Starting phenix.real_space_refine on Fri Aug 22 18:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ny6_49925/08_2025/9ny6_49925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ny6_49925/08_2025/9ny6_49925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ny6_49925/08_2025/9ny6_49925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ny6_49925/08_2025/9ny6_49925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ny6_49925/08_2025/9ny6_49925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ny6_49925/08_2025/9ny6_49925.map" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 4200 2.51 5 N 1137 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6681 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2227 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 276} Chain: "D" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2227 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 276} Chain: "E" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2227 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 276} Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6681 At special positions: 0 Unit cell: (85.14, 98.384, 102.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1326 8.00 N 1137 7.00 C 4200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 252.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 4.4% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.650A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 10 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.701A pdb=" N GLU D 61 " --> pdb=" O TYR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'E' and resid 7 through 10 Processing helix chain 'E' and resid 55 through 63 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.513A pdb=" N ASN E 69 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 71 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY C 110 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 86 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL C 108 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLY E 122 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 140 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR C 161 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 142 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE C 158 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU E 179 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ASP C 160 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N GLN E 181 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ILE C 162 " --> pdb=" O GLN E 181 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N TYR E 183 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N GLU C 164 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D 189 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.513A pdb=" N ASN E 69 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 71 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY C 110 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 86 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ARG E 130 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER C 113 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP E 132 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C 115 " --> pdb=" O ASP E 132 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 129 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL E 131 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N HIS D 146 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN C 165 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ILE D 148 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE C 158 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU E 179 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ASP C 160 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N GLN E 181 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ILE C 162 " --> pdb=" O GLN E 181 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N TYR E 183 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N GLU C 164 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D 189 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 44 through 47 removed outlier: 7.791A pdb=" N ASN D 45 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU C 68 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL D 47 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 70 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 65 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN E 89 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 67 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU E 91 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASN C 69 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 130 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 131 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL E 140 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR D 161 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL E 142 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE D 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 144 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS E 146 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP D 160 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU C 179 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE D 162 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN C 181 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU D 164 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR C 183 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE D 166 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N VAL E 189 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU C 179 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR E 191 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN C 181 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY D 195 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS E 192 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL D 197 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 47 removed outlier: 7.791A pdb=" N ASN D 45 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU C 68 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL D 47 