Starting phenix.real_space_refine on Sun May 18 07:18:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm8_37645/05_2025/8wm8_37645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm8_37645/05_2025/8wm8_37645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wm8_37645/05_2025/8wm8_37645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm8_37645/05_2025/8wm8_37645.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm8_37645/05_2025/8wm8_37645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm8_37645/05_2025/8wm8_37645.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 25 5.16 5 C 5396 2.51 5 N 1374 2.21 5 O 1459 1.98 5 H 8522 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16776 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4116 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4198 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 17, 'TRANS': 247} Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4170 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 17, 'TRANS': 245} Chain: "C" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4288 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'NO3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.02, per 1000 atoms: 0.48 Number of scatterers: 16776 At special positions: 0 Unit cell: (81.32, 118.77, 95.23, 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 25 16.00 O 1459 8.00 N 1374 7.00 C 5396 6.00 H 8522 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: 4.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 56.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.852A pdb=" N CYS D 103 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU D 104 " --> pdb=" O ASN D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 109 through 119 removed outlier: 4.008A pdb=" N ALA D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 140 removed outlier: 3.710A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.663A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 204 removed outlier: 3.548A pdb=" N GLU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.769A pdb=" N ASP D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.643A pdb=" N ASN B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.553A pdb=" N LEU B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.686A pdb=" N PHE B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 67' Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.832A pdb=" N SER B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.823A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 129 removed outlier: 4.034A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 4.340A pdb=" N VAL B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.664A pdb=" N ILE B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.871A pdb=" N ASN B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.620A pdb=" N ILE B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 195 through 208 Proline residue: B 201 - end of helix Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.804A pdb=" N GLY B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.610A pdb=" N ASN B 239 " --> pdb=" O TRP B 235 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 240' Processing helix chain 'B' and resid 244 through 275 removed outlier: 3.950A pdb=" N GLU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.530A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.024A pdb=" N ASN A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.549A pdb=" N ILE A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.569A pdb=" N THR A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.736A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.562A pdb=" N LEU A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.697A pdb=" N VAL A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.534A pdb=" N ILE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.507A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 123 removed outlier: 3.745A pdb=" N ALA C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.805A pdb=" N ARG C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 removed outlier: 3.825A pdb=" N GLU C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.837A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.831A pdb=" N VAL C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 removed outlier: 4.187A pdb=" N TYR C 244 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 47 removed outlier: 6.433A pdb=" N LYS D 28 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP D 41 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL D 26 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 43 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU D 24 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 45 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL D 22 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU D 24 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL D 80 