Starting phenix.real_space_refine on Mon May 4 00:33:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua0_63974/05_2026/9ua0_63974.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua0_63974/05_2026/9ua0_63974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ua0_63974/05_2026/9ua0_63974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua0_63974/05_2026/9ua0_63974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ua0_63974/05_2026/9ua0_63974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua0_63974/05_2026/9ua0_63974.map" } resolution = 3.39 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= 0.040 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: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5263 2.51 5 N 1356 2.21 5 O 1404 1.98 5 H 8359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4100 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 4037 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 13, 'TRANS': 237} Chain: "C" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4193 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 14, 'TRANS': 249} Chain: "D" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4080 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Time building chain proxies: 3.49, per 1000 atoms: 0.21 Number of scatterers: 16410 At special positions: 0 Unit cell: (85.6, 94.16, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1404 8.00 N 1356 7.00 C 5263 6.00 H 8359 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 572.3 milliseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 61.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 removed outlier: 3.610A pdb=" N VAL A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 4.261A pdb=" N LEU A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.554A pdb=" N SER A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.504A pdb=" N LYS A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 135 through 145 removed outlier: 4.449A pdb=" N ILE A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.553A pdb=" N LEU A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.621A pdb=" N ARG A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 197 through 224 Proline residue: A 203 - end of helix removed outlier: 3.687A pdb=" N ILE A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.735A pdb=" N TRP A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 275 Processing helix chain 'B' and resid 27 through 36 Processing helix chain 'B' and resid 37 through 48 removed outlier: 4.035A pdb=" N GLY B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 82 through 103 removed outlier: 4.167A pdb=" N SER B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.941A pdb=" N LEU B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 removed outlier: 3.813A pdb=" N LYS B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Proline residue: B 123 - end of helix removed outlier: 3.812A pdb=" N THR B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.551A pdb=" N TRP B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.699A pdb=" N ALA B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 196 through 223 Proline residue: B 203 - end of helix removed outlier: 3.516A pdb=" N THR B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 removed outlier: 3.749A pdb=" N TYR B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 274 removed outlier: 4.033A pdb=" N VAL B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.898A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.032A pdb=" N VAL C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU C 120 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 155 removed outlier: 3.647A pdb=" N ALA C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 149 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.755A pdb=" N ASN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.809A pdb=" N VAL C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 262 removed outlier: 3.749A pdb=" N ARG C 259 " --> pdb=" O ASN C 255 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.558A pdb=" N MET D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.796A pdb=" N ALA D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 removed outlier: 3.646A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.347A pdb=" N GLN D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 3.636A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.985A pdb=" N MET D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 272 removed outlier: 3.757A pdb=" N TYR D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.022A pdb=" N ILE C 28 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.417A pdb=" N MET C 81 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL C 195 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER C 39 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 222 " --> pdb=" O MET C 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 41 through 47 removed outlier: 6.427A pdb=" N LYS D 42 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 28 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL D 44 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN D 26 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D 27 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE D 79 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.022A pdb=" N VAL D 99 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG D 224 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 57 " --> pdb=" O VAL D 226 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1140 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: 3.66 Time building geometry restraints manager: 2.06 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: 8354 1.03 - 1.23: 20 1.23 - 1.42: 3297 1.42 - 1.62: 4869 1.62 - 1.81: 51 Bond restraints: 16591 Sorted by residual: bond pdb=" CB MET B 227 " pdb=" CG MET B 227 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.75e-01 bond pdb=" CG MET C 182 " pdb=" HG2 MET C 182 " ideal model delta sigma weight residual 0.970 0.955 0.015 2.00e-02 2.50e+03 5.63e-01 bond pdb=" CG PRO C 136 " pdb=" CD PRO C 136 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 5.01e-01 bond pdb=" CG PRO D 124 " pdb=" CD PRO D 124 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 4.90e-01 bond pdb=" CG PRO A 71 " pdb=" CD PRO A 71 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.22e-01 ... (remaining 16586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 29479 1.47 - 2.95: 640 2.95 - 4.42: 74 4.42 - 5.90: 5 5.90 - 7.37: 2 Bond angle restraints: 30200 Sorted by residual: angle pdb=" N VAL C 123 " pdb=" CA VAL C 123 " pdb=" C VAL C 123 " ideal model delta sigma weight residual 112.96 108.12 4.84 1.00e+00 1.00e+00 2.34e+01 angle pdb=" N ASP C 70 " pdb=" CA ASP C 70 " pdb=" C ASP C 70 " ideal model delta sigma weight residual 113.23 109.39 3.84 1.22e+00 6.72e-01 9.89e+00 angle pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" C ILE A 105 " ideal model delta sigma weight residual 111.81 109.11 2.70 8.60e-01 1.35e+00 9.83e+00 angle pdb=" CA TRP B 41 " pdb=" CB TRP B 41 " pdb=" CG TRP B 41 " ideal model delta sigma weight residual 113.60 118.17 -4.57 1.90e+00 2.77e-01 5.79e+00 angle pdb=" CA ARG D 246 " pdb=" C ARG D 246 " pdb=" N PRO D 247 " ideal model delta sigma weight residual 118.44 121.99 -3.55 1.59e+00 3.96e-01 5.00e+00 ... (remaining 30195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6656 17.97 - 35.94: 751 35.94 - 53.90: 231 53.90 - 71.87: 58 71.87 - 89.84: 10 Dihedral angle restraints: 7706 sinusoidal: 4256 harmonic: 3450 Sorted by residual: dihedral pdb=" CA SER A 98 " pdb=" C SER A 98 " pdb=" N ILE A 99 " pdb=" CA ILE A 99 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO C 231 " pdb=" C PRO C 231 " pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ALA A 100 " pdb=" C ALA A 100 " pdb=" N ALA A 101 " pdb=" CA ALA A 101 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 7703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 845 0.030 - 0.060: 300 0.060 - 0.090: 97 0.090 - 0.120: 58 0.120 - 0.150: 11 Chirality restraints: 1311 Sorted by residual: chirality pdb=" CA ILE D 171 " pdb=" N ILE D 171 " pdb=" C ILE D 171 " pdb=" CB ILE D 171 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE D 24 " pdb=" N ILE D 24 " pdb=" C ILE D 24 " pdb=" CB ILE D 24 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE C 228 " pdb=" N ILE C 228 " pdb=" C ILE C 228 " pdb=" CB ILE C 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1308 not shown) Planarity restraints: 2375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 37 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PHE B 37 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE B 37 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 38 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 29 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 30 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 193 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C PHE B 193 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE B 193 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 194 " 0.010 2.00e-02 2.50e+03 ... (remaining 2372 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 366 2.11 - 2.73: 29356 2.73 - 3.35: 47897 3.35 - 3.98: 59565 3.98 - 4.60: 94763 Nonbonded interactions: 231947 Sorted by model distance: nonbonded pdb=" HE1 TRP D 201 " pdb=" O CYS D 206 " model vdw 1.487 2.450 nonbonded pdb=" O ILE A 58 " pdb=" HG1 THR A 64 " model vdw 1.591 2.450 nonbonded pdb=" O GLN B 85 " pdb=" H ILE B 233 " model vdw 1.592 2.450 nonbonded pdb=" HZ3 LYS C 180 " pdb=" OE1 GLN C 183 " model vdw 1.628 2.450 nonbonded pdb=" HG1 THR D 229 " pdb=" O ASN D 235 " model vdw 1.642 2.450 ... (remaining 231942 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 24 through 274) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 0.025 8232 Z= 0.133 Angle : 0.577 7.374 11205 Z= 0.302 Chirality : 0.040 0.150 1311 Planarity : 0.004 0.046 1408 Dihedral : 17.777 89.839 3008 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.46 % Allowed : 26.16 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.28), residues: 1019 helix: -0.20 (0.23), residues: 579 sheet: -1.71 (0.63), residues: 78 loop : -2.34 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.009 0.001 TYR B 70 PHE 0.009 0.001 PHE C 4 TRP 0.008 0.001 TRP B 41 HIS 0.002 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8232) covalent geometry : angle 0.57718 (11205) hydrogen bonds : bond 0.20421 ( 388) hydrogen bonds : angle 7.51516 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 166 average time/residue: 0.2016 time to fit residues: 46.6339 Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 45 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3683 r_free = 0.3683 target = 0.136066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113682 restraints weight = 37261.038| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.84 r_work: 0.3229 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8232 Z= 0.167 Angle : 0.603 5.783 11205 Z= 0.317 Chirality : 0.041 0.155 1311 Planarity : 0.005 0.052 1408 Dihedral : 4.709 22.414 1105 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.16 % Allowed : 25.23 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.27), residues: 1019 helix: -0.13 (0.22), residues: 589 sheet: -1.99 (0.62), residues: 78 loop : -2.47 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.008 0.001 TYR D 259 PHE 0.014 0.001 PHE A 153 TRP 0.009 0.001 TRP B 41 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8232) covalent geometry : angle 0.60309 (11205) hydrogen bonds : bond 0.05472 ( 388) hydrogen bonds : angle 5.20710 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7642 (ttm170) REVERT: D 192 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7992 (tm-30) outliers start: 10 outliers final: 5 residues processed: 161 average time/residue: 0.2240 time to fit residues: 49.0101 Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3727 r_free = 0.3727 target = 0.140020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117695 restraints weight = 36985.807| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.84 r_work: 0.3270 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8232 Z= 0.116 Angle : 0.557 5.082 11205 Z= 0.290 Chirality : 0.040 0.155 1311 Planarity : 0.005 0.053 1408 Dihedral : 4.623 22.207 1103 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.74 % Allowed : 24.07 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.27), residues: 1019 helix: 0.04 (0.22), residues: 590 sheet: -2.22 (0.60), residues: 78 loop : -2.40 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 246 TYR 0.008 0.001 TYR D 259 PHE 0.009 0.001 PHE B 235 TRP 0.009 0.001 TRP B 41 HIS 0.002 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8232) covalent geometry : angle 0.55723 (11205) hydrogen bonds : bond 0.04478 ( 388) hydrogen bonds : angle 4.81705 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7971 (ttmm) REVERT: C 121 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7458 (ttm170) REVERT: C 198 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7264 (m-30) outliers start: 15 outliers final: 7 residues processed: 165 average time/residue: 0.2112 time to fit residues: 48.3468 Evaluate side-chains 158 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116594 restraints weight = 36769.384| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.81 r_work: 0.3260 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8232 Z= 0.150 Angle : 0.566 5.146 11205 Z= 0.294 Chirality : 0.040 0.157 1311 Planarity : 0.005 0.055 1408 Dihedral : 4.634 23.046 1103 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.08 % Allowed : 24.31 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.27), residues: 1019 helix: 0.07 (0.22), residues: 590 sheet: -2.32 (0.59), residues: 78 loop : -2.39 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.008 0.001 TYR C 243 PHE 0.009 0.001 PHE A 153 TRP 0.008 0.001 TRP A 217 HIS 0.002 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8232) covalent geometry : angle 0.56620 (11205) hydrogen bonds : bond 0.04180 ( 388) hydrogen bonds : angle 4.72093 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 248 GLU cc_start: 0.7777 (mp0) cc_final: 0.7476 (mp0) REVERT: C 121 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: C 198 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: D 252 GLN cc_start: 0.9210 (mp10) cc_final: 0.8666 (mp10) outliers start: 18 outliers final: 11 residues processed: 163 average time/residue: 0.1960 time to fit residues: 44.9901 