Starting phenix.real_space_refine on Tue Mar 3 20:57:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o0z_12684/03_2026/7o0z_12684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o0z_12684/03_2026/7o0z_12684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2026/7o0z_12684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2026/7o0z_12684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2026/7o0z_12684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2026/7o0z_12684.map" } resolution = 3.7 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 5649 2.51 5 N 1516 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1999 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Chain: "E" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1997 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.19, per 1000 atoms: 0.25 Number of scatterers: 8730 At special positions: 0 Unit cell: (84.132, 103.626, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1539 8.00 N 1516 7.00 C 5649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 326.7 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 59.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 39 through 42 removed outlier: 3.903A pdb=" N LYS B 42 " --> pdb=" O GLY B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.737A pdb=" N LEU B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.551A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.536A pdb=" N ASP B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.596A pdb=" N LEU B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.820A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.507A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.699A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.522A pdb=" N MET B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.514A pdb=" N THR C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.660A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.504A pdb=" N ALA C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.513A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.622A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 232 through 241 removed outlier: 4.039A pdb=" N TRP C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 removed outlier: 3.764A pdb=" N LEU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 4.065A pdb=" N ALA C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.256A pdb=" N GLY C 306 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 3.757A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 43 removed outlier: 3.619A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.775A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.527A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.598A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 131 removed outlier: 3.959A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 removed outlier: 3.754A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP D 141 " --> pdb=" O GLY D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 168 removed outlier: 3.875A pdb=" N ILE D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.537A pdb=" N GLY D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 209 through 214 removed outlier: 4.010A pdb=" N LEU D 213 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.819A pdb=" N ILE D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.967A pdb=" N LEU D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 17 removed outlier: 4.049A pdb=" N LYS E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.526A pdb=" N LEU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 75 removed outlier: 4.213A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 85 removed outlier: 3.705A pdb=" N GLY E 84 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.755A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 132 removed outlier: 3.511A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 139 through 168 removed outlier: 4.022A pdb=" N ARG E 145 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE E 148 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.562A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.758A pdb=" N ALA E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.865A pdb=" N LEU E 212 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 213 " --> pdb=" O PRO E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 213' Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.512A pdb=" N ASN E 225 " --> pdb=" O TYR E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 245 