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.518A pdb=" N LEU D 208 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL D 225 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS D 54 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 25 removed outlier: 6.529A pdb=" N ARG C 12 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS C 9 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY C 65 " --> pdb=" O HIS C 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162 removed outlier: 7.129A pdb=" N LEU C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER C 39 " --> pdb=" O VAL C 210 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 927 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: 5.78 Time building geometry restraints manager: 5.04 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: 8514 1.03 - 1.23: 9 1.23 - 1.42: 3400 1.42 - 1.62: 4997 1.62 - 1.81: 42 Bond restraints: 16962 Sorted by residual: bond pdb=" N NO3 A 301 " pdb=" O3 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.264 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" N NO3 A 301 " pdb=" O2 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.264 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" N NO3 A 301 " pdb=" O1 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.263 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C ILE B 209 " pdb=" O ILE B 209 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.19e-02 7.06e+03 1.28e+00 bond pdb=" C GLY D 35 " pdb=" N PRO D 36 " ideal model delta sigma weight residual 1.333 1.343 -0.010 1.01e-02 9.80e+03 9.72e-01 ... (remaining 16957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 29168 1.19 - 2.38: 1571 2.38 - 3.56: 100 3.56 - 4.75: 33 4.75 - 5.94: 6 Bond angle restraints: 30878 Sorted by residual: angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 113.41 107.47 5.94 1.22e+00 6.72e-01 2.37e+01 angle pdb=" N ASN A 117 " pdb=" CA ASN A 117 " pdb=" C ASN A 117 " ideal model delta sigma weight residual 114.62 109.17 5.45 1.14e+00 7.69e-01 2.28e+01 angle pdb=" N VAL C 106 " pdb=" CA VAL C 106 " pdb=" C VAL C 106 " ideal model delta sigma weight residual 111.62 108.23 3.39 7.90e-01 1.60e+00 1.84e+01 angle pdb=" N ASP D 178 " pdb=" CA ASP D 178 " pdb=" C ASP D 178 " ideal model delta sigma weight residual 110.41 106.28 4.13 1.23e+00 6.61e-01 1.13e+01 angle pdb=" CA ASN A 117 " pdb=" C ASN A 117 " pdb=" N ALA A 118 " ideal model delta sigma weight residual 119.71 116.30 3.41 1.17e+00 7.31e-01 8.47e+00 ... (remaining 30873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7061 17.96 - 35.92: 570 35.92 - 53.88: 221 53.88 - 71.84: 37 71.84 - 89.80: 16 Dihedral angle restraints: 7905 sinusoidal: 4361 harmonic: 3544 Sorted by residual: dihedral pdb=" CA TRP A 235 " pdb=" C TRP A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N ILE A 158 " pdb=" CA ILE A 158 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP A 23 " pdb=" C TRP A 23 " pdb=" N LYS A 24 " pdb=" CA LYS A 24 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 851 0.030 - 0.059: 303 0.059 - 0.089: 118 0.089 - 0.118: 62 0.118 - 0.148: 13 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA ILE B 172 " pdb=" N ILE B 172 " pdb=" C ILE B 172 " pdb=" CB ILE B 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 172 " pdb=" N ILE A 172 " pdb=" C ILE A 172 " pdb=" CB ILE A 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE D 241 " pdb=" N ILE D 241 " pdb=" C ILE D 241 " pdb=" CB ILE D 241 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1344 not shown) Planarity restraints: 2447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 112 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 113 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 146 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 147 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 245 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO D 246 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 246 " 0.022 5.00e-02 4.00e+02 ... (remaining 2444 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 795 2.18 - 2.78: 34458 2.78 - 3.39: 46449 3.39 - 3.99: 59381 3.99 - 4.60: 92618 Nonbonded interactions: 233701 Sorted by model distance: nonbonded pdb=" O PRO A 160 " pdb="HD21 ASN A 164 " model vdw 1.572 2.450 nonbonded pdb=" OD1 ASP D 267 " pdb="HD21 ASN D 271 " model vdw 1.592 2.450 nonbonded pdb=" O PHE D 219 " pdb="HH11 ARG D 247 " model vdw 1.614 2.450 nonbonded pdb=" OD1 ASN D 263 " pdb=" HH TYR C 244 " model vdw 1.650 2.450 nonbonded pdb=" OD1 ASP C 8 " pdb=" HD1 HIS C 9 " model vdw 1.675 2.450 ... (remaining 233696 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 15 through 277) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 16 through 277)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.930 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.002 0.044 8440 Z= 0.114 Angle : 0.581 5.941 11494 Z= 0.328 Chirality : 0.040 0.148 1347 Planarity : 0.004 0.046 1458 Dihedral : 14.853 89.805 