Starting phenix.real_space_refine on Tue Jul 29 00:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0o_32246/07_2025/7w0o_32246.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0o_32246/07_2025/7w0o_32246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0o_32246/07_2025/7w0o_32246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0o_32246/07_2025/7w0o_32246.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0o_32246/07_2025/7w0o_32246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0o_32246/07_2025/7w0o_32246.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2064 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5799 2.51 5 N 1543 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9106 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "D" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 11} Chain: "R" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2352 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.17, per 1000 atoms: 0.57 Number of scatterers: 9106 At special positions: 0 Unit cell: (92.4, 123.2, 136.4, 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 68 16.00 O 1696 8.00 N 1543 7.00 C 5799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.04 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.582A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.910A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.875A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.637A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.910A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.651A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.541A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.742A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.688A pdb=" N ASN C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 76 removed outlier: 3.582A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 56 removed outlier: 3.790A pdb=" N LEU R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 82 through 89 removed outlier: 4.197A pdb=" N THR R 89 " --> pdb=" O TRP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 131 removed outlier: 4.037A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN R 112 " --> pdb=" O LEU R 108 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR R 114 " --> pdb=" O PHE R 110 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 117 " --> pdb=" O MET R 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP R 126 " --> pdb=" O GLY R 122 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 162 removed outlier: 3.551A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA R 158 " --> pdb=" O TRP R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'R' and resid 190 through 209 removed outlier: 3.808A pdb=" N GLU R 194 " --> pdb=" O THR R 190 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY R 209 " --> pdb=" O SER R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 removed outlier: 3.538A pdb=" N PHE R 214 " --> pdb=" O PHE R 210 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 261 removed outlier: 4.104A pdb=" N ARG R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 277 Processing helix chain 'R' and resid 280 through 310 Proline residue: R 292 - end of helix removed outlier: 3.891A pdb=" N THR R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.931A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.066A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 190 removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 34 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.244A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 339 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.866A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.529A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.903A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 170 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.710A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.874A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.925A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.532A pdb=" N CYS S 22 " --> pdb=" O LEU S 79 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP S 73 " --> pdb=" O THR S 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.587A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL S 48 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.587A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.649A pdb=" N TYR S 228 " --> pdb=" O PHE S 177 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE S 177 " --> pdb=" O TYR S 228 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 156 through 159 removed outlier: 3.559A pdb=" N SER S 206 " --> pdb=" O THR S 213 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR S 215 " --> pdb=" O SER S 204 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 969 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: 2.26 Time building geometry restraints manager: 2.47 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: 