removed outlier: 3.659A pdb=" N SER E 240 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 272 removed outlier: 3.508A pdb=" N LEU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.771A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 9 through 12 removed outlier: 5.380A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.174A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 201 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE B 35 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA B 202 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 250 removed outlier: 3.576A pdb=" N LEU B 250 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 5.468A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 4 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 149 through 153 removed outlier: 6.468A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 248 through 251 removed outlier: 3.550A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2832 1.34 - 1.46: 1611 1.46 - 1.57: 4401 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 8888 Sorted by residual: bond pdb=" C LEU D 209 " pdb=" N PRO D 210 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.11e-02 8.12e+03 5.66e+00 bond pdb=" CB ASN C 38 " pdb=" CG ASN C 38 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.87e+00 bond pdb=" C ILE E 51 " pdb=" N PRO E 52 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.06e-02 8.90e+03 3.17e+00 bond pdb=" CG LEU C 151 " pdb=" CD2 LEU C 151 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.03e+00 bond pdb=" CA LEU D 209 " pdb=" C LEU D 209 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.26e-02 6.30e+03 2.97e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 11785 3.08 - 6.16: 232 6.16 - 9.25: 36 9.25 - 12.33: 7 12.33 - 15.41: 1 Bond angle restraints: 12061 Sorted by residual: angle pdb=" C SER B 231 " pdb=" N GLU B 232 " pdb=" CA GLU B 232 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" CA LEU C 188 " pdb=" CB LEU C 188 " pdb=" CG LEU C 188 " ideal model delta sigma weight residual 116.30 131.71 -15.41 3.50e+00 8.16e-02 1.94e+01 angle pdb=" C VAL C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta sigma weight residual 124.31 131.61 -7.30 1.67e+00 3.59e-01 1.91e+01 angle pdb=" C GLN C 304 " pdb=" N GLU C 305 " pdb=" CA GLU C 305 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 ... (remaining 12056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 4490 15.57 - 31.13: 576 31.13 - 46.70: 157 46.70 - 62.26: 26 62.26 - 77.83: 8 Dihedral angle restraints: 5257 sinusoidal: 2047 harmonic: 3210 Sorted by residual: dihedral pdb=" CA GLU B 232 " pdb=" C GLU B 232 " pdb=" N ARG B 233 " pdb=" CA ARG B 233 " ideal model delta harmonic sigma weight residual 180.00 146.88 33.12 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA GLU B 305 " pdb=" C GLU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET E 66 " pdb=" C MET E 66 " pdb=" N PRO E 67 " pdb=" CA PRO E 67 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1327 0.106 - 0.212: 84 0.212 - 0.317: 12 0.317 - 0.423: 1 0.423 - 0.529: 1 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB VAL C 260 " pdb=" CA VAL C 260 " pdb=" CG1 VAL C 260 " pdb=" CG2 VAL C 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB ILE B 200 " pdb=" CA ILE B 200 " pdb=" CG1 ILE B 200 " pdb=" CG2 ILE B 200 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1422 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO E 67 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " -0.049 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO D 67 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 51 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 52 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " -0.036 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2934 2.84 - 3.35: 7686 3.35 - 3.87: 15151 3.87 - 4.38: 16958 4.38 - 4.90: 27991 Nonbonded interactions: 70720 Sorted by model distance: nonbonded pdb=" O ILE D 51 " pdb=" OG1 THR D 54 " model vdw 2.319 3.040 nonbonded pdb=" O TRP E 259 " pdb=" OG SER E 263 " model vdw 2.324 3.040 nonbonded pdb=" O ALA D 59 " pdb=" OG1 THR D 63 " model vdw 2.341 3.040 nonbonded pdb=" O SER B 90 " pdb=" OG1 THR B 94 " model vdw 2.342 3.040 nonbonded pdb=" OE1 GLU D 81 " pdb=" OG1 THR D 86 " model vdw 2.342 3.040 ... (remaining 70715 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 231 or resid 236 through 274)) selection = (chain 'E' and (resid 2 through 43 or resid 50 through 274)) } 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: 0.560 