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 70 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 65 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN E 89 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 67 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU E 91 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASN C 69 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 130 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 131 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY C 122 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N VAL E 142 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 124 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE E 144 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP D 104 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA C 124 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N GLY D 106 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE E 83 " --> pdb=" O PRO D 105 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS D 107 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.386A pdb=" N ILE C 83 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLY D 122 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 140 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASP C 139 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE E 162 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR C 141 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU E 164 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA C 143 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 10.699A pdb=" N PHE E 166 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N LYS C 145 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLN D 180 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN E 165 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN D 182 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.386A pdb=" N ILE C 83 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLY D 122 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 140 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU D 128 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR E 115 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG D 130 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE E 117 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP D 132 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN D 69 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL D 66 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN E 45 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU D 68 " --> pdb=" O ASN E 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.547A pdb=" N THR C 286 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 207 through 209 removed outlier: 6.590A pdb=" N ILE C 226 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ALA C 253 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 228 " --> pdb=" O ALA C 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.840A pdb=" N PHE D 218 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA D 259 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY D 288 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR D 261 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE D 290 " --> pdb=" O TYR D 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 207 through 209 removed outlier: 6.590A pdb=" N ILE D 207 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.024A pdb=" N PHE E 218 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR E 286 " --> pdb=" O ALA E 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 207 through 209 removed outlier: 6.706A pdb=" N ILE E 207 " --> pdb=" O THR E 229 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2274 1.34 - 1.46: 1381 1.46 - 1.58: 3148 1.58 - 1.69: 1 1.69 - 1.81: 27 Bond restraints: 6831 Sorted by residual: bond pdb=" CB PRO C 232 " pdb=" CG PRO C 232 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.59e+00 bond pdb=" CB ASP E 29 " pdb=" CG ASP E 29 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.40e+00 bond pdb=" N MET E 169 " pdb=" CA MET E 169 " ideal model delta sigma weight residual 1.460 1.443 0.017 1.45e-02 4.76e+03 1.38e+00 bond pdb=" CB GLU E 34 " pdb=" CG GLU E 34 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB TRP E 216 " pdb=" CG TRP E 216 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.35e+00 ... (remaining 6826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 9238 2.63 - 5.25: 72 5.25 - 7.88: 9 7.88 - 10.51: 1 10.51 - 13.14: 1 Bond angle restraints: 9321 Sorted by residual: angle pdb=" CA PRO C 232 " pdb=" N PRO C 232 " pdb=" CD PRO C 232 " ideal model delta sigma weight residual 112.00 104.42 7.58 1.40e+00 5.10e-01 2.93e+01 angle pdb=" N GLU E 34 " pdb=" CA GLU E 34 " pdb=" C GLU E 34 " ideal model delta sigma weight residual 110.80 102.04 8.76 2.13e+00 2.20e-01 1.69e+01 angle pdb=" CA LEU D 184 " pdb=" CB LEU D 184 " pdb=" CG LEU D 184 " ideal model delta sigma weight residual 116.30 129.44 -13.14 3.50e+00 8.16e-02 1.41e+01 angle pdb=" C GLY E 215 " pdb=" N TRP E 216 " pdb=" CA TRP E 216 " ideal model delta sigma weight residual 121.66 114.64 7.02 1.92e+00 2.71e-01 1.34e+01 angle pdb=" C ARG E 103 " pdb=" N ASP E 104 " pdb=" CA ASP E 104 " ideal model delta sigma weight residual 120.09 124.47 -4.38 1.25e+00 6.40e-01 1.23e+01 ... (remaining 9316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 3621 15.10 - 30.20: 285 30.20 - 45.30: 70 45.30 - 60.40: 19 60.40 - 75.50: 4 Dihedral angle restraints: 3999 sinusoidal: 1521 harmonic: 2478 Sorted by residual: dihedral pdb=" CA TYR E 16 " pdb=" C TYR E 16 " pdb=" N VAL E 17 " pdb=" CA VAL E 17 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA VAL E 23 " pdb=" C VAL E 23 " pdb=" N PHE E 24 " pdb=" CA PHE E 24 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA VAL E 18 " pdb=" C VAL E 18 " pdb=" N ASP E 19 " pdb=" CA ASP E 19 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 3996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 711 0.039 - 0.079: 186 0.079 - 0.118: 137 0.118 - 0.157: 11 0.157 - 0.196: 5 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CG LEU E 209 " pdb=" CB LEU E 209 " pdb=" CD1 LEU E 209 " pdb=" CD2 LEU E 209 