2875 1.34 - 1.46: 1518 1.46 - 1.57: 4811 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 9304 Sorted by residual: bond pdb=" CB PRO C 91 " pdb=" CG PRO C 91 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.36e+00 bond pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.23e+00 bond pdb=" CG1 ILE R 216 " pdb=" CD1 ILE R 216 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 bond pdb=" CG GLU A 14 " pdb=" CD GLU A 14 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG PRO D 24 " pdb=" CD PRO D 24 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.09e+00 ... (remaining 9299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12183 1.70 - 3.40: 325 3.40 - 5.10: 73 5.10 - 6.80: 18 6.80 - 8.50: 6 Bond angle restraints: 12605 Sorted by residual: angle pdb=" N GLU B 10 " pdb=" CA GLU B 10 " pdb=" CB GLU B 10 " ideal model delta sigma weight residual 110.16 116.12 -5.96 1.48e+00 4.57e-01 1.62e+01 angle pdb=" N GLU A 14 " pdb=" CA GLU A 14 " pdb=" CB GLU A 14 " ideal model delta sigma weight residual 110.12 115.10 -4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" CA MET D 23 " pdb=" CB MET D 23 " pdb=" CG MET D 23 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N GLN A 304 " pdb=" CA GLN A 304 " pdb=" CB GLN A 304 " ideal model delta sigma weight residual 110.39 116.14 -5.75 1.75e+00 3.27e-01 1.08e+01 angle pdb=" N PHE R 78 " pdb=" CA PHE R 78 " pdb=" C PHE R 78 " ideal model delta sigma weight residual 114.04 110.16 3.88 1.24e+00 6.50e-01 9.81e+00 ... (remaining 12600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4998 17.46 - 34.91: 418 34.91 - 52.37: 79 52.37 - 69.82: 8 69.82 - 87.28: 5 Dihedral angle restraints: 5508 sinusoidal: 2145 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 172.97 -79.97 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CA CYS R 119 " pdb=" C CYS R 119 " pdb=" N LEU R 120 " pdb=" CA LEU R 120 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR R 77 " pdb=" C THR R 77 " pdb=" N PHE R 78 " pdb=" CA PHE R 78 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1012 0.042 - 0.085: 297 0.085 - 0.127: 100 0.127 - 0.170: 11 0.170 - 0.212: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA GLN A 304 " pdb=" N GLN A 304 " pdb=" C GLN A 304 " pdb=" CB GLN A 304 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA GLN A 306 " pdb=" N GLN A 306 " pdb=" C GLN A 306 " pdb=" CB GLN A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1419 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 90 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 91 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 286 " 0.015 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE R 286 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 286 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 286 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE R 286 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 286 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 236 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.034 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 772 2.74 - 3.28: 9355 3.28 - 3.82: 14185 3.82 - 4.36: 15742 4.36 - 4.90: 27125 Nonbonded interactions: 67179 Sorted by model distance: nonbonded pdb=" O PRO R 292 " pdb=" OG1 THR R 295 " model vdw 2.199 3.040 nonbonded pdb=" O VAL R 212 " pdb=" OG1 THR R 215 " model vdw 2.209 3.040 nonbonded pdb=" NE1 TRP S 47 " pdb=" O ALA S 49 " model vdw 2.252 3.120 nonbonded pdb=" O MET R 272 " pdb=" OG SER R 275 " model vdw 2.278 3.040 nonbonded pdb=" NE1 TRP R 95 " pdb=" O GLY R 98 " model vdw 2.291 3.120 ... (remaining 67174 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 21.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9305 Z= 0.135 Angle : 0.716 8.501 12607 Z= 0.377 Chirality : 0.045 0.212 1422 Planarity : 0.005 0.103 1593 Dihedral : 13.045 87.278 3337 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 1143 helix: 0.85 (0.27), residues: 366 sheet: -0.92 (0.33), residues: 262 loop : -2.48 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 279 HIS 0.006 0.001 HIS S 35 PHE 0.044 0.002 PHE R 286 TYR 0.028 0.001 TYR A 302 ARG 0.010 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.18468 ( 339) hydrogen bonds : angle 6.60182 ( 969) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.84619 ( 2) covalent geometry : bond 0.00296 ( 9304) covalent geometry : angle 0.71570 (12605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8378 (mtmm) REVERT: A 191 PHE cc_start: 0.8011 (t80) cc_final: 0.7804 (t80) REVERT: A 204 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8405 (mm-40) REVERT: A 212 ILE cc_start: 0.8915 (tp) cc_final: 0.8681 (tp) REVERT: A 240 MET cc_start: 0.4663 (mtp) cc_final: 0.4397 (mtp) REVERT: A 245 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6248 (mm-30) REVERT: A 248 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7981 (mtmm) REVERT: A 251 ASP cc_start: 0.8678 (t0) cc_final: 0.8368 (t0) REVERT: A 264 ILE cc_start: 0.8523 (mm) cc_final: 0.8233 (mm) REVERT: A 266 LEU cc_start: 0.7761 (tp) cc_final: 0.7532 (tp) REVERT: A 274 PHE cc_start: 0.8572 (t80) cc_final: 0.8239 (t80) REVERT: A 276 GLU cc_start: 0.7988 (pp20) cc_final: 0.7611 (pp20) REVERT: A 277 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7224 (mtmm) REVERT: A 302 TYR cc_start: 0.7145 (t80) cc_final: 0.6896 (t80) REVERT: A 303 ILE cc_start: 0.8137 (mm) cc_final: 0.7931 (tp) REVERT: A 306 GLN cc_start: 0.7773 (mp10) cc_final: 0.7339 (mp10) REVERT: A 316 THR cc_start: 0.7699 (p) cc_final: 0.7392 (p) REVERT: A 317 LYS cc_start: 0.7671 (mttp) cc_final: 0.7283 (mttm) REVERT: A 341 ASP cc_start: 0.8155 (t0) cc_final: 0.7913 (t0) REVERT: A 343 ILE cc_start: 0.8394 (tp) cc_final: 0.7767 (tp) REVERT: A 345 LYS cc_start: 0.7682 (tppp) cc_final: 0.7383 (tppp) REVERT: A 347 ASN cc_start: 0.8128 (m110) cc_final: 0.7575 (m-40) REVERT: A 350 ASP cc_start: 0.7704 (m-30) cc_final: 0.7376 (m-30) REVERT: B 22 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8243 (mtt-85) REVERT: B 45 MET cc_start: 0.7589 (mmm) cc_final: 0.7003 (mmp) REVERT: B 125 ASN cc_start: 0.8356 (t0) cc_final: 0.7754 (t0) REVERT: B 127 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7875 (mmtp) REVERT: B 148 CYS cc_start: 0.7472 (t) cc_final: 0.7113 (t) REVERT: B 170 ASP cc_start: 0.7309 (p0) cc_final: 0.6878 (p0) REVERT: B 217 MET cc_start: 0.7813 (ppp) cc_final: 0.7460 (ppp) REVERT: B 219 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7328 (tpp80) REVERT: B 225 HIS cc_start: 0.8483 (m170) cc_final: 0.8183 (m170) REVERT: B 233 CYS cc_start: 0.7872 (t) cc_final: 0.7656 (t) REVERT: B 247 ASP cc_start: 0.7659 (t0) cc_final: 0.7219 (t0) REVERT: B 253 PHE cc_start: 0.8216 (m-80) cc_final: 0.7687 (m-80) REVERT: B 290 ASP cc_start: 0.7249 (t0) cc_final: 0.7035 (t0) REVERT: B 298 ASP cc_start: 0.8210 (t0) cc_final: 0.7696 (t0) REVERT: B 322 ASP cc_start: 0.7682 (m-30) cc_final: 0.7346 (m-30) REVERT: C 44 ARG cc_start: 0.8883 (mpp80) cc_final: 0.8639 (ptt-90) REVERT: C 48 GLU cc_start: 0.9016 (mp0) cc_final: 0.8497 (mp0) REVERT: C 51 LYS cc_start: 0.9241 (ptpp) cc_final: 0.8766 (pttm) REVERT: C 52 MET cc_start: 0.8470 (mmp) cc_final: 0.7945 (mmp) REVERT: C 69 MET cc_start: 0.8566 (mtm) cc_final: 0.8138 (mtm) REVERT: C 73 GLU cc_start: 0.8123 (pp20) cc_final: 0.7774 (pp20) REVERT: R 108 LEU cc_start: 0.7847 (tp) cc_final: 0.7543 (tp) REVERT: R 114 TYR cc_start: 0.7835 (m-80) cc_final: 0.7400 (m-80) REVERT: R 117 VAL cc_start: 0.8863 (p) cc_final: 0.8656 (m) REVERT: R 120 LEU cc_start: 0.9004 (tp) cc_final: 0.8788 (tp) REVERT: R 182 TYR cc_start: 0.8489 (p90) cc_final: 0.8161 (p90) REVERT: R 183 MET cc_start: 0.6444 (tmm) cc_final: 0.5938 (tmm) REVERT: R 252 VAL cc_start: 0.7834 (p) cc_final: 0.7575 (m) REVERT: R 257 PHE cc_start: 0.8113 (t80) cc_final: 0.7837 (t80) REVERT: R 268 LYS cc_start: 0.9082 (pttt) cc_final: 0.8859 (pttt) REVERT: R 295 THR cc_start: 0.8591 (p) cc_final: 0.7503 (p) REVERT: R 299 TYR cc_start: 0.7688 (m-80) cc_final: 0.7397 (m-80) REVERT: S 34 MET cc_start: 0.7646 (pmm) cc_final: 0.7219 (ptm) REVERT: S 79 LEU cc_start: 0.7486 (tp) cc_final: 0.7118 (tp) REVERT: S 160 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6724 (mtm110) REVERT: S 166 LEU cc_start: 0.8654 (tp) cc_final: 0.8434 (tp) REVERT: S 174 LEU cc_start: 0.8063 (tt) cc_final: 0.7819 (tt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2691 time to fit residues: 128.8964 Evaluate side-chains 352 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0370 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 75 HIS R 137 ASN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122080 restraints weight = 17046.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126586 restraints weight = 9029.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129556 restraints weight = 5791.908| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9305 Z= 0.142 Angle : 0.725 11.477 12607 Z= 0.371 Chirality : 0.045 0.183 1422 Planarity : 0.005 0.069 1593 Dihedral : 5.097 28.516 1262 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 2.11 % Allowed : 13.58 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.24), residues: 1143 helix: 1.03 (0.27), residues: 370 sheet: -0.81 (0.33), residues: 251 loop : -2.50 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 85 HIS 0.005 0.001 HIS S 35 PHE 0.032 0.002 PHE R 286 TYR 0.025 0.002 TYR R 88 ARG 0.007 0.001 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 339) hydrogen bonds : angle 5.33857 ( 969) SS BOND : bond 0.00393 ( 1) SS BOND : angle 1.12152 ( 2) covalent geometry : bond 0.00309 ( 9304) covalent geometry : angle 0.72469 (12605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 365 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7478 (ptp90) cc_final: 0.7177 (ptp90) REVERT: A 212 ILE cc_start: 0.8881 (tp) cc_final: 0.8656 (tp) REVERT: A 240 MET cc_start: 0.4612 (mtp) cc_final: 0.4400 (mtp) REVERT: A 245 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6172 (mm-30) REVERT: A 248 