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.090 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.007 0.073 8888 Z= 0.347 Angle : 1.083 15.411 12061 Z= 0.564 Chirality : 0.062 0.529 1425 Planarity : 0.007 0.078 1520 Dihedral : 15.074 77.831 3207 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.44 % Allowed : 13.92 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.96 (0.16), residues: 1126 helix: -4.61 (0.08), residues: 633 sheet: -2.85 (0.39), residues: 114 loop : -2.56 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 307 TYR 0.019 0.002 TYR C 86 PHE 0.019 0.002 PHE E 143 TRP 0.016 0.002 TRP B 240 HIS 0.009 0.002 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00728 ( 8888) covalent geometry : angle 1.08307 (12061) hydrogen bonds : bond 0.30049 ( 432) hydrogen bonds : angle 10.77127 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7798 (pttp) cc_final: 0.6941 (ptpp) REVERT: B 47 LYS cc_start: 0.9761 (mttm) cc_final: 0.9474 (mttp) REVERT: B 111 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9078 (pt0) REVERT: C 42 LYS cc_start: 0.9462 (ttpt) cc_final: 0.8466 (ttmm) REVERT: C 46 MET cc_start: 0.9000 (ttp) cc_final: 0.8780 (ttp) REVERT: C 47 LYS cc_start: 0.9808 (mttt) cc_final: 0.9423 (mtmm) REVERT: C 89 LEU cc_start: 0.9567 (mt) cc_final: 0.9103 (tp) REVERT: C 141 GLN cc_start: 0.9609 (pp30) cc_final: 0.9370 (pp30) REVERT: C 200 ILE cc_start: 0.9928 (mt) cc_final: 0.9549 (tt) REVERT: D 147 MET cc_start: 0.9313 (mmt) cc_final: 0.8927 (mmm) REVERT: D 171 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8836 (tttm) REVERT: E 76 ASP cc_start: 0.8812 (p0) cc_final: 0.8548 (p0) REVERT: E 88 MET cc_start: 0.9159 (tpp) cc_final: 0.8780 (tpp) REVERT: E 97 ARG cc_start: 0.9122 (mtt180) cc_final: 0.7786 (mmm-85) REVERT: E 147 MET cc_start: 0.9314 (mtt) cc_final: 0.8743 (mmt) REVERT: E 170 GLU cc_start: 0.8909 (pm20) cc_final: 0.8050 (pm20) REVERT: E 222 ARG cc_start: 0.9452 (mtm180) cc_final: 0.9225 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 141 average time/residue: 0.1033 time to fit residues: 19.7825 Evaluate side-chains 91 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 194 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 ASN C 38 ASN C 176 GLN C 194 HIS C 270 GLN D 6 ASN D 225 ASN E 99 GLN E 225 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.042691 restraints weight = 46100.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044172 restraints weight = 24435.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045201 restraints weight = 15819.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045930 restraints weight = 11512.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046412 restraints weight = 9139.524| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8888 Z= 0.139 Angle : 0.659 8.691 12061 Z= 0.337 Chirality : 0.041 0.208 1425 Planarity : 0.005 0.040 1520 Dihedral : 5.304 33.632 1234 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.99 % Allowed : 18.56 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.21), residues: 1126 helix: -2.31 (0.16), residues: 644 sheet: -2.44 (0.43), residues: 104 loop : -2.39 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 248 TYR 0.017 0.001 TYR B 293 PHE 0.011 0.001 PHE D 146 TRP 0.037 0.001 TRP E 259 HIS 0.004 0.001 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8888) covalent geometry : angle 0.65880 (12061) hydrogen bonds : bond 0.04060 ( 432) hydrogen bonds : angle 5.50570 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7543 (pttp) cc_final: 0.7215 (pttm) REVERT: B 47 LYS cc_start: 0.9754 (mttm) cc_final: 0.9492 (mttp) REVERT: B 89 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8949 (tt) REVERT: C 38 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7325 (p0) REVERT: C 42 LYS cc_start: 0.9480 (ttpt) cc_final: 0.8558 (ttmm) REVERT: C 47 LYS cc_start: 0.9811 (mttt) cc_final: 0.9493 (mtmm) REVERT: C 48 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9477 (mm) REVERT: C 89 LEU cc_start: 0.9643 (mt) cc_final: 0.9130 (tp) REVERT: D 11 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8969 (mm-30) REVERT: D 81 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 146 PHE cc_start: 0.8999 (m-80) cc_final: 0.8631 (t80) REVERT: D 147 MET cc_start: 0.9172 (mmt) cc_final: 0.8810 (mmp) REVERT: D 221 TYR cc_start: 0.8974 (t80) cc_final: 0.8257 (t80) REVERT: D 259 TRP cc_start: 0.8530 (m100) cc_final: 0.8207 (m100) REVERT: E 76 ASP cc_start: 0.8803 (p0) cc_final: 0.8586 (p0) REVERT: E 83 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8793 (mm-30) REVERT: E 88 MET cc_start: 0.9151 (tpp) cc_final: 0.8848 (tpp) REVERT: E 147 MET cc_start: 0.9275 (mtt) cc_final: 0.8841 (mtp) REVERT: E 170 GLU cc_start: 0.8428 (pm20) cc_final: 0.7771 (pm20) outliers start: 18 outliers final: 8 residues processed: 128 average time/residue: 0.0832 time to fit residues: 15.4898 Evaluate side-chains 101 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 263 HIS C 38 ASN C 214 GLN C 263 HIS E 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041659 restraints weight = 47253.