3077 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.26), residues: 1047 helix: -1.14 (0.24), residues: 517 sheet: -2.40 (0.66), residues: 66 loop : -2.07 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.002 0.001 HIS C 240 PHE 0.015 0.001 PHE D 20 TYR 0.011 0.001 TYR D 102 ARG 0.004 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.28261 ( 318) hydrogen bonds : angle 9.87400 ( 927) covalent geometry : bond 0.00238 ( 8440) covalent geometry : angle 0.58135 (11494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3588 time to fit residues: 94.5389 Evaluate side-chains 150 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** A 170 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 = 0.3789 r_free = 0.3789 target = 0.149810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116356 restraints weight = 34751.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122490 restraints weight = 15534.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126336 restraints weight = 9481.950| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8440 Z= 0.171 Angle : 0.645 6.587 11494 Z= 0.337 Chirality : 0.043 0.143 1347 Planarity : 0.005 0.053 1458 Dihedral : 5.195 25.161 1122 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 0.56 % Allowed : 9.03 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.25), residues: 1047 helix: -1.10 (0.22), residues: 527 sheet: -2.70 (0.62), residues: 65 loop : -2.31 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 159 HIS 0.006 0.001 HIS C 197 PHE 0.013 0.001 PHE A 95 TYR 0.018 0.002 TYR A 116 ARG 0.005 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.06266 ( 318) hydrogen bonds : angle 6.51172 ( 927) covalent geometry : bond 0.00382 ( 8440) covalent geometry : angle 0.64474 (11494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 TYR cc_start: 0.8102 (m-10) cc_final: 0.7449 (m-10) REVERT: A 144 GLN cc_start: 0.6765 (mp-120) cc_final: 0.6547 (mp10) REVERT: A 236 ASP cc_start: 0.8054 (t0) cc_final: 0.7766 (t0) REVERT: C 75 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7435 (mp0) outliers start: 5 outliers final: 3 residues processed: 164 average time/residue: 0.3461 time to fit residues: 83.2194 Evaluate side-chains 156 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116419 restraints weight = 34378.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122258 restraints weight = 15823.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125921 restraints weight = 9804.617| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8440 Z= 0.123 Angle : 0.590 6.146 11494 Z= 0.308 Chirality : 0.042 0.149 1347 Planarity : 0.005 0.056 1458 Dihedral : 5.096 25.103 1122 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 0.56 % Allowed : 10.48 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.25), residues: 1047 helix: -1.04 (0.22), residues: 537 sheet: -2.59 (0.64), residues: 60 loop : -2.28 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.005 0.001 HIS C 197 PHE 0.012 0.001 PHE A 95 TYR 0.010 0.001 TYR B 238 ARG 0.004 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 318) hydrogen bonds : angle 5.82234 ( 927) covalent geometry : bond 0.00278 ( 8440) covalent geometry : angle 0.58956 (11494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8157 (t80) cc_final: 0.7952 (t80) REVERT: A 236 ASP cc_start: 0.7993 (t0) cc_final: 0.7721 (t0) REVERT: C 75 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7379 (mp0) outliers start: 5 outliers final: 5 residues processed: 162 average time/residue: 0.3594 time to fit residues: 87.8703 Evaluate side-chains 155 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114135 restraints weight = 34922.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119874 restraints weight = 16198.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123442 restraints weight = 10109.507| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8440 Z= 0.169 Angle : 0.603 6.732 11494 Z= 0.314 Chirality : 0.042 0.145 1347 Planarity : 0.005 0.057 1458 Dihedral : 5.179 25.424 1122 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 0.67 % Allowed : 13.04 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.25), residues: 1047 helix: -1.01 (0.22), residues: 541 sheet: -2.63 (0.59), residues: 70 loop : -2.35 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS D 137 PHE 0.016 0.001 PHE A 95 TYR 0.011 0.001 TYR B 176 ARG 0.004 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 318) hydrogen bonds : angle 5.59663 ( 927) covalent geometry : bond 0.00391 ( 8440) covalent geometry : angle 0.60285 (11494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8149 (t80) cc_final: 0.7880 (t80) REVERT: A 156 THR cc_start: 0.8746 (t) cc_final: 0.8531 (t) REVERT: A 236 ASP cc_start: 0.8127 (t0) cc_final: 0.7872 (t0) REVERT: C 75 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7428 (mp0) outliers start: 6 outliers final: 6 residues processed: 150 average time/residue: 0.3432 time to fit residues: 76.8359 Evaluate side-chains 153 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115533 restraints weight = 34949.