Starting phenix.real_space_refine on Wed Jun 18 15:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hi1_34809/06_2025/8hi1_34809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hi1_34809/06_2025/8hi1_34809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hi1_34809/06_2025/8hi1_34809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hi1_34809/06_2025/8hi1_34809.map" model { file = "/net/cci-nas-00/data/ceres_data/8hi1_34809/06_2025/8hi1_34809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hi1_34809/06_2025/8hi1_34809.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.102 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.82, per 1000 atoms: 0.47 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: 5.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 8.96 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: 7.55 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10143 1.03 - 1.23: 40 1.23 - 1.42: 4676 1.42 - 1.62: 6383 1.62 - 1.81: 62 Bond restraints: 21304 Sorted by residual: bond pdb=" CB ILE D 74 " pdb=" CG2 ILE D 74 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB GLN F 24 " pdb=" CG GLN F 24 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB VAL E 32 " pdb=" CG1 VAL E 32 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" C ASP C 65 " pdb=" N ILE C 66 " ideal model delta sigma weight residual 1.329 1.300 0.029 2.19e-02 2.09e+03 1.74e+00 bond pdb=" CG LEU D 60 " pdb=" CD1 LEU D 60 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.61: 38372 10.61 - 21.23: 1 21.23 - 31.84: 0 31.84 - 42.45: 0 42.45 - 53.06: 2 Bond angle restraints: 38375 Sorted by residual: angle pdb=" C SER C 294 " pdb=" N LEU C 295 " pdb=" H LEU C 295 " ideal model delta sigma weight residual 124.38 71.32 53.06 3.00e+00 1.11e-01 3.13e+02 angle pdb=" CA LEU C 295 " pdb=" N LEU C 295 " pdb=" H LEU C 295 " ideal model delta sigma weight residual 114.08 61.54 52.54 3.00e+00 1.11e-01 3.07e+02 angle pdb=" C SER C 294 " pdb=" N LEU C 295 " pdb=" CA LEU C 295 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" N VAL C 121 " pdb=" CA VAL C 121 " pdb=" C VAL C 121 " ideal model delta sigma weight residual 112.43 108.68 3.75 9.20e-01 1.18e+00 1.66e+01 angle pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" N GLN C 141 " ideal model delta sigma weight residual 118.42 122.66 -4.24 1.31e+00 5.83e-01 1.05e+01 ... (remaining 38370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 9134 31.74 - 63.48: 588 63.48 - 95.23: 11 95.23 - 126.97: 0 126.97 - 158.71: 2 Dihedral angle restraints: 9735 sinusoidal: 5645 harmonic: 4090 Sorted by residual: dihedral pdb=" CA ARG B 90 " pdb=" C ARG B 90 " pdb=" N GLN B 91 " pdb=" CA GLN B 91 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN E 36 " pdb=" C ASN E 36 " pdb=" N SER E 37 " pdb=" CA SER E 37 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C4' DT H 29 " pdb=" C3' DT H 29 " pdb=" O3' DT H 29 " pdb=" P DT H 30 " ideal model delta sinusoidal sigma weight residual 220.00 61.29 158.71 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1070 0.033 - 0.066: 457 0.066 - 0.099: 170 0.099 - 0.131: 45 0.131 - 0.164: 9 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA VAL C 35 " pdb=" N VAL C 35 " pdb=" C VAL C 35 " pdb=" CB VAL C 35 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ILE B 25 " pdb=" N ILE B 25 " pdb=" C ILE B 25 " pdb=" CB ILE B 25 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1748 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 207 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 208 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 207 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO D 208 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 207 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 208 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.024 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1038 2.17 - 2.78: 39824 2.78 - 3.38: 53178 3.38 - 3.99: 70414 3.99 - 4.60: 112154 Nonbonded interactions: 276608 Sorted by model distance: nonbonded pdb="HH22 ARG B 49 " pdb=" OE1 GLU E 25 " model vdw 1.562 2.450 nonbonded pdb=" HH TYR D 229 " pdb=" OD2 ASP D 275 " model vdw 1.601 2.450 nonbonded pdb="HH12 ARG C 169 " pdb=" OP1 DG H 28 " model vdw 1.627 2.450 nonbonded pdb="HH11 ARG C 123 " pdb=" O SER C 136 " model vdw 1.628 2.450 nonbonded pdb="HH22 ARG C 169 " pdb=" OG SER C 187 " model vdw 1.629 2.450 ... (remaining 276603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2)) or (resid 247 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2)) or (resid 248 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 249 through 250 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 251 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2 or name CD1)) or (resid 252 and (name N or name CA or name C or name O or name \ HA2 or name HA3)) or resid 253 through 296 or (resid 297 through 298 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 299 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 300 