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043080 restraints weight = 25165.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044062 restraints weight = 16371.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.044745 restraints weight = 12006.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045251 restraints weight = 9578.360| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8888 Z= 0.189 Angle : 0.675 9.244 12061 Z= 0.337 Chirality : 0.043 0.200 1425 Planarity : 0.004 0.037 1520 Dihedral : 4.875 31.858 1234 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.98 % Allowed : 20.44 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.24), residues: 1126 helix: -0.69 (0.19), residues: 645 sheet: -2.20 (0.44), residues: 104 loop : -2.06 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 248 TYR 0.015 0.001 TYR B 293 PHE 0.013 0.001 PHE D 157 TRP 0.020 0.001 TRP E 259 HIS 0.004 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8888) covalent geometry : angle 0.67533 (12061) hydrogen bonds : bond 0.03610 ( 432) hydrogen bonds : angle 4.98846 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7520 (pttp) cc_final: 0.7193 (pttm) REVERT: B 47 LYS cc_start: 0.9779 (mttm) cc_final: 0.9521 (mttp) REVERT: B 89 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8888 (tt) REVERT: B 133 MET cc_start: 0.9413 (mtm) cc_final: 0.8961 (mtm) REVERT: C 42 LYS cc_start: 0.9525 (ttpt) cc_final: 0.8801 (ttmt) REVERT: C 47 LYS cc_start: 0.9836 (mttt) cc_final: 0.9527 (mtmm) REVERT: C 89 LEU cc_start: 0.9591 (mt) cc_final: 0.9327 (tp) REVERT: C 133 MET cc_start: 0.9296 (mtm) cc_final: 0.8710 (ptp) REVERT: C 295 MET cc_start: 0.9434 (mmm) cc_final: 0.9133 (mmm) REVERT: D 11 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9093 (mm-30) REVERT: D 58 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9505 (mm) REVERT: D 81 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8361 (mm-30) REVERT: D 146 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8599 (t80) REVERT: D 147 MET cc_start: 0.9208 (mmt) cc_final: 0.8853 (mmp) REVERT: D 221 TYR cc_start: 0.9108 (t80) cc_final: 0.8345 (t80) REVERT: E 76 ASP cc_start: 0.8825 (p0) cc_final: 0.8574 (p0) REVERT: E 83 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8849 (mt-10) REVERT: E 97 ARG cc_start: 0.8805 (mtt180) cc_final: 0.8389 (mmm-85) REVERT: E 147 MET cc_start: 0.9267 (mtt) cc_final: 0.8833 (mtp) REVERT: E 170 GLU cc_start: 0.8384 (pm20) cc_final: 0.7636 (pm20) REVERT: E 223 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9398 (mm) outliers start: 27 outliers final: 13 residues processed: 114 average time/residue: 0.0714 time to fit residues: 12.2351 Evaluate side-chains 97 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 0.0030 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 HIS C 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042312 restraints weight = 47294.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.043750 restraints weight = 25182.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044751 restraints weight = 16434.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.045454 restraints weight = 12067.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045944 restraints weight = 9598.775| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8888 Z= 0.137 Angle : 0.618 9.238 12061 Z= 0.306 Chirality : 0.042 0.222 1425 Planarity : 0.004 0.037 1520 Dihedral : 4.701 31.639 1234 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.76 % Allowed : 22.87 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.31 (0.25), residues: 1126 helix: -0.03 (0.20), residues: 648 sheet: -2.13 (0.44), residues: 114 loop : -1.80 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 248 TYR 0.018 0.001 TYR E 93 PHE 0.013 0.001 PHE D 157 TRP 0.023 0.001 TRP E 259 HIS 0.013 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8888) covalent geometry : angle 0.61809 (12061) hydrogen bonds : bond 0.03270 ( 432) hydrogen bonds : angle 4.64917 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7473 (pttp) cc_final: 0.7156 (pttm) REVERT: B 47 LYS cc_start: 0.9767 (mttm) cc_final: 0.9509 (mttp) REVERT: B 89 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8802 (tt) REVERT: B 133 MET cc_start: 0.9397 (mtm) cc_final: 0.9045 (mtm) REVERT: C 42 LYS cc_start: 0.9555 (ttpt) cc_final: 0.8820 (ttmt) REVERT: C 43 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9376 (p) REVERT: C 47 LYS cc_start: 0.9836 (mttt) cc_final: 0.9628 (mttp) REVERT: C 89 LEU cc_start: 0.9536 (mt) cc_final: 0.9256 (tp) REVERT: C 133 MET cc_start: 0.9265 (mtm) cc_final: 0.8690 (ptp) REVERT: D 11 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9038 (mm-30) REVERT: D 58 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9500 (mm) REVERT: D 81 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8267 (mm-30) REVERT: D 83 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8473 (mt-10) REVERT: D 147 MET cc_start: 0.9200 (mmt) cc_final: 0.8940 (mmp) REVERT: D 221 TYR cc_start: 0.9049 (t80) cc_final: 0.8342 (t80) REVERT: E 76 ASP cc_start: 0.8856 (p0) cc_final: 0.8590 (p0) REVERT: E 83 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8845 (mt-10) REVERT: E 147 MET cc_start: 0.9291 (mtt) cc_final: 0.8864 (mtp) REVERT: E 170 GLU cc_start: 0.8304 (pm20) cc_final: 0.7566 (pm20) outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 0.0709 time to fit residues: 12.1666 Evaluate side-chains 95 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 65 optimal weight: 0.2980 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.041568 restraints weight = 47842.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042993 restraints weight = 25476.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043960 restraints weight = 16588.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044639 restraints weight = 12197.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045146 restraints weight = 9752.568| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8888 Z= 0.175 Angle : 0.640 10.342 12061 Z= 0.316 Chirality : 0.042 0.198 1425 Planarity : 0.004 0.042 1520 Dihedral : 4.594 31.321 1234 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.76 % Allowed : 23.09 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.82 (0.26), residues: 1126 helix: 0.38 (0.21), residues: 649 sheet: -1.89 (0.46), residues: 112 loop : -1.65 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 145 TYR 0.022 0.002 TYR E 93 PHE 0.012 0.001 PHE D 157 TRP 0.021 0.001 TRP E 259 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8888) covalent geometry : angle 0.64019 (12061) hydrogen bonds : bond 0.03192 ( 432) hydrogen bonds : angle 4.56173 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7499 (pttp) cc_final: 0.7117 (pttm) REVERT: B 47 LYS cc_start: 0.9777 (mttm) cc_final: 0.9500 (mttp) REVERT: B 89 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8737 (tt) REVERT: B 133 MET cc_start: 0.9413 (mtm) cc_final: 0.9163 (mtm) REVERT: B 166 ASP cc_start: 0.8747 (p0) cc_final: 0.8507 (p0) REVERT: B 261 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8074 (p0) REVERT: C 42 LYS cc_start: 0.9604 (ttpt) cc_final: 0.8955 (ttmm) REVERT: C 43 THR cc_start: 0.9653 (OUTLIER) cc_final: 0.9403 (p) REVERT: C 47 LYS cc_start: 0.9850 (mttt) cc_final: 0.9610 (mttp) REVERT: C 48 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9422 (mm) REVERT: C 89 LEU cc_start: 0.9512 (mt) cc_final: 0.9285 (tp) REVERT: D 11 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9016 (mm-30) REVERT: D 81 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8161 (mm-30) REVERT: D 83 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8470 (mt-10) REVERT: D 147 MET cc_start: 0.9326 (mmt) cc_final: 0.8960 (mmp) REVERT: D 221 TYR cc_start: 0.9050 (t80) cc_final: 0.8538 (t80) REVERT: E 76 ASP cc_start: 0.8917 (p0) cc_final: 0.8633 (p0) REVERT: E 83 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8806 (mt-10) REVERT: E 147 MET cc_start: 0.9312 (mtt) cc_final: 0.8978 (mtp) REVERT: E 170 GLU cc_start: 0.8285 (pm20) cc_final: 0.7517 (pm20) outliers start: 34 outliers final: 20 residues processed: 113 average time/residue: 0.0733 time to fit residues: 12.4582 Evaluate side-chains 103 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040674 restraints weight = 48632.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.042053 restraints weight = 25829.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042988 restraints weight = 16896.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.043653 restraints weight = 12504.