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121240 restraints weight = 16023.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124897 restraints weight = 9971.094| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8440 Z= 0.129 Angle : 0.581 6.156 11494 Z= 0.300 Chirality : 0.041 0.149 1347 Planarity : 0.005 0.057 1458 Dihedral : 5.130 25.652 1122 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 0.78 % Allowed : 14.27 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.25), residues: 1047 helix: -0.91 (0.22), residues: 541 sheet: -2.63 (0.59), residues: 70 loop : -2.31 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.003 0.001 HIS D 137 PHE 0.020 0.001 PHE A 154 TYR 0.012 0.001 TYR A 116 ARG 0.004 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 318) hydrogen bonds : angle 5.32036 ( 927) covalent geometry : bond 0.00305 ( 8440) covalent geometry : angle 0.58140 (11494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8142 (t80) cc_final: 0.7871 (t80) REVERT: A 144 GLN cc_start: 0.6748 (mp-120) cc_final: 0.6489 (mp10) REVERT: A 156 THR cc_start: 0.8764 (t) cc_final: 0.8537 (t) REVERT: A 236 ASP cc_start: 0.8089 (t0) cc_final: 0.7844 (t0) REVERT: C 75 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7412 (mp0) outliers start: 7 outliers final: 7 residues processed: 156 average time/residue: 0.3532 time to fit residues: 81.8220 Evaluate side-chains 154 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114957 restraints weight = 34834.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120726 restraints weight = 16096.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124357 restraints weight = 10043.966| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8440 Z= 0.131 Angle : 0.578 6.367 11494 Z= 0.299 Chirality : 0.042 0.146 1347 Planarity : 0.005 0.057 1458 Dihedral : 5.111 25.546 1122 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 0.78 % Allowed : 15.72 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.26), residues: 1047 helix: -0.83 (0.23), residues: 536 sheet: -2.63 (0.59), residues: 70 loop : -2.26 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.003 0.001 HIS D 137 PHE 0.018 0.001 PHE A 154 TYR 0.010 0.001 TYR B 176 ARG 0.004 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 318) hydrogen bonds : angle 5.16369 ( 927) covalent geometry : bond 0.00310 ( 8440) covalent geometry : angle 0.57847 (11494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8136 (t80) cc_final: 0.7867 (t80) REVERT: A 144 GLN cc_start: 0.6732 (mp-120) cc_final: 0.6458 (mp10) REVERT: A 156 THR cc_start: 0.8782 (t) cc_final: 0.8553 (t) REVERT: A 236 ASP cc_start: 0.8106 (t0) cc_final: 0.7811 (t0) REVERT: C 75 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7444 (mp0) outliers start: 7 outliers final: 7 residues processed: 155 average time/residue: 0.3472 time to fit residues: 79.6814 Evaluate side-chains 152 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 0.0170 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114473 restraints weight = 34836.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120168 restraints weight = 16097.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123737 restraints weight = 10045.994| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8440 Z= 0.141 Angle : 0.584 6.332 11494 Z= 0.302 Chirality : 0.042 0.147 1347 Planarity : 0.005 0.057 1458 Dihedral : 5.133 25.759 1122 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 1.00 % Allowed : 15.94 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.26), residues: 1047 helix: -0.84 (0.23), residues: 541 sheet: -2.63 (0.60), residues: 70 loop : -2.22 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.003 0.001 HIS C 122 PHE 0.018 0.001 PHE A 154 TYR 0.011 0.001 TYR B 176 ARG 0.005 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 318) hydrogen bonds : angle 5.09071 ( 927) covalent geometry : bond 0.00334 ( 8440) covalent geometry : angle 0.58416 (11494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8143 (t80) cc_final: 0.7875 (t80) REVERT: A 144 GLN cc_start: 0.6786 (mp-120) cc_final: 0.6518 (mp10) REVERT: A 236 ASP cc_start: 0.8088 (t0) cc_final: 0.7805 (t0) REVERT: C 75 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7425 (mp0) outliers start: 9 outliers final: 9 residues processed: 152 average time/residue: 0.3359 time to fit residues: 75.2537 Evaluate side-chains 155 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113838 restraints weight = 34836.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119519 restraints weight = 16272.