Evaluate side-chains 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 230 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3728 r_free = 0.3728 target = 0.140105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117875 restraints weight = 36689.899| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.81 r_work: 0.3277 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8232 Z= 0.116 Angle : 0.550 4.972 11205 Z= 0.286 Chirality : 0.039 0.155 1311 Planarity : 0.005 0.054 1408 Dihedral : 4.606 22.835 1103 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.85 % Allowed : 25.23 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.27), residues: 1019 helix: 0.19 (0.22), residues: 590 sheet: -2.32 (0.59), residues: 78 loop : -2.35 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.007 0.001 TYR B 70 PHE 0.009 0.001 PHE C 253 TRP 0.009 0.001 TRP A 217 HIS 0.002 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8232) covalent geometry : angle 0.55035 (11205) hydrogen bonds : bond 0.03933 ( 388) hydrogen bonds : angle 4.61999 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7909 (ttmm) REVERT: B 248 GLU cc_start: 0.7786 (mp0) cc_final: 0.7467 (mp0) REVERT: C 121 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7467 (ttm170) REVERT: C 198 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7306 (m-30) outliers start: 16 outliers final: 9 residues processed: 163 average time/residue: 0.2043 time to fit residues: 46.4333 Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3721 r_free = 0.3721 target = 0.139360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117014 restraints weight = 36625.075| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.81 r_work: 0.3265 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8232 Z= 0.153 Angle : 0.561 5.079 11205 Z= 0.292 Chirality : 0.040 0.157 1311 Planarity : 0.005 0.055 1408 Dihedral : 4.573 23.292 1102 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.31 % Allowed : 24.42 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.27), residues: 1019 helix: 0.16 (0.22), residues: 596 sheet: -2.34 (0.59), residues: 78 loop : -2.32 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 183 TYR 0.008 0.001 TYR B 70 PHE 0.008 0.001 PHE A 153 TRP 0.008 0.001 TRP A 217 HIS 0.002 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8232) covalent geometry : angle 0.56098 (11205) hydrogen bonds : bond 0.03924 ( 388) hydrogen bonds : angle 4.60762 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 248 GLU cc_start: 0.7832 (mp0) cc_final: 0.7539 (mp0) REVERT: C 121 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7495 (ttm170) REVERT: C 198 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: D 252 GLN cc_start: 0.9233 (mp10) cc_final: 0.8600 (mp10) outliers start: 20 outliers final: 11 residues processed: 166 average time/residue: 0.1950 time to fit residues: 45.7293 Evaluate side-chains 159 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 227 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3731 r_free = 0.3731 target = 0.139286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117311 restraints weight = 36300.417| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.78 r_work: 0.3280 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8232 Z= 0.125 Angle : 0.551 4.978 11205 Z= 0.285 Chirality : 0.040 0.154 1311 Planarity : 0.005 0.055 1408 Dihedral : 4.543 23.167 1102 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.74 % Allowed : 25.58 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.28), residues: 1019 helix: 0.27 (0.22), residues: 595 sheet: -2.31 (0.60), residues: 78 loop : -2.28 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.007 0.001 TYR B 70 PHE 0.008 0.001 PHE B 235 TRP 0.009 0.001 TRP A 217 HIS 0.003 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8232) covalent geometry : angle 0.55099 (11205) hydrogen bonds : bond 0.03739 ( 388) hydrogen bonds : angle 4.53388 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7918 (ttmm) REVERT: B 248 GLU cc_start: 0.7829 (mp0) cc_final: 0.7541 (mp0) REVERT: C 198 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: C 258 LYS cc_start: 0.8478 (ttpp) cc_final: 0.7841 (tptt) outliers start: 15 outliers final: 12 residues processed: 160 average time/residue: 0.1898 time to fit residues: 42.8776 Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3733 r_free = 0.3733 target = 0.140525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118214 restraints weight = 36686.559| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.83 r_work: 0.3278 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8232 Z= 0.121 Angle : 0.544 4.936 11205 Z= 0.282 Chirality : 0.039 0.156 1311 Planarity : 0.005 0.056 1408 Dihedral : 4.479 23.064 1102 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.74 % Allowed : 25.58 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 