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044093 restraints weight = 10043.056| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8888 Z= 0.260 Angle : 0.731 8.878 12061 Z= 0.360 Chirality : 0.044 0.206 1425 Planarity : 0.004 0.048 1520 Dihedral : 4.706 30.763 1234 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.98 % Allowed : 23.31 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.62 (0.26), residues: 1126 helix: 0.52 (0.21), residues: 652 sheet: -1.76 (0.47), residues: 107 loop : -1.56 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 173 TYR 0.024 0.002 TYR E 93 PHE 0.013 0.002 PHE D 157 TRP 0.021 0.001 TRP E 259 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 8888) covalent geometry : angle 0.73104 (12061) hydrogen bonds : bond 0.03379 ( 432) hydrogen bonds : angle 4.70330 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7513 (pttp) cc_final: 0.7136 (pttm) REVERT: B 47 LYS cc_start: 0.9782 (mttm) cc_final: 0.9450 (mttp) REVERT: B 89 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 133 MET cc_start: 0.9406 (mtm) cc_final: 0.9198 (mtm) REVERT: B 261 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8157 (p0) REVERT: C 42 LYS cc_start: 0.9613 (ttpt) cc_final: 0.8952 (ttmt) REVERT: C 47 LYS cc_start: 0.9860 (mttt) cc_final: 0.9658 (mttp) REVERT: C 48 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9452 (mm) REVERT: C 133 MET cc_start: 0.9372 (mtm) cc_final: 0.8663 (ptp) REVERT: D 11 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8977 (mm-30) REVERT: D 68 LEU cc_start: 0.9593 (tp) cc_final: 0.9318 (tt) REVERT: D 81 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8189 (mm-30) REVERT: D 147 MET cc_start: 0.9367 (mmt) cc_final: 0.9031 (mmp) REVERT: D 221 TYR cc_start: 0.9047 (t80) cc_final: 0.8603 (t80) REVERT: E 76 ASP cc_start: 0.8890 (p0) cc_final: 0.8573 (p0) REVERT: E 97 ARG cc_start: 0.8719 (mtt180) cc_final: 0.7822 (mmm-85) REVERT: E 147 MET cc_start: 0.9361 (mtt) cc_final: 0.8980 (mtp) REVERT: E 170 GLU cc_start: 0.8294 (pm20) cc_final: 0.7332 (pm20) REVERT: E 223 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9427 (mm) REVERT: E 259 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7885 (m-10) outliers start: 36 outliers final: 24 residues processed: 105 average time/residue: 0.0843 time to fit residues: 13.0222 Evaluate side-chains 105 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.042314 restraints weight = 47208.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.043725 restraints weight = 24937.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044708 restraints weight = 16277.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045367 restraints weight = 11968.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045864 restraints weight = 9598.043| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8888 Z= 0.124 Angle : 0.627 9.611 12061 Z= 0.303 Chirality : 0.042 0.195 1425 Planarity : 0.003 0.041 1520 Dihedral : 4.530 31.424 1234 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.31 % Allowed : 24.42 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.45 (0.26), residues: 1126 helix: 0.73 (0.21), residues: 656 sheet: -1.84 (0.48), residues: 106 loop : -1.62 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 145 TYR 0.025 0.001 TYR B 86 PHE 0.009 0.001 PHE D 157 TRP 0.019 0.001 TRP E 259 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8888) covalent geometry : angle 0.62748 (12061) hydrogen bonds : bond 0.03008 ( 432) hydrogen bonds : angle 4.39445 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7459 (pttp) cc_final: 0.7096 (pttm) REVERT: B 47 LYS cc_start: 0.9768 (mttm) cc_final: 0.9400 (mttp) REVERT: B 89 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8742 (tt) REVERT: B 261 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7975 (p0) REVERT: C 42 LYS cc_start: 0.9637 (ttpt) cc_final: 0.8904 (ttmm) REVERT: C 47 LYS cc_start: 0.9860 (mttt) cc_final: 0.9652 (mttp) REVERT: C 133 MET cc_start: 0.9320 (mtm) cc_final: 0.8699 (ptp) REVERT: D 11 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8984 (mm-30) REVERT: D 68 LEU cc_start: 0.9557 (tp) cc_final: 0.9289 (tt) REVERT: D 81 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8232 (mm-30) REVERT: D 147 MET cc_start: 0.9354 (mmt) cc_final: 0.8975 (mmp) REVERT: D 221 TYR cc_start: 0.9027 (t80) cc_final: 0.8526 (t80) REVERT: E 76 ASP cc_start: 0.8861 (p0) cc_final: 0.8535 (p0) REVERT: E 88 MET cc_start: 0.8803 (tpp) cc_final: 0.8461 (tpp) REVERT: E 147 MET cc_start: 0.9329 (mtt) cc_final: 0.8984 (mtp) REVERT: E 170 GLU cc_start: 0.8004 (pm20) cc_final: 0.7448 (pm20) REVERT: E 223 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9395 (mm) outliers start: 30 outliers final: 19 residues processed: 111 average time/residue: 0.0792 time to fit residues: 13.1737 Evaluate side-chains 100 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.041629 restraints weight = 47721.