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 301 and ( \ name N or name CA or name C or name O or name CB or name CG or name SD or name C \ E )) or (resid 302 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 303 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 304 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) o \ r (resid 305 and (name N or name CA or name C or name O or name CB or name CG or \ name ND1 or name CD2 or name CE1 or name NE2)) or (resid 306 and (name N or nam \ e CA or name C or name O )))) selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 24 through \ 74 or (resid 75 and (name N or name CA or name C or name O or name HA2 or name H \ A3)) or resid 76 through 306)) } ncs_group { reference = (chain 'B' and (resid 4 through 85 or (resid 86 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 8 \ 7 through 88 or (resid 89 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or (resid 90 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ )) or (resid 91 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or (resid 92 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or (resid 93 and (name N or name CA or name C or na \ me O or name CB )) or resid 94 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB or name OG or name HA or name HB2 or name HB3 or \ name HG )) or resid 102 through 281)) selection = (chain 'D' and (resid 4 through 140 or resid 181 through 281)) } ncs_group { reference = (chain 'E' and resid 2 through 92) selection = (chain 'F' and resid 2 through 92) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.350 Extract box with map and model: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 51.680 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11161 Z= 0.215 Angle : 0.694 11.317 15328 Z= 0.413 Chirality : 0.043 0.164 1751 Planarity : 0.004 0.064 1760 Dihedral : 17.864 158.710 4263 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP E 22 HIS 0.010 0.002 HIS C 198 PHE 0.014 0.002 PHE E 82 TYR 0.013 0.001 TYR F 61 ARG 0.006 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.17387 ( 458) hydrogen bonds : angle 6.77442 ( 1275) covalent geometry : bond 0.00508 (11161) covalent geometry : angle 0.69383 (15328) *********************** 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 : 1.902 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: 0.3268 (tpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.6861 time to fit residues: 159.3627 Evaluate side-chains 103 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN B 5 ASN B 127 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 100 HIS D 277 GLN E 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.209750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161543 restraints weight = 33235.120| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.45 r_work: 0.3713 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11161 Z= 0.181 Angle : 0.654 18.318 15328 Z= 0.366 Chirality : 0.042 0.153 1751 Planarity : 0.005 0.056 1760 Dihedral : 18.262 162.027 1971 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.15 % Allowed : 9.32 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.19), residues: 1214 helix: -2.37 (0.18), residues: 515 sheet: -3.01 (0.30), residues: 186 loop : -3.88 (0.22), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 22 HIS 0.011 0.002 HIS C 198 PHE 0.023 0.002 PHE A 176 TYR 0.016 0.001 TYR D 92 ARG 0.008 0.001 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.05220 ( 458) hydrogen bonds : angle 4.95293 ( 1275) covalent geometry : bond 0.00419 (11161) covalent geometry : angle 0.65381 (15328) *********************** 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 128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7378 (t0) cc_final: 0.6918 (t0) REVERT: A 125 MET cc_start: 0.6005 (mtt) cc_final: 0.4231 (ttp) REVERT: A 224 ASP cc_start: 0.6116 (m-30) cc_final: 0.5862 (m-30) REVERT: B 54 MET cc_start: 0.8321 (mmt) cc_final: 0.7618 (mmt) REVERT: C 45 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7310 (mpp80) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.5733 time to fit residues: 97.9694 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.199303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152358 restraints weight = 33470.980| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.66 r_work: 0.3613 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11161 Z= 0.242 Angle : 0.673 18.074 15328 Z= 0.377 Chirality : 0.045 0.154 1751 Planarity : 0.005 0.069 1760 Dihedral : 18.427 161.426 1971 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.31 % Allowed : 11.