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA GLU E 34 " pdb=" N GLU E 34 " pdb=" C GLU E 34 " pdb=" CB GLU E 34 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB ILE E 35 " pdb=" CA ILE E 35 " pdb=" CG1 ILE E 35 " pdb=" CG2 ILE E 35 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 1047 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 231 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 232 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 232 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 232 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 216 " 0.031 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP E 216 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP E 216 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 216 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 216 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 216 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 216 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 216 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 29 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C ASP E 29 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP E 29 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY E 30 " -0.015 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 423 2.73 - 3.27: 6675 3.27 - 3.81: 11383 3.81 - 4.36: 13387 4.36 - 4.90: 22874 Nonbonded interactions: 54742 Sorted by model distance: nonbonded pdb=" N GLU C 76 " pdb=" OE1 GLU C 76 " model vdw 2.186 3.120 nonbonded pdb=" O THR C 50 " pdb=" OG SER E 79 " model vdw 2.188 3.040 nonbonded pdb=" NZ LYS C 145 " pdb=" O HIS C 146 " model vdw 2.243 3.120 nonbonded pdb=" O LEU D 230 " pdb=" OG SER D 255 " model vdw 2.247 3.040 nonbonded pdb=" O SER C 73 " pdb=" OG SER E 99 " model vdw 2.264 3.040 ... (remaining 54737 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 7.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 6831 Z= 0.126 Angle : 0.612 13.137 9321 Z= 0.318 Chirality : 0.048 0.196 1050 Planarity : 0.005 0.113 1251 Dihedral : 12.369 75.495 2427 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 16.88 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.29), residues: 876 helix: -1.25 (1.01), residues: 21 sheet: -0.45 (0.36), residues: 200 loop : -0.70 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 170 TYR 0.026 0.001 TYR D 141 PHE 0.010 0.001 PHE E 24 TRP 0.067 0.003 TRP E 216 HIS 0.002 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6831) covalent geometry : angle 0.61236 ( 9321) hydrogen bonds : bond 0.24428 ( 148) hydrogen bonds : angle 9.88972 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.223 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0565 time to fit residues: 3.5874 Evaluate side-chains 39 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 overall best weight: 7.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN D 175 ASN E 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.086961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058394 restraints weight = 27804.560| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.22 r_work: 0.2979 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6831 Z= 0.177 Angle : 0.566 8.329 9321 Z= 0.292 Chirality : 0.048 0.138 1050 Planarity : 0.004 0.044 1251 Dihedral : 4.562 26.967 942 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.09 % Allowed : 15.76 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.28), residues: 876 helix: -0.96 (1.04), residues: 21 sheet: -0.50 (0.35), residues: 210 loop : -0.72 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 25 TYR 0.014 0.001 TYR D 141 PHE 0.007 0.001 PHE C 242 TRP 0.039 0.002 TRP E 216 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6831) covalent geometry : angle 0.56591 ( 9321) hydrogen bonds : bond 0.03328 ( 148) hydrogen bonds : angle 6.34818 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.236 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 53 average time/residue: 0.0497 time to fit residues: 4.1709 Evaluate side-chains 46 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 chunk 11 optimal weight: 30.0000 chunk 41 optimal weight: 40.0000 chunk 27 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 5 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN ** D 244 GLN ** 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 = 0.3903 r_free = 0.3903 target = 0.082705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056068 restraints weight = 28378.735| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.35 r_work: 0.2878 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 6831 Z= 0.368 Angle : 0.684 6.795 9321 Z= 0.366 Chirality : 0.050 0.171 1050 Planarity : 0.005 0.048 1251 Dihedral : 5.524 41.198 942 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.85 % Favored : 92.92 % Rotamer: Outliers : 5.02 % Allowed : 13.67 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.28), residues: 876 helix: -0.47 (1.09), residues: 21 sheet: -0.85 (0.35), residues: 194 loop : -0.92 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 26 TYR 0.021 0.002 TYR E 183 PHE 0.014 0.002 PHE E 24 TRP 0.033 0.003 TRP E 216 HIS 0.005 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00818 ( 6831) covalent geometry : angle 0.68444 ( 9321) hydrogen bonds : bond 0.04410 ( 148) hydrogen bonds : angle 6.57897 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 36 time to evaluate : 0.252 Fit side-chains REVERT: C 193 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8431 (tp) REVERT: E 153 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8930 (mp10) REVERT: E 161 TYR cc_start: 0.7338 (t80) cc_final: 0.6691 (t80) outliers start: 36 outliers final: 20 residues processed: 70 average time/residue: 0.0539 time to fit residues: 5.8074 Evaluate side-chains 57 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 0.0980 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 19 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 27 optimal weight: 50.0000 overall best weight: 8.