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123107 restraints weight = 10215.326| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8440 Z= 0.166 Angle : 0.595 6.710 11494 Z= 0.308 Chirality : 0.042 0.145 1347 Planarity : 0.005 0.059 1458 Dihedral : 5.196 26.070 1122 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.34 % Allowed : 15.50 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.26), residues: 1047 helix: -0.80 (0.23), residues: 540 sheet: -2.73 (0.58), residues: 71 loop : -2.23 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.002 0.001 HIS D 137 PHE 0.018 0.001 PHE A 95 TYR 0.015 0.001 TYR B 176 ARG 0.005 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 318) hydrogen bonds : angle 5.08805 ( 927) covalent geometry : bond 0.00391 ( 8440) covalent geometry : angle 0.59533 (11494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.7621 (t80) cc_final: 0.7367 (t80) REVERT: D 115 TYR cc_start: 0.8151 (t80) cc_final: 0.7885 (t80) REVERT: A 144 GLN cc_start: 0.6899 (mp-120) cc_final: 0.6641 (mp10) REVERT: A 236 ASP cc_start: 0.8106 (t0) cc_final: 0.7877 (t0) REVERT: C 75 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7458 (mp0) outliers start: 12 outliers final: 12 residues processed: 152 average time/residue: 0.3419 time to fit residues: 77.2998 Evaluate side-chains 158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115244 restraints weight = 34745.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121040 restraints weight = 15984.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124660 restraints weight = 9952.061| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8440 Z= 0.114 Angle : 0.575 6.983 11494 Z= 0.295 Chirality : 0.042 0.152 1347 Planarity : 0.005 0.059 1458 Dihedral : 5.104 26.097 1122 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 1.23 % Allowed : 15.94 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.26), residues: 1047 helix: -0.65 (0.23), residues: 541 sheet: -2.64 (0.60), residues: 71 loop : -2.15 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.004 0.001 HIS D 137 PHE 0.018 0.001 PHE A 154 TYR 0.017 0.001 TYR D 102 ARG 0.004 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 318) hydrogen bonds : angle 4.94380 ( 927) covalent geometry : bond 0.00273 ( 8440) covalent geometry : angle 0.57485 (11494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.7581 (t80) cc_final: 0.7316 (t80) REVERT: D 115 TYR cc_start: 0.8095 (t80) cc_final: 0.7863 (t80) REVERT: A 144 GLN cc_start: 0.6716 (mp-120) cc_final: 0.6458 (mp10) REVERT: A 236 ASP cc_start: 0.8108 (t0) cc_final: 0.7830 (t0) REVERT: C 75 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7419 (mp0) outliers start: 11 outliers final: 11 residues processed: 155 average time/residue: 0.3430 time to fit residues: 80.2769 Evaluate side-chains 159 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116726 restraints weight = 34424.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122538 restraints weight = 15766.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126162 restraints weight = 9816.813| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8440 Z= 0.111 Angle : 0.572 7.114 11494 Z= 0.294 Chirality : 0.042 0.147 1347 Planarity : 0.005 0.059 1458 Dihedral : 5.041 25.511 1122 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.23 % Allowed : 16.39 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 1047 helix: -0.56 (0.23), residues: 541 sheet: -2.58 (0.60), residues: 71 loop : -2.10 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.005 0.001 HIS D 137 PHE 0.018 0.001 PHE A 154 TYR 0.011 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 318) hydrogen bonds : angle 4.86539 ( 927) covalent geometry : bond 0.00266 ( 8440) covalent geometry : angle 0.57247 (11494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.7617 (t80) cc_final: 0.7348 (t80) REVERT: D 115 TYR cc_start: 0.8103 (t80) cc_final: 0.7875 (t80) REVERT: A 144 GLN cc_start: 0.6786 (mp-120) cc_final: 0.6519 (mp10) REVERT: A 236 ASP cc_start: 0.8084 (t0) cc_final: 0.7806 (t0) outliers start: 11 outliers final: 11 residues processed: 156 average time/residue: 0.3616 time to fit residues: 82.8388 Evaluate side-chains 162 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116207 restraints weight = 34596.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122035 restraints weight = 15883.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125648 restraints weight = 9855.798| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8440 Z= 0.115 Angle : 0.579 7.150 11494 Z= 0.296 Chirality : 0.042 0.148 1347 Planarity : 0.005 0.059 1458 Dihedral : 5.005 25.337 1122 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.11 % Allowed : 17.17 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.26), residues: 1047 helix: -0.50 (0.23), residues: 547 sheet: -2.56 (0.60), residues: 71 loop : -2.11 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.005 0.001 HIS D 137 PHE 0.017 0.001 PHE A 154 TYR 0.012 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 318) hydrogen bonds : angle 4.81985 ( 927) covalent geometry : bond 0.00275 ( 8440) covalent geometry : angle 0.57863 (11494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.72 seconds wall clock time: 88 minutes 4.37 seconds (5284.37 seconds total)