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7984 (mtmm) REVERT: A 251 ASP cc_start: 0.8691 (t0) cc_final: 0.8385 (t0) REVERT: A 264 ILE cc_start: 0.8479 (mm) cc_final: 0.8213 (mm) REVERT: A 276 GLU cc_start: 0.8014 (pp20) cc_final: 0.7749 (pp20) REVERT: A 302 TYR cc_start: 0.7191 (t80) cc_final: 0.6622 (t80) REVERT: A 303 ILE cc_start: 0.8239 (mm) cc_final: 0.7904 (tp) REVERT: A 304 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: A 313 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7151 (tpt90) REVERT: A 314 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7796 (mmmt) REVERT: A 333 GLN cc_start: 0.7914 (tp40) cc_final: 0.7124 (tp40) REVERT: A 343 ILE cc_start: 0.8399 (tp) cc_final: 0.7714 (tp) REVERT: A 345 LYS cc_start: 0.7775 (tppp) cc_final: 0.7440 (tppp) REVERT: A 347 ASN cc_start: 0.8263 (m110) cc_final: 0.7841 (m110) REVERT: A 350 ASP cc_start: 0.7679 (m-30) cc_final: 0.7344 (m-30) REVERT: B 45 MET cc_start: 0.7606 (mmm) cc_final: 0.7068 (mmp) REVERT: B 46 ARG cc_start: 0.6823 (mpp-170) cc_final: 0.6292 (mpp-170) REVERT: B 125 ASN cc_start: 0.8175 (t0) cc_final: 0.7901 (t0) REVERT: B 127 LYS cc_start: 0.8287 (mmtp) cc_final: 0.7932 (mmtp) REVERT: B 148 CYS cc_start: 0.7215 (t) cc_final: 0.6806 (t) REVERT: B 170 ASP cc_start: 0.7322 (p0) cc_final: 0.6885 (p0) REVERT: B 205 ASP cc_start: 0.7641 (t0) cc_final: 0.7382 (t0) REVERT: B 219 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7576 (tpp80) REVERT: B 233 CYS cc_start: 0.7929 (t) cc_final: 0.7531 (t) REVERT: B 247 ASP cc_start: 0.7685 (t0) cc_final: 0.7141 (t0) REVERT: B 284 LEU cc_start: 0.8868 (mp) cc_final: 0.8576 (mm) REVERT: B 298 ASP cc_start: 0.8293 (t0) cc_final: 0.7822 (t0) REVERT: B 322 ASP cc_start: 0.7685 (m-30) cc_final: 0.7258 (m-30) REVERT: C 51 LYS cc_start: 0.9282 (ptpp) cc_final: 0.8680 (pttm) REVERT: C 52 MET cc_start: 0.8484 (mmp) cc_final: 0.7994 (mmp) REVERT: C 69 MET cc_start: 0.8528 (mtm) cc_final: 0.8101 (mtm) REVERT: C 73 GLU cc_start: 0.8104 (pp20) cc_final: 0.7724 (pp20) REVERT: D 23 MET cc_start: 0.7414 (ppp) cc_final: 0.6826 (ppp) REVERT: R 114 TYR cc_start: 0.7880 (m-80) cc_final: 0.7234 (m-80) REVERT: R 120 LEU cc_start: 0.8982 (tp) cc_final: 0.8738 (tp) REVERT: R 182 TYR cc_start: 0.8489 (p90) cc_final: 0.8199 (p90) REVERT: R 183 MET cc_start: 0.6664 (tmm) cc_final: 0.5963 (tmm) REVERT: R 257 PHE cc_start: 0.8024 (t80) cc_final: 0.7764 (t80) REVERT: R 261 TRP cc_start: 0.6392 (t-100) cc_final: 0.5911 (t-100) REVERT: R 265 HIS cc_start: 0.7915 (m-70) cc_final: 0.7128 (m-70) REVERT: R 295 THR cc_start: 0.8538 (p) cc_final: 0.7461 (p) REVERT: R 299 TYR cc_start: 0.7772 (m-80) cc_final: 0.7547 (m-80) REVERT: S 34 MET cc_start: 0.7638 (pmm) cc_final: 0.7293 (ptm) REVERT: S 79 LEU cc_start: 0.7266 (tp) cc_final: 0.6893 (tp) REVERT: S 93 MET cc_start: 0.7030 (mmm) cc_final: 0.6759 (mmm) REVERT: S 160 ARG cc_start: 0.7368 (mtm110) cc_final: 0.7068 (mtm110) REVERT: S 239 PHE cc_start: 0.8043 (m-80) cc_final: 0.7820 (m-80) outliers start: 21 outliers final: 16 residues processed: 370 average time/residue: 0.2568 time to fit residues: 123.0049 Evaluate side-chains 369 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 352 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS C 75 HIS S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.153026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121130 restraints weight = 17192.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125633 restraints weight = 9087.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128589 restraints weight = 5844.638| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9305 Z= 0.136 Angle : 0.712 12.620 12607 Z= 0.361 Chirality : 0.045 0.177 1422 Planarity : 0.005 0.058 1593 Dihedral : 5.034 28.465 1262 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.42 % Allowed : 18.11 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.24), residues: 1143 helix: 0.92 (0.27), residues: 380 sheet: -0.76 (0.31), residues: 266 loop : -2.49 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 85 HIS 0.006 0.001 HIS S 35 PHE 0.023 0.002 PHE R 312 TYR 0.026 0.001 TYR R 88 ARG 0.010 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 339) hydrogen bonds : angle 4.91970 ( 969) SS BOND : bond 0.00567 ( 1) SS BOND : angle 1.09261 ( 2) covalent geometry : bond 0.00297 ( 9304) covalent geometry : angle 0.71161 (12605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 362 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7371 (ptp90) cc_final: 0.7000 (ptp90) REVERT: A 53 MET cc_start: 0.6995 (mpp) cc_final: 0.6755 (mpp) REVERT: A 212 ILE cc_start: 0.8864 (tp) cc_final: 0.8658 (tp) REVERT: A 240 MET cc_start: 0.4580 (mtp) cc_final: 0.4367 (mtp) REVERT: A 245 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6197 (mm-30) REVERT: A 248 LYS cc_start: 0.8338 (mtmm) cc_final: 0.7932 (mtmm) REVERT: A 251 ASP cc_start: 0.8709 (t0) cc_final: 0.8387 (t0) REVERT: A 264 ILE cc_start: 0.8449 (mm) cc_final: 0.8161 (mm) REVERT: A 276 GLU