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN ** D 244 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.083846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055645 restraints weight = 28036.938| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.09 r_work: 0.2925 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6831 Z= 0.184 Angle : 0.563 6.473 9321 Z= 0.294 Chirality : 0.048 0.137 1050 Planarity : 0.004 0.044 1251 Dihedral : 5.085 49.915 942 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.48 % Favored : 94.29 % Rotamer: Outliers : 3.63 % Allowed : 15.62 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.28), residues: 876 helix: -0.41 (1.01), residues: 21 sheet: -0.93 (0.35), residues: 193 loop : -0.86 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 14 TYR 0.011 0.001 TYR C 16 PHE 0.016 0.001 PHE C 240 TRP 0.023 0.002 TRP E 216 HIS 0.002 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6831) covalent geometry : angle 0.56289 ( 9321) hydrogen bonds : bond 0.03109 ( 148) hydrogen bonds : angle 6.00474 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: D 169 MET cc_start: 0.8650 (pmm) cc_final: 0.8118 (pmm) REVERT: E 99 SER cc_start: 0.9174 (p) cc_final: 0.8795 (t) REVERT: E 169 MET cc_start: 0.8940 (pmm) cc_final: 0.8453 (pmm) outliers start: 26 outliers final: 19 residues processed: 62 average time/residue: 0.0733 time to fit residues: 6.4063 Evaluate side-chains 50 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 0.0570 chunk 74 optimal weight: 10.0000 overall best weight: 6.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 244 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.084240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056069 restraints weight = 28308.201| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.16 r_work: 0.2936 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6831 Z= 0.148 Angle : 0.551 6.810 9321 Z= 0.284 Chirality : 0.048 0.132 1050 Planarity : 0.004 0.044 1251 Dihedral : 4.910 50.630 942 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Rotamer: Outliers : 4.32 % Allowed : 15.20 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.28), residues: 876 helix: -0.17 (1.06), residues: 21 sheet: -0.93 (0.35), residues: 196 loop : -0.77 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 25 TYR 0.010 0.001 TYR C 16 PHE 0.012 0.001 PHE C 240 TRP 0.018 0.002 TRP E 216 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6831) covalent geometry : angle 0.55055 ( 9321) hydrogen bonds : bond 0.02914 ( 148) hydrogen bonds : angle 5.79116 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 34 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: C 239 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6303 (p90) REVERT: D 169 MET cc_start: 0.8692 (pmm) cc_final: 0.8153 (pmm) REVERT: E 153 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8977 (mp10) outliers start: 31 outliers final: 21 residues processed: 65 average time/residue: 0.0612 time to fit residues: 5.9056 Evaluate side-chains 56 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 243 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 48 optimal weight: 30.0000 chunk 58 optimal weight: 0.1980 chunk 82 optimal weight: 30.0000 chunk 39 optimal weight: 50.0000 overall best weight: 17.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 244 GLN ** 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 = 0.3889 r_free = 0.3889 target = 0.081560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053211 restraints weight = 29156.902| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.02 r_work: 0.2860 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 6831 Z= 0.353 Angle : 0.675 6.498 9321 Z= 0.358 Chirality : 0.050 0.205 1050 Planarity : 0.005 0.044 1251 Dihedral : 5.522 53.700 942 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.58 % Rotamer: Outliers : 5.02 % Allowed : 14.37 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.28), residues: 876 helix: -0.11 (1.06), residues: 21 sheet: -1.08 (0.35), residues: 189 loop : -0.92 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 25 TYR 0.020 0.002 TYR E 183 PHE 0.018 0.002 PHE E 24 TRP 0.018 0.003 TRP E 216 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00779 ( 6831) covalent geometry : angle 0.67527 ( 9321) hydrogen bonds : bond 0.03735 ( 148) hydrogen bonds : angle 6.33723 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 36 time to evaluate : 0.201 Fit side-chains REVERT: C 161 TYR cc_start: 0.8337 (t80) cc_final: 0.8035 (t80) REVERT: C 193 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8409 (tp) REVERT: D 169 MET cc_start: 0.8701 (pmm) cc_final: 0.8191 (pmm) REVERT: E 153 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8950 (mp10) REVERT: E 169 MET cc_start: 0.9085 (pmm) cc_final: 0.8735 (pmm) outliers start: 36 outliers final: 26 residues processed: 72 average time/residue: 0.0610 time to fit residues: 6.5480 Evaluate side-chains 62 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 34 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 53 optimal weight: 50.0000 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 70 optimal weight: 0.0040 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 17 optimal weight: 50.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN E 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.084352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056500 restraints weight = 28209.971| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.18 r_work: 0.2961 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.002 0.039 6831 Z= 0.109 Angle : 0.575 7.686 9321 Z= 0.293 Chirality : 0.049 0.167 1050 Planarity : 0.004 0.047 1251 Dihedral : 5.019 58.823 942 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.21 % Rotamer: Outliers : 3.21 % Allowed : 15.90 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.28), residues: 876 helix: -0.17 (1.07), residues: 21 sheet: -1.01 (0.35), residues: 198 loop : -0.78 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 103 TYR 0.010 0.001 TYR C 281 PHE 0.011 0.001 PHE C 52 TRP 0.013 0.001 TRP E 216 HIS 0.009 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6831) covalent geometry : angle 0.57475 ( 9321) hydrogen bonds : bond 0.02678 ( 148) hydrogen bonds : angle 5.65145 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: C 193 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8154 (tp) REVERT: E 169 MET cc_start: 0.9012 (pmm) cc_final: 0.8703 (pmm) outliers