1019 helix: 0.36 (0.22), residues: 594 sheet: -2.28 (0.61), residues: 78 loop : -2.24 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.006 0.001 TYR B 70 PHE 0.008 0.001 PHE B 235 TRP 0.009 0.001 TRP A 217 HIS 0.002 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8232) covalent geometry : angle 0.54433 (11205) hydrogen bonds : bond 0.03625 ( 388) hydrogen bonds : angle 4.47813 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7950 (ttmm) REVERT: B 248 GLU cc_start: 0.7816 (mp0) cc_final: 0.7552 (mp0) REVERT: C 198 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: C 258 LYS cc_start: 0.8476 (ttpp) cc_final: 0.7832 (tptt) outliers start: 15 outliers final: 13 residues processed: 164 average time/residue: 0.1801 time to fit residues: 41.9722 Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3720 r_free = 0.3720 target = 0.139352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116900 restraints weight = 36885.073| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.83 r_work: 0.3260 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8232 Z= 0.164 Angle : 0.569 5.943 11205 Z= 0.295 Chirality : 0.040 0.158 1311 Planarity : 0.005 0.054 1408 Dihedral : 4.540 23.384 1102 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.31 % Allowed : 25.23 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.27), residues: 1019 helix: 0.31 (0.22), residues: 595 sheet: -2.35 (0.60), residues: 78 loop : -2.26 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 210 TYR 0.008 0.001 TYR A 97 PHE 0.009 0.001 PHE A 153 TRP 0.009 0.001 TRP B 41 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8232) covalent geometry : angle 0.56925 (11205) hydrogen bonds : bond 0.03739 ( 388) hydrogen bonds : angle 4.50805 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7952 (ttmm) REVERT: B 248 GLU cc_start: 0.7867 (mp0) cc_final: 0.7653 (mp0) REVERT: C 121 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7522 (ttm170) REVERT: C 198 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: C 258 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7796 (tptt) REVERT: D 198 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8015 (mp) outliers start: 20 outliers final: 14 residues processed: 165 average time/residue: 0.1982 time to fit residues: 45.4295 Evaluate side-chains 168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3715 r_free = 0.3715 target = 0.137532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115430 restraints weight = 36492.882| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.79 r_work: 0.3262 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8232 Z= 0.123 Angle : 0.557 6.266 11205 Z= 0.288 Chirality : 0.040 0.155 1311 Planarity : 0.005 0.055 1408 Dihedral : 4.492 23.235 1102 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.97 % Allowed : 25.69 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.28), residues: 1019 helix: 0.42 (0.22), residues: 594 sheet: -2.35 (0.60), residues: 78 loop : -2.20 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.007 0.001 TYR A 97 PHE 0.008 0.001 PHE B 235 TRP 0.009 0.001 TRP A 217 HIS 0.003 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8232) covalent geometry : angle 0.55723 (11205) hydrogen bonds : bond 0.03584 ( 388) hydrogen bonds : angle 4.45967 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7980 (ttmm) REVERT: C 198 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: C 258 LYS cc_start: 0.8474 (ttpp) cc_final: 0.7771 (tptt) REVERT: D 198 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8001 (mp) outliers start: 17 outliers final: 13 residues processed: 164 average time/residue: 0.1943 time to fit residues: 45.1026 Evaluate side-chains 163 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 161 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 = 0.3898 r_free = 0.3898 target = 0.157399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134340 restraints weight = 36727.797| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.79 r_work: 0.3415 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8232 Z= 0.120 Angle : 0.564 6.376 11205 Z= 0.291 Chirality : 0.040 0.156 1311 Planarity : 0.005 0.054 1408 Dihedral : 4.469 23.173 1102 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.97 % Allowed : 25.69 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.28), residues: 1019 helix: 0.48 (0.22), residues: 595 sheet: -2.37 (0.59), residues: 78 loop : -2.19 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 246 TYR 0.007 0.001 TYR B 70 PHE 0.007 0.001 PHE B 235 TRP 0.009 0.001 TRP A 217 HIS 0.004 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8232) covalent geometry : angle 0.56376 (11205) hydrogen bonds : bond 0.03537 ( 388) hydrogen bonds : angle 4.41869 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.59 seconds wall clock time: 56 minutes 20.44 seconds (3380.44 seconds total)