cc_start: 0.7975 (pp20) cc_final: 0.7700 (pp20) REVERT: A 302 TYR cc_start: 0.7288 (t80) cc_final: 0.6801 (t80) REVERT: A 303 ILE cc_start: 0.8290 (mm) cc_final: 0.8010 (mm) REVERT: A 313 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7243 (tpt90) REVERT: A 318 GLU cc_start: 0.7487 (pm20) cc_final: 0.7180 (pm20) REVERT: A 333 GLN cc_start: 0.7927 (tp40) cc_final: 0.7146 (tp40) REVERT: A 343 ILE cc_start: 0.8482 (tp) cc_final: 0.7770 (tp) REVERT: A 345 LYS cc_start: 0.7760 (tppp) cc_final: 0.7308 (tppp) REVERT: A 347 ASN cc_start: 0.8213 (m110) cc_final: 0.7809 (m110) REVERT: A 350 ASP cc_start: 0.7684 (m-30) cc_final: 0.7356 (m-30) REVERT: B 15 LYS cc_start: 0.9093 (ptpp) cc_final: 0.8569 (pttm) REVERT: B 22 ARG cc_start: 0.7410 (tpm170) cc_final: 0.7177 (tpm170) REVERT: B 45 MET cc_start: 0.7647 (mmm) cc_final: 0.7238 (mmp) REVERT: B 46 ARG cc_start: 0.6858 (mpp-170) cc_final: 0.6245 (mpp-170) REVERT: B 125 ASN cc_start: 0.8188 (t0) cc_final: 0.7921 (t0) REVERT: B 127 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7854 (mmtp) REVERT: B 128 THR cc_start: 0.8889 (t) cc_final: 0.8233 (p) REVERT: B 132 ASN cc_start: 0.7248 (m110) cc_final: 0.7043 (m110) REVERT: B 153 ASP cc_start: 0.7989 (t0) cc_final: 0.7201 (p0) REVERT: B 170 ASP cc_start: 0.7269 (p0) cc_final: 0.6877 (p0) REVERT: B 205 ASP cc_start: 0.7601 (t0) cc_final: 0.7355 (t0) REVERT: B 219 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7612 (tpp80) REVERT: B 233 CYS cc_start: 0.7866 (t) cc_final: 0.7458 (t) REVERT: B 235 PHE cc_start: 0.7493 (t80) cc_final: 0.7083 (t80) REVERT: B 247 ASP cc_start: 0.7727 (t0) cc_final: 0.7110 (t0) REVERT: B 298 ASP cc_start: 0.8306 (t0) cc_final: 0.7724 (t0) REVERT: B 322 ASP cc_start: 0.7600 (m-30) cc_final: 0.7232 (m-30) REVERT: C 48 GLU cc_start: 0.8755 (mp0) cc_final: 0.8142 (mm-30) REVERT: C 51 LYS cc_start: 0.9271 (ptpp) cc_final: 0.8010 (pttm) REVERT: C 52 MET cc_start: 0.8460 (mmp) cc_final: 0.7983 (mmp) REVERT: C 69 MET cc_start: 0.8586 (mtm) cc_final: 0.8109 (mtm) REVERT: C 73 GLU cc_start: 0.8092 (pp20) cc_final: 0.7726 (pp20) REVERT: D 20 ARG cc_start: 0.7924 (tmm-80) cc_final: 0.7133 (tmm-80) REVERT: R 82 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7994 (tt) REVERT: R 114 TYR cc_start: 0.7906 (m-80) cc_final: 0.7202 (m-80) REVERT: R 120 LEU cc_start: 0.9031 (tp) cc_final: 0.8789 (tp) REVERT: R 182 TYR cc_start: 0.8398 (p90) cc_final: 0.8116 (p90) REVERT: R 183 MET cc_start: 0.6735 (tmm) cc_final: 0.5826 (tmm) REVERT: R 261 TRP cc_start: 0.6533 (t-100) cc_final: 0.6250 (t-100) REVERT: R 265 HIS cc_start: 0.7897 (m-70) cc_final: 0.7358 (m-70) REVERT: R 286 PHE cc_start: 0.8245 (m-80) cc_final: 0.7571 (m-80) REVERT: R 295 THR cc_start: 0.8398 (p) cc_final: 0.7188 (p) REVERT: R 299 TYR cc_start: 0.7782 (m-80) cc_final: 0.7543 (m-80) REVERT: S 79 LEU cc_start: 0.7536 (tp) cc_final: 0.7112 (tp) REVERT: S 160 ARG cc_start: 0.7353 (mtm110) cc_final: 0.7035 (mtm110) REVERT: S 239 PHE cc_start: 0.8069 (m-80) cc_final: 0.7814 (m-10) outliers start: 34 outliers final: 26 residues processed: 376 average time/residue: 0.2855 time to fit residues: 140.3016 Evaluate side-chains 382 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 355 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.153799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121784 restraints weight = 17041.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126238 restraints weight = 9001.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129233 restraints weight = 5785.284| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9305 Z= 0.130 Angle : 0.722 13.225 12607 Z= 0.363 Chirality : 0.045 0.163 1422 Planarity : 0.004 0.055 1593 Dihedral : 4.940 29.048 1262 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.43 % Allowed : 20.42 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1143 helix: 1.17 (0.27), residues: 365 sheet: -0.57 (0.31), residues: 265 loop : -2.50 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 85 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.002 PHE R 312 TYR 0.016 0.001 TYR R 309 ARG 0.010 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 339) hydrogen bonds : angle 4.81821 ( 969) SS BOND : bond 0.00337 ( 1) SS BOND : angle 1.07643 ( 2) covalent geometry : bond 0.00287 ( 9304) covalent geometry : angle 0.72192 (12605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 350 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7471 (ptp90) cc_final: 0.7147 (ptp90) REVERT: A 53 MET cc_start: 0.7003 (mpp) cc_final: 0.6783 (mpp) REVERT: A 212 ILE cc_start: 0.8865 (tp) cc_final: 0.8642 (tp) REVERT: A 240 MET cc_start: 0.4547 (mtp) cc_final: 0.4332 (mtp) REVERT: A 245 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6181 (mm-30) REVERT: A 248 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7937 (mtmm) REVERT: A 251 ASP cc_start: 0.8682 (t0) cc_final: 0.8471 (t0) REVERT: A 264 ILE cc_start: 0.8414 (mm) cc_final: 0.8181 (mm) REVERT: A 276 GLU cc_start: 0.7981 (pp20) cc_final: 