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.20), residues: 1214 helix: -1.85 (0.19), residues: 517 sheet: -2.71 (0.33), residues: 186 loop : -3.65 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 166 HIS 0.017 0.002 HIS C 198 PHE 0.016 0.002 PHE D 24 TYR 0.012 0.002 TYR E 61 ARG 0.013 0.001 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.05713 ( 458) hydrogen bonds : angle 4.82693 ( 1275) covalent geometry : bond 0.00560 (11161) covalent geometry : angle 0.67292 (15328) *********************** 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 130 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7483 (t0) cc_final: 0.7058 (t0) REVERT: A 125 MET cc_start: 0.5927 (mtt) cc_final: 0.4087 (ttp) REVERT: C 45 ARG cc_start: 0.7635 (mtt180) cc_final: 0.7225 (mpp80) REVERT: C 240 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6570 (pt0) REVERT: D 58 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7557 (mt) REVERT: E 24 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6618 (tt0) outliers start: 24 outliers final: 12 residues processed: 124 average time/residue: 0.5798 time to fit residues: 104.5559 Evaluate side-chains 110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 90 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.202405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155801 restraints weight = 33499.566| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.60 r_work: 0.3658 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2968 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= 0.146 Angle : 0.590 18.717 15328 Z= 0.334 Chirality : 0.041 0.148 1751 Planarity : 0.004 0.067 1760 Dihedral : 18.274 162.925 1971 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.73 % Allowed : 13.64 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.21), residues: 1214 helix: -1.30 (0.21), residues: 521 sheet: -2.35 (0.34), residues: 176 loop : -3.61 (0.21), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 166 HIS 0.007 0.001 HIS C 29 PHE 0.011 0.001 PHE A 176 TYR 0.009 0.001 TYR D 92 ARG 0.009 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 458) hydrogen bonds : angle 4.46860 ( 1275) covalent geometry : bond 0.00335 (11161) covalent geometry : angle 0.59010 (15328) *********************** 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 124 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7429 (t0) cc_final: 0.6952 (t0) REVERT: A 125 MET cc_start: 0.5873 (mtt) cc_final: 0.4118 (ttp) REVERT: B 90 ARG cc_start: 0.7591 (tpm170) cc_final: 0.7361 (mmp80) REVERT: C 45 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7214 (mpp80) REVERT: C 240 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6462 (pt0) outliers start: 18 outliers final: 15 residues processed: 116 average time/residue: 0.5055 time to fit residues: 83.9891 Evaluate side-chains 110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR 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 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.198001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151871 restraints weight = 33501.260| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.56 r_work: 0.3619 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11161 Z= 0.227 Angle : 0.649 18.424 15328 Z= 0.364 Chirality : 0.044 0.151 1751 Planarity : 0.005 0.055 1760 Dihedral : 18.401 162.504 1971 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.11 % Allowed : 14.22 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.21), residues: 1214 helix: -1.28 (0.21), residues: 521 sheet: -2.20 (0.36), residues: 176 loop : -3.65 (0.21), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 22 HIS 0.014 0.002 HIS C 29 PHE 0.014 0.002 PHE D 24 TYR 0.011 0.001 TYR E 61 ARG 0.006 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.05266 ( 458) hydrogen bonds : angle 4.53538 ( 1275) covalent geometry : bond 0.00535 (11161) covalent geometry : angle 0.64867 (15328) *********************** 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 124 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7548 (t0) cc_final: 0.7100 (t0) REVERT: A 125 MET cc_start: 0.5993 (mtt) cc_final: 0.4183 (ttp) REVERT: B 218 ASP cc_start: 0.8174 (t0) cc_final: 0.7838 (t0) REVERT: C 45 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7324 (mpp80) REVERT: C 141 GLN cc_start: 0.6777 (tm-30) cc_final: 0.6566 (tm-30) REVERT: C 237 LEU cc_start: 0.7414 (tp) cc_final: 0.7177 (mt) REVERT: C 240 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6562 (pt0) REVERT: D 58 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7426 (mt) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.6295 time to fit residues: 111.1042 Evaluate side-chains 119 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 202 ILE 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 90 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 84 VAL 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 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 42 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.201860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154275 restraints weight = 32920.986| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.54 r_work: 0.3665 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3490 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= 0.126 Angle : 0.569 18.995 15328 Z= 0.321 Chirality : 0.040 0.172 1751 Planarity : 0.004 