start: 23 outliers final: 21 residues processed: 63 average time/residue: 0.0697 time to fit residues: 6.1964 Evaluate side-chains 60 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 40.0000 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 40.0000 chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** D 244 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.083708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055769 restraints weight = 28355.068| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.12 r_work: 0.2927 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6831 Z= 0.150 Angle : 0.577 8.957 9321 Z= 0.294 Chirality : 0.048 0.151 1050 Planarity : 0.004 0.046 1251 Dihedral : 4.949 56.677 942 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.25 % Favored : 94.52 % Rotamer: Outliers : 3.63 % Allowed : 15.34 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.28), residues: 876 helix: -0.11 (1.08), residues: 21 sheet: -0.94 (0.35), residues: 193 loop : -0.73 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 25 TYR 0.011 0.001 TYR C 281 PHE 0.013 0.001 PHE E 24 TRP 0.012 0.001 TRP E 216 HIS 0.008 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6831) covalent geometry : angle 0.57713 ( 9321) hydrogen bonds : bond 0.02849 ( 148) hydrogen bonds : angle 5.66228 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: C 193 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8150 (tp) REVERT: C 219 MET cc_start: -0.0130 (mpp) cc_final: -0.0380 (mpp) REVERT: E 169 MET cc_start: 0.9012 (pmm) cc_final: 0.8668 (pmm) outliers start: 26 outliers final: 22 residues processed: 63 average time/residue: 0.0719 time to fit residues: 6.3420 Evaluate side-chains 58 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 40.0000 chunk 23 optimal weight: 50.0000 chunk 6 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 50.0000 chunk 58 optimal weight: 0.0270 overall best weight: 1.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.085571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.057951 restraints weight = 28054.073| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.19 r_work: 0.3004 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6831 Z= 0.094 Angle : 0.584 9.919 9321 Z= 0.292 Chirality : 0.049 0.212 1050 Planarity : 0.004 0.047 1251 Dihedral : 4.752 56.806 942 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.21 % Rotamer: Outliers : 3.07 % Allowed : 16.04 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.28), residues: 876 helix: -0.31 (1.05), residues: 21 sheet: -0.75 (0.36), residues: 188 loop : -0.68 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.010 0.001 TYR C 161 PHE 0.012 0.001 PHE E 283 TRP 0.010 0.001 TRP E 216 HIS 0.008 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 6831) covalent geometry : angle 0.58420 ( 9321) hydrogen bonds : bond 0.02424 ( 148) hydrogen bonds : angle 5.29274 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 193 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7835 (tp) outliers start: 22 outliers final: 18 residues processed: 62 average time/residue: 0.0696 time to fit residues: 5.9519 Evaluate side-chains 54 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 0.0570 chunk 8 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 50.0000 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 0.1980 overall best weight: 4.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** D 244 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.084456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056563 restraints weight = 28088.666| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.18 r_work: 0.2953 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6831 Z= 0.127 Angle : 0.601 9.910 9321 Z= 0.299 Chirality : 0.049 0.176 1050 Planarity : 0.004 0.046 1251 Dihedral : 4.690 54.474 942 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.79 % Favored : 94.98 % Rotamer: Outliers : 2.79 % Allowed : 16.88 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.28), residues: 876 helix: -0.22 (1.08), residues: 21 sheet: -0.78 (0.35), residues: 197 loop : -0.62 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 25 TYR 0.011 0.001 TYR C 281 PHE 0.010 0.001 PHE E 283 TRP 0.011 0.001 TRP E 216 HIS 0.007 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6831) covalent geometry : angle 0.60081 ( 9321) hydrogen bonds : bond 0.02644 ( 148) hydrogen bonds : angle 5.38814 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: C 193 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7950 (tp) REVERT: C 219 MET cc_start: -0.0297 (mpp) cc_final: -0.0617 (mpp) outliers start: 20 outliers final: 19 residues processed: 52 average time/residue: 0.0561 time to fit residues: 4.4704 Evaluate side-chains 52 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 43 optimal weight: 40.0000 chunk 80 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 0.0010 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 44 optimal weight: 0.9980 overall best weight: 4.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** D 244 GLN ** 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 = 0.3966 r_free = 0.3966 target = 0.084683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056700 restraints weight = 28040.371| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 4.21 r_work: 0.2962 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6831 Z= 0.116 Angle : 0.609 13.702 9321 Z= 0.303 Chirality : 0.049 0.206 1050 Planarity : 0.004 0.046 1251 Dihedral : 4.638 53.732 942 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.91 % Favored : 94.86 % Rotamer: Outliers : 3.35 % Allowed : 16.32 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.28), residues: 876 helix: -0.28 (1.05), residues: 21 sheet: -0.70 (0.36), residues: 196 loop : -0.61 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 25 TYR 0.010 0.001 TYR C 281 PHE 0.011 0.001 PHE E 283 TRP 0.011 0.001 TRP E 216 HIS 0.007 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6831) covalent geometry : angle 0.60942 ( 9321) hydrogen bonds : bond 0.02550 ( 148) hydrogen bonds : angle 5.22537 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.33 seconds wall clock time: 36 minutes 58.01 seconds (2218.01 seconds total)