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043039 restraints weight = 25200.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044007 restraints weight = 16430.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.044688 restraints weight = 12069.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045186 restraints weight = 9649.522| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8888 Z= 0.180 Angle : 0.671 9.520 12061 Z= 0.325 Chirality : 0.043 0.197 1425 Planarity : 0.003 0.043 1520 Dihedral : 4.503 31.113 1234 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.31 % Allowed : 24.64 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.34 (0.26), residues: 1126 helix: 0.77 (0.21), residues: 657 sheet: -1.83 (0.46), residues: 112 loop : -1.44 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 145 TYR 0.019 0.002 TYR B 86 PHE 0.010 0.001 PHE E 157 TRP 0.028 0.001 TRP E 259 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8888) covalent geometry : angle 0.67147 (12061) hydrogen bonds : bond 0.03082 ( 432) hydrogen bonds : angle 4.44861 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7499 (pttp) cc_final: 0.7130 (pttm) REVERT: B 47 LYS cc_start: 0.9776 (mttm) cc_final: 0.9411 (mttp) REVERT: B 89 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8747 (tt) REVERT: B 166 ASP cc_start: 0.8853 (p0) cc_final: 0.8139 (p0) REVERT: B 261 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7991 (p0) REVERT: C 42 LYS cc_start: 0.9646 (ttpt) cc_final: 0.9065 (ttmm) REVERT: C 47 LYS cc_start: 0.9859 (mttt) cc_final: 0.9619 (mttp) REVERT: C 133 MET cc_start: 0.9335 (mtm) cc_final: 0.8645 (ptp) REVERT: D 11 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9013 (mm-30) REVERT: D 68 LEU cc_start: 0.9560 (tp) cc_final: 0.9290 (tt) REVERT: D 81 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 147 MET cc_start: 0.9394 (mmt) cc_final: 0.9045 (mmp) REVERT: D 221 TYR cc_start: 0.9042 (t80) cc_final: 0.8555 (t80) REVERT: E 76 ASP cc_start: 0.8882 (p0) cc_final: 0.8542 (p0) REVERT: E 81 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8316 (mm-30) REVERT: E 88 MET cc_start: 0.8888 (tpp) cc_final: 0.8512 (tpp) REVERT: E 147 MET cc_start: 0.9345 (mtt) cc_final: 0.8975 (mtp) REVERT: E 170 GLU cc_start: 0.8174 (pm20) cc_final: 0.7438 (pm20) REVERT: E 223 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9379 (mm) outliers start: 30 outliers final: 22 residues processed: 106 average time/residue: 0.0749 time to fit residues: 12.1380 Evaluate side-chains 102 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042442 restraints weight = 46610.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.043874 restraints weight = 24757.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044878 restraints weight = 16188.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045551 restraints weight = 11884.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046064 restraints weight = 9502.102| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8888 Z= 0.124 Angle : 0.643 10.459 12061 Z= 0.308 Chirality : 0.042 0.192 1425 Planarity : 0.003 0.042 1520 Dihedral : 4.455 31.523 1234 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.87 % Allowed : 25.08 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.26 (0.26), residues: 1126 helix: 0.85 (0.21), residues: 658 sheet: -1.77 (0.48), residues: 105 loop : -1.48 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 145 TYR 0.017 0.001 TYR B 86 PHE 0.008 0.001 PHE C 85 TRP 0.026 0.001 TRP E 259 HIS 0.004 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8888) covalent geometry : angle 0.64319 (12061) hydrogen bonds : bond 0.02992 ( 432) hydrogen bonds : angle 4.31079 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7431 (pttp) cc_final: 0.6564 (ptpp) REVERT: B 89 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 166 ASP cc_start: 0.8779 (p0) cc_final: 0.8070 (p0) REVERT: B 261 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7883 (p0) REVERT: C 42 LYS cc_start: 0.9640 (ttpt) cc_final: 0.8990 (ttmm) REVERT: C 133 MET cc_start: 0.9321 (mtm) cc_final: 0.8637 (ptp) REVERT: D 11 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9011 (mm-30) REVERT: D 68 LEU cc_start: 0.9535 (tp) cc_final: 0.9258 (tt) REVERT: D 81 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 147 MET cc_start: 0.9400 (mmt) cc_final: 0.9020 (mmp) REVERT: D 221 TYR cc_start: 0.9054 (t80) cc_final: 0.8556 (t80) REVERT: E 76 ASP cc_start: 0.8859 (p0) cc_final: 0.8519 (p0) REVERT: E 88 MET cc_start: 0.8866 (tpp) cc_final: 0.8446 (tpp) REVERT: E 97 ARG cc_start: 0.8495 (mtt180) cc_final: 0.7689 (mmm-85) REVERT: E 147 MET cc_start: 0.9327 (mtt) cc_final: 0.8987 (mtp) REVERT: E 170 GLU cc_start: 0.8064 (pm20) cc_final: 0.7317 (pm20) REVERT: E 223 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9384 (mm) outliers start: 26 outliers final: 19 residues processed: 108 average time/residue: 0.0742 time to fit residues: 12.2551 Evaluate side-chains 106 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 70 optimal weight: 0.4980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041667 restraints weight = 47121.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.043068 restraints weight = 24978.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.044052 restraints weight = 16344.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.044728 restraints weight = 12011.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045191 restraints weight = 9603.641| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8888 Z= 0.191 Angle : 0.694 10.226 12061 Z= 0.334 Chirality : 0.043 0.197 1425 Planarity : 0.004 0.045 1520 Dihedral : 4.495 31.194 1234 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.76 % Allowed : 24.97 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.14 (0.26), residues: 1126 helix: 0.91 (0.21), residues: 656 sheet: -1.77 (0.48), residues: 102 loop : -1.33 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 145 TYR 0.017 0.002 TYR B 86 PHE 0.010 0.001 PHE D 157 TRP 0.029 0.001 TRP E 259 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8888) covalent geometry : angle 0.69420 (12061) hydrogen bonds : bond 0.03137 ( 432) hydrogen bonds : angle 4.43811 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7420 (pttp) cc_final: 0.7011 (pttm) REVERT: B 89 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 133 MET cc_start: 0.9096 (ptp) cc_final: 0.8777 (ptp) REVERT: B 166 ASP cc_start: 0.8872 (p0) cc_final: 0.8174 (p0) REVERT: B 261 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8001 (p0) REVERT: C 42 LYS cc_start: 0.9652 (ttpt) cc_final: 0.9052 (ttmt) REVERT: C 133 MET cc_start: 0.9355 (mtm) cc_final: 0.8699 (ptp) REVERT: D 11 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8875 (tp30) REVERT: D 68 LEU cc_start: 0.9547 (tp) cc_final: 0.9264 (tt) REVERT: D 147 MET cc_start: 0.9444 (mmt) cc_final: 0.9177 (mmp) REVERT: D 221 TYR cc_start: 0.9043 (t80) cc_final: 0.8789 (t80) REVERT: E 76 ASP cc_start: 0.8898 (p0) cc_final: 0.8508 (p0) REVERT: E 81 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8230 (mm-30) REVERT: E 88 MET cc_start: 0.8950 (tpp) cc_final: 0.8516 (tpp) REVERT: E 147 MET cc_start: 0.9365 (mtt) cc_final: 0.8987 (mtp) REVERT: E 223 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9378 (mm) outliers start: 25 outliers final: 21 residues processed: 99 average time/residue: 0.0774 time to fit residues: 11.6872 Evaluate side-chains 102 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042693 restraints weight = 46503.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044162 restraints weight = 24304.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045159 restraints weight = 15698.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045851 restraints weight = 11484.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046318 restraints weight = 9162.478| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8888 Z= 0.119 Angle : 0.664 10.740 12061 Z= 0.314 Chirality : 0.042 0.190 1425 Planarity : 0.003 0.042 1520 Dihedral : 4.483 31.659 1234 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.76 % Allowed : 25.52 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.10 (0.26), residues: 1126 helix: 1.01 (0.21), residues: 651 sheet: -1.83 (0.49), residues: 98 loop : -1.40 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 145 TYR 0.016 0.001 TYR B 86 PHE 0.009 0.001 PHE C 85 TRP 0.023 0.001 TRP E 259 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8888) covalent geometry : angle 0.66432 (12061) hydrogen bonds : bond 0.03043 ( 432) hydrogen bonds : angle 4.30617 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.77 seconds wall clock time: 22 minutes 57.77 seconds (1377.77 seconds total)