0.7742 (pp20) REVERT: A 302 TYR cc_start: 0.7189 (t80) cc_final: 0.6863 (t80) REVERT: A 313 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7064 (tpt90) REVERT: A 314 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7775 (mmmt) REVERT: A 316 THR cc_start: 0.7762 (p) cc_final: 0.7198 (p) REVERT: A 318 GLU cc_start: 0.7456 (pm20) cc_final: 0.7247 (pm20) REVERT: A 333 GLN cc_start: 0.7918 (tp40) cc_final: 0.7166 (tp40) REVERT: A 343 ILE cc_start: 0.8492 (tp) cc_final: 0.7804 (tp) REVERT: A 345 LYS cc_start: 0.7739 (tppp) cc_final: 0.7317 (tppp) REVERT: A 347 ASN cc_start: 0.8192 (m110) cc_final: 0.7782 (m-40) REVERT: A 350 ASP cc_start: 0.7677 (m-30) cc_final: 0.7344 (m-30) REVERT: B 15 LYS cc_start: 0.9088 (ptpp) cc_final: 0.8572 (pttm) REVERT: B 22 ARG cc_start: 0.7499 (tpm170) cc_final: 0.7174 (tpm170) REVERT: B 45 MET cc_start: 0.7605 (mmm) cc_final: 0.7276 (mmp) REVERT: B 46 ARG cc_start: 0.6814 (mpp-170) cc_final: 0.6197 (mpp-170) REVERT: B 125 ASN cc_start: 0.8167 (t0) cc_final: 0.7935 (t0) REVERT: B 127 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7767 (mmtp) REVERT: B 132 ASN cc_start: 0.7600 (m110) cc_final: 0.7188 (m110) REVERT: B 153 ASP cc_start: 0.7953 (t0) cc_final: 0.7249 (p0) REVERT: B 164 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7462 (m) REVERT: B 170 ASP cc_start: 0.7217 (p0) cc_final: 0.6990 (p0) REVERT: B 205 ASP cc_start: 0.7657 (t0) cc_final: 0.7426 (t0) REVERT: B 219 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7619 (tpp80) REVERT: B 233 CYS cc_start: 0.7794 (t) cc_final: 0.7399 (t) REVERT: B 235 PHE cc_start: 0.7490 (t80) cc_final: 0.7028 (t80) REVERT: B 247 ASP cc_start: 0.7717 (t0) cc_final: 0.7117 (t0) REVERT: B 298 ASP cc_start: 0.8280 (t0) cc_final: 0.7716 (t0) REVERT: B 322 ASP cc_start: 0.7603 (m-30) cc_final: 0.7208 (m-30) REVERT: C 48 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: C 51 LYS cc_start: 0.9260 (ptpp) cc_final: 0.8038 (pttm) REVERT: C 52 MET cc_start: 0.8444 (mmp) cc_final: 0.7969 (mmp) REVERT: C 69 MET cc_start: 0.8560 (mtm) cc_final: 0.8235 (mtm) REVERT: R 82 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7970 (tt) REVERT: R 113 MET cc_start: 0.8012 (ppp) cc_final: 0.7625 (ppp) REVERT: R 114 TYR cc_start: 0.7820 (m-80) cc_final: 0.6918 (m-80) REVERT: R 183 MET cc_start: 0.6825 (tmm) cc_final: 0.6021 (tmm) REVERT: R 187 MET cc_start: 0.3989 (mpp) cc_final: 0.3045 (ptp) REVERT: R 261 TRP cc_start: 0.6760 (t-100) cc_final: 0.6189 (t-100) REVERT: R 265 HIS cc_start: 0.8098 (m-70) cc_final: 0.7345 (m-70) REVERT: R 286 PHE cc_start: 0.8312 (m-80) cc_final: 0.7536 (m-80) REVERT: R 295 THR cc_start: 0.8319 (p) cc_final: 0.7082 (p) REVERT: R 299 TYR cc_start: 0.7804 (m-80) cc_final: 0.7510 (m-80) REVERT: S 6 GLU cc_start: 0.6847 (mp0) cc_final: 0.6382 (mp0) REVERT: S 19 LYS cc_start: 0.7555 (tmmt) cc_final: 0.7324 (tmmt) REVERT: S 83 MET cc_start: 0.7535 (mpp) cc_final: 0.7119 (mpp) REVERT: S 160 ARG cc_start: 0.7349 (mtm110) cc_final: 0.6907 (mtm110) outliers start: 44 outliers final: 35 residues processed: 370 average time/residue: 0.3552 time to fit residues: 171.0337 Evaluate side-chains 386 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121190 restraints weight = 17114.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125672 restraints weight = 9019.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128669 restraints weight = 5801.872| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9305 Z= 0.138 Angle : 0.717 10.516 12607 Z= 0.363 Chirality : 0.045 0.173 1422 Planarity : 0.004 0.055 1593 Dihedral : 4.966 28.966 1262 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.13 % Allowed : 21.13 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1143 helix: 1.09 (0.27), residues: 366 sheet: -0.54 (0.32), residues: 256 loop : -2.54 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 279 HIS 0.006 0.001 HIS S 35 PHE 0.025 0.002 PHE R 312 TYR 0.014 0.001 TYR R 309 ARG 0.011 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 339) hydrogen bonds : angle 4.84010 ( 969) SS BOND : bond 0.00730 ( 1) SS BOND : angle 0.69651 ( 2) covalent geometry : bond 0.00306 ( 9304) covalent geometry : angle 0.71660 (12605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7472 (ptp90) cc_final: 0.7143 (ptp90) REVERT: A 53 MET cc_start: 0.6939 (mpp) cc_final: 0.6701 (mpp) REVERT: A 212 ILE cc_start: 0.8852 (tp) cc_final: 0.8646 (tp) REVERT: A 216 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 240 MET cc_start: 0.4594 (mtp) cc_final: 0.4380 (mtp) REVERT: A 245 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6194 (mm-30) REVERT: A 248 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7954 (mtmm) REVERT: A 251 ASP cc_start: 0.8716 (t0) cc_final: 0.8478 (t0) REVERT: A 264 ILE cc_start: 0.8351 (mm) cc_final: 0.8142 (mm) REVERT: A 287 TYR cc_start: 0.8479 (m-80) cc_final: 0.7750 (m-80) REVERT: A 304 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: A 313 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7162 (tpt90) REVERT: A 316 THR cc_start: 0.7800 (p) cc_final: 0.7321 (p) REVERT: A 317 LYS cc_start: 0.7963 (mttt) cc_final: 0.7390 (mttm) REVERT: A 318 GLU cc_start: 0.7447 (pm20) cc_final: 0.7231 (pm20) REVERT: A 333 GLN cc_start: 0.7901 (tp40) cc_final: 0.7155 (tp40) REVERT: A 343 ILE cc_start: 0.8509 (tp) cc_final: 0.7805 (tp) REVERT: A 347 ASN cc_start: 0.8193 (m110) cc_final: 0.7793 (m-40) REVERT: A 350 ASP cc_start: 0.7694 (m-30) cc_final: 0.7378 (m-30) REVERT: B 15 LYS cc_start: 0.9095 (ptpp) cc_final: 0.8660 (pttm) REVERT: B 22 ARG cc_start: 0.7559 (tpm170) cc_final: 0.7315 (tpm170) REVERT: B 45 MET cc_start: 0.7593 (mmm) cc_final: 0.7275 (mmp) REVERT: B 46 ARG cc_start: 0.6941 (mpp-170) cc_final: 0.6363 (mpp-170) REVERT: B 125 ASN cc_start: 0.8162 (t0) cc_final: 0.7940 (t0) REVERT: B 127 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7772 (mmtp) REVERT: B 132 ASN cc_start: 0.7595 (m110) cc_final: 0.7203 (m110) REVERT: B 153 ASP cc_start: 0.7932 (t0) cc_final: 0.7254 (p0) REVERT: B 164 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7494 (m) REVERT: B 170 ASP cc_start: 0.7112 (p0) cc_final: 0.6734 (p0) REVERT: B 219 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7617 (tpp80) REVERT: B 233 CYS cc_start: 0.7781 (t) cc_final: 0.7516 (t) REVERT: B 234 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7113 (t80) REVERT: B 235 PHE cc_start: 0.7525 (t80) cc_final: 0.6966 (t80) REVERT: B 247 ASP cc_start: 0.7758 (t0) cc_final: 0.7140 (t0) REVERT: B 298 ASP cc_start: 0.8342 (t0) cc_final: 0.7772 (t0) REVERT: C 48 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: C 51 LYS cc_start: 0.9264 (ptpp) cc_final: 0.8082 (pttm) REVERT: C 52 MET cc_start: 0.8462 (mmp) cc_final: 0.7995 (mmp) REVERT: C 69 MET cc_start: 0.8566 (mtm) cc_final: 0.8133 (mtm) REVERT: C 73 GLU cc_start: 0.8103 (pp20) cc_final: 0.7775 (pp20) REVERT: R 82 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7839 (tt) REVERT: R 113 MET cc_start: 0.7982 (ppp) cc_final: 0.7596 (ppp) REVERT: R 114 TYR cc_start: 0.7837 (m-80) cc_final: 0.6899 (m-80) REVERT: R 182 TYR cc_start: 0.8109 (p90) cc_final: 0.7787 (p90) REVERT: R 183 MET cc_start: 0.6643 (tmm) cc_final: 0.5984 (tmm) REVERT: R 253 LEU cc_start: 0.8507 (mp) cc_final: 0.8186 (mp) REVERT: R 261 TRP cc_start: 0.6817 (t-100) cc_final: 0.6090 (t-100) REVERT: R 265 HIS cc_start: 0.8163 (m-70) cc_final: 0.7358 (m-70) REVERT: R 286 PHE cc_start: 0.8220 (m-80) cc_final: 0.7487 (m-80) REVERT: R 295 THR cc_start: 0.8267 (p) cc_final: 0.6972 (p) REVERT: R 299 TYR cc_start: 0.7763 (m-80) cc_final: 0.7477 (m-80) REVERT: S 6 GLU cc_start: 0.6873 (mp0) cc_final: 0.6388 (mp0) REVERT: S 19 LYS cc_start: 0.7523 (tmmt) cc_final: 0.7299 (tmmt) REVERT: S 38 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7275 (ptm160) REVERT: S 160 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7085 (mtm110) outliers start: 51 outliers final: 37 residues processed: 373 average time/residue: 0.3334 time to fit residues: 161.6785 Evaluate side-chains 388 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 346 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.148315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117259 restraints weight = 16918.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121514 restraints weight = 9053.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124254 restraints weight = 5861.299| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9305 Z= 0.262 Angle : 0.808 12.085 12607 Z= 0.421 Chirality : 0.048 0.171 1422 Planarity : 0.005 0.060 1593 Dihedral : 5.385 27.087 1262 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.53 % Allowed : 22.84 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1143 helix: 0.87 (0.27), residues: 372 sheet: -0.72 (0.33), residues: 251 loop : -2.63 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 332 HIS 0.015 0.002 HIS S 35 PHE 0.026 0.003 PHE A 191 TYR 0.021 0.002 TYR R 35 ARG 0.011 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 339) hydrogen bonds : angle 5.14730 ( 969) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.74801 ( 2) covalent geometry : bond 0.00570 ( 9304) covalent geometry : angle 0.80825 (12605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7049 (mpp) cc_final: 0.6711 (mpp) REVERT: A 212 ILE cc_start: 0.8824 (tp) cc_final: 0.8623 (tp) REVERT: A 216 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 245 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6340 (mm-30) REVERT: A 248 LYS cc_start: 0.8496 (mtmm) cc_final: 0.7947 (mtmm) REVERT: A 251 ASP cc_start: 0.8837 (t0) cc_final: 0.8510 (t0) REVERT: A 264 ILE cc_start: 0.8329 (mm) cc_final: 0.8108 (mm) REVERT: A 287 TYR cc_start: 0.8494 (m-80) cc_final: 0.7803 (m-80) REVERT: A 290 TYR cc_start: 0.7062 (t80) cc_final: 0.5885 (t80) REVERT: A 304 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: A 316 THR cc_start: 0.7961 (p) cc_final: 0.7659 (p) REVERT: A 317 LYS cc_start: 0.8219 (mttt) cc_final: 0.7694 (mttm) REVERT: A 331 