0.036 1760 Dihedral : 18.220 163.374 1971 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.54 % Allowed : 16.04 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.21), residues: 1214 helix: -0.90 (0.21), residues: 520 sheet: -1.87 (0.36), residues: 180 loop : -3.45 (0.21), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 22 HIS 0.005 0.001 HIS C 94 PHE 0.009 0.001 PHE A 176 TYR 0.008 0.001 TYR D 92 ARG 0.002 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 458) hydrogen bonds : angle 4.19547 ( 1275) covalent geometry : bond 0.00287 (11161) covalent geometry : angle 0.56856 (15328) *********************** 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 129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7405 (t0) cc_final: 0.6887 (t0) REVERT: A 125 MET cc_start: 0.5829 (mtt) cc_final: 0.4012 (ttp) REVERT: B 76 ASP cc_start: 0.8645 (t0) cc_final: 0.8366 (t0) REVERT: B 227 ASP cc_start: 0.7775 (m-30) cc_final: 0.7532 (m-30) REVERT: C 45 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7228 (mpp80) REVERT: C 140 MET cc_start: 0.3971 (ttt) cc_final: 0.2877 (tpt) REVERT: C 240 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6447 (pt0) REVERT: D 58 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7344 (mt) REVERT: E 42 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6702 (mptt) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.4661 time to fit residues: 83.8809 Evaluate side-chains 110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 90 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN 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 52 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4340 r_free = 0.4340 target = 0.198309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151876 restraints weight = 33320.940| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.63 r_work: 0.3643 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3657 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= 0.209 Angle : 0.620 18.813 15328 Z= 0.348 Chirality : 0.043 0.196 1751 Planarity : 0.004 0.041 1760 Dihedral : 18.332 162.737 1971 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.11 % Allowed : 16.33 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1214 helix: -0.95 (0.21), residues: 518 sheet: -1.85 (0.37), residues: 177 loop : -3.39 (0.22), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 22 HIS 0.011 0.002 HIS C 29 PHE 0.014 0.002 PHE E 3 TYR 0.011 0.001 TYR E 61 ARG 0.003 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 458) hydrogen bonds : angle 4.31690 ( 1275) covalent geometry : bond 0.00496 (11161) covalent geometry : angle 0.61980 (15328) *********************** 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 123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7464 (t0) cc_final: 0.6966 (t0) REVERT: A 125 MET cc_start: 0.5915 (mtt) cc_final: 0.4089 (ttp) REVERT: B 218 ASP cc_start: 0.8157 (t0) cc_final: 0.7758 (t0) REVERT: C 45 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7277 (mpp80) REVERT: C 140 MET cc_start: 0.4326 (ttt) cc_final: 0.3159 (tpt) REVERT: C 237 LEU cc_start: 0.7466 (tp) cc_final: 0.7183 (mt) REVERT: C 240 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6537 (pt0) REVERT: D 58 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7454 (mt) REVERT: E 42 LYS cc_start: 0.7131 (mtpp) cc_final: 0.6832 (mptt) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.4742 time to fit residues: 82.5893 Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE 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 91 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 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 123 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.202186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154262 restraints weight = 33377.803| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.58 r_work: 0.3651 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11161 Z= 0.133 Angle : 0.567 19.144 15328 Z= 0.320 Chirality : 0.041 0.201 1751 Planarity : 0.004 0.061 1760 Dihedral : 18.226 163.353 1971 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.34 % Allowed : 17.68 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.22), residues: 1214 helix: -0.66 (0.22), residues: 520 sheet: -1.61 (0.36), residues: 180 loop : -3.32 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 22 HIS 0.005 0.001 HIS C 198 PHE 0.011 0.001 PHE F 3 TYR 0.008 0.001 TYR D 92 ARG 0.010 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 458) hydrogen bonds : angle 4.05736 ( 1275) covalent geometry : bond 0.00308 (11161) covalent geometry : angle 0.56736 (15328) *********************** 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 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7417 (t0) cc_final: 0.6858 (t0) REVERT: A 125 MET cc_start: 0.5803 (mtt) cc_final: 0.3946 (ttp) REVERT: C 45 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7219 (mpp80) REVERT: C 140 MET cc_start: 0.3976 (ttt) cc_final: 0.2858 (tpt) REVERT: D 58 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7294 (mt) REVERT: E 42 LYS cc_start: 0.7058 (mtpp) cc_final: 0.6769 (mptt) outliers start: 14 outliers final: 11 residues processed: 116 average time/residue: 0.5094 time to fit residues: 85.0875 Evaluate side-chains 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 58 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4348 r_free = 0.4348 target = 0.199119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151965 restraints weight = 33238.049| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.53 r_work: 0.3634 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11161 Z= 0.173 Angle : 0.592 19.011 15328 Z= 0.333 Chirality : 0.042 0.178 1751 Planarity : 0.004 0.042 1760 Dihedral : 18.299 162.944 1971 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.44 % Allowed : 17.68 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.22), residues: 1214 helix: -0.65 (0.22), residues: 518 sheet: -1.52 (0.38), residues: 177 loop : -3.25 (0.22), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 166 HIS 0.009 0.002 HIS C 29 PHE 0.014 0.001 PHE E 3 TYR 0.009 0.001 TYR D 92 ARG 0.007 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 458) hydrogen bonds : angle 4.12674 ( 1275) covalent geometry : bond 0.00409 (11161) covalent geometry : angle 0.59224 (15328) *********************** 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 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7447 (t0) cc_final: 0.6914 (t0) REVERT: A 125 MET cc_start: 0.5864 (mtt) cc_final: 0.3971 (ttp) REVERT: C 45 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7240 (mpp80) REVERT: C 140 MET cc_start: 0.4235 (ttt) cc_final: 0.3010 (tpt) REVERT: C 240 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6278 (pt0) REVERT: D 58 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7421 (mt) REVERT: E 42 LYS cc_start: 0.7089 (mtpp) cc_final: 0.6707 (mptt) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.4719 time to fit residues: 74.1804 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 : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 58 LEU Chi-restraints excluded: chain D residue 84 VAL 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 Chi-restraints excluded: chain F residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.200760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152962 restraints weight = 33307.166| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.55 r_work: 0.3607 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11161 Z= 0.146 Angle : 0.574 19.134 15328 Z= 0.323 Chirality : 0.041 0.175 1751 Planarity : 0.004 0.049 1760 Dihedral : 18.258 163.356 1971 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.63 % Allowed : 17.58 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.22), residues: 1214 helix: -0.46 (0.22), residues: 516 sheet: -1.40 (0.38), residues: 175 loop : -3.16 (0.22), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 166 HIS 0.006 0.001 HIS C 29 PHE 0.011 0.001 PHE F 3 TYR 0.007 0.001 TYR D 92 ARG 0.007 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 458) hydrogen bonds : angle 4.01769 ( 1275) covalent geometry : bond 0.00342 (11161) covalent geometry : angle 0.57370 (15328) ********************** 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 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7435 (t0) cc_final: 0.6891 (t0) REVERT: A 125 MET cc_start: 0.5798 (mtt) cc_final: 0.3929 (ttp) REVERT: C 45 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7233 (mpp80) REVERT: C 140 MET cc_start: 0.4201 (ttt) cc_final: 0.2970 (tpt) REVERT: C 240 GLU cc_start: 0.6690 (tm-30) cc_final: 0.6278 (pt0) REVERT: D 58 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7365 (mt) REVERT: E 42 LYS cc_start: 0.7031 (mtpp) cc_final: 0.6657 (mptt) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 0.4798 time to fit residues: 81.6105 Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 58 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153351 restraints weight = 33298.659| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.60 r_work: 0.3665 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 11161 Z= 0.189 Angle : 0.847 59.155 15328 Z= 0.517 Chirality : 0.041 0.205 1751 Planarity : 0.004 0.048 1760 Dihedral : 18.259 163.333 1971 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.63 % Allowed : 17.48 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.22), residues: 1214 helix: -0.45 (0.22), residues: 516 sheet: -1.38 (0.38), residues: 174 loop : -3.16 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 166 HIS 0.006 0.001 HIS C 29 PHE 0.011 0.001 PHE E 3 TYR 0.007 0.001 TYR D 92 ARG 0.006 0.000 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 458) hydrogen bonds : angle 4.01979 ( 1275) covalent geometry : bond 0.00404 (11161) covalent geometry : angle 0.84724 (15328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13693.41 seconds wall clock time: 235 minutes 11.42 seconds (14111.42 seconds total)