ASN cc_start: 0.7688 (p0) cc_final: 0.7182 (p0) REVERT: A 343 ILE cc_start: 0.8546 (tp) cc_final: 0.7828 (tp) REVERT: A 347 ASN cc_start: 0.8317 (m110) cc_final: 0.7864 (m-40) REVERT: A 350 ASP cc_start: 0.7775 (m-30) cc_final: 0.7443 (m-30) REVERT: B 15 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8641 (ptpp) REVERT: B 22 ARG cc_start: 0.7670 (tpm170) cc_final: 0.7437 (tpm170) REVERT: B 45 MET cc_start: 0.7607 (mmm) cc_final: 0.7237 (mmp) REVERT: B 46 ARG cc_start: 0.6953 (mpp-170) cc_final: 0.6368 (mpp-170) REVERT: B 127 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7891 (mmtp) REVERT: B 132 ASN cc_start: 0.7690 (m110) cc_final: 0.7313 (m110) REVERT: B 153 ASP cc_start: 0.7987 (t0) cc_final: 0.7347 (p0) REVERT: B 164 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7536 (m) REVERT: B 170 ASP cc_start: 0.7083 (p0) cc_final: 0.6860 (p0) REVERT: B 205 ASP cc_start: 0.7714 (t0) cc_final: 0.7457 (t0) REVERT: B 219 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7593 (tpp80) REVERT: B 233 CYS cc_start: 0.8000 (t) cc_final: 0.7764 (t) REVERT: B 247 ASP cc_start: 0.7876 (t0) cc_final: 0.7279 (t0) REVERT: B 254 ASP cc_start: 0.7837 (t0) cc_final: 0.7497 (t0) REVERT: B 284 LEU cc_start: 0.8771 (mp) cc_final: 0.8519 (mm) REVERT: B 292 PHE cc_start: 0.7119 (m-80) cc_final: 0.6867 (m-80) REVERT: B 298 ASP cc_start: 0.8300 (t0) cc_final: 0.7831 (t0) REVERT: C 48 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: C 51 LYS cc_start: 0.9287 (ptpp) cc_final: 0.8067 (pttm) REVERT: C 52 MET cc_start: 0.8541 (mmp) cc_final: 0.7933 (mmp) REVERT: C 69 MET cc_start: 0.8610 (mtm) cc_final: 0.8160 (mtm) REVERT: C 73 GLU cc_start: 0.8163 (pp20) cc_final: 0.7808 (pp20) REVERT: R 113 MET cc_start: 0.8053 (ppp) cc_final: 0.7645 (ppp) REVERT: R 114 TYR cc_start: 0.7891 (m-80) cc_final: 0.6837 (m-80) REVERT: R 182 TYR cc_start: 0.8263 (p90) cc_final: 0.7712 (p90) REVERT: R 183 MET cc_start: 0.6784 (tmm) cc_final: 0.6210 (tmm) REVERT: R 216 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7812 (mp) REVERT: R 253 LEU cc_start: 0.8604 (mp) cc_final: 0.8391 (mp) REVERT: R 261 TRP cc_start: 0.6822 (t-100) cc_final: 0.6100 (t-100) REVERT: R 265 HIS cc_start: 0.8174 (m-70) cc_final: 0.7363 (m-70) REVERT: R 286 PHE cc_start: 0.8357 (m-80) cc_final: 0.7539 (m-80) REVERT: R 295 THR cc_start: 0.8308 (p) cc_final: 0.6934 (p) REVERT: R 299 TYR cc_start: 0.7920 (m-80) cc_final: 0.7707 (m-80) REVERT: S 6 GLU cc_start: 0.6866 (mp0) cc_final: 0.6459 (mp0) REVERT: S 160 ARG cc_start: 0.7319 (mtm110) cc_final: 0.6914 (mtm110) REVERT: S 234 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6456 (tm-30) outliers start: 55 outliers final: 41 residues processed: 378 average time/residue: 0.3265 time to fit residues: 160.8655 Evaluate side-chains 393 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.151363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119958 restraints weight = 17051.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124275 restraints weight = 9071.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127093 restraints weight = 5860.843| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9305 Z= 0.152 Angle : 0.788 10.471 12607 Z= 0.398 Chirality : 0.046 0.193 1422 Planarity : 0.005 0.058 1593 Dihedral : 5.209 27.971 1262 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.13 % Allowed : 25.65 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1143 helix: 0.91 (0.28), residues: 373 sheet: -0.67 (0.33), residues: 253 loop : -2.56 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 279 HIS 0.007 0.001 HIS S 35 PHE 0.026 0.002 PHE A 191 TYR 0.018 0.001 TYR R 35 ARG 0.011 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 339) hydrogen bonds : angle 4.91449 ( 969) SS BOND : bond 0.00331 ( 1) SS BOND : angle 0.53704 ( 2) covalent geometry : bond 0.00339 ( 9304) covalent geometry : angle 0.78764 (12605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6729 (mpp) REVERT: A 212 ILE cc_start: 0.8812 (tp) cc_final: 0.8612 (tp) REVERT: A 216 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 243 MET cc_start: 0.7255 (tpp) cc_final: 0.6973 (tpp) REVERT: A 245 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6238 (mm-30) REVERT: A 248 LYS cc_start: 0.8462 (mtmm) cc_final: 0.7887 (mtmm) REVERT: A 264 ILE cc_start: 0.8314 (mm) cc_final: 0.8114 (mm) REVERT: A 287 TYR cc_start: 0.8437 (m-80) cc_final: 0.7774 (m-80) REVERT: A 290 TYR cc_start: 0.6897 (t80) cc_final: 0.5855 (t80) REVERT: A 304 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 313 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7059 (tpt90) REVERT: A 316 THR cc_start: 0.7871 (p) cc_final: 0.7643 (p) REVERT: A 317 LYS cc_start: 0.8094 (mttt) cc_final: 0.7637 (mttm) REVERT: A 343 ILE cc_start: 0.8533 (tp) cc_final: 0.7810 (tp) REVERT: A 347 ASN cc_start: 0.8257 (m110) cc_final: 0.7782 (m-40) REVERT: A 350 ASP cc_start: 0.7665 (m-30) cc_final: 0.7314 (m-30) REVERT: B 22 ARG cc_start: 0.7617 (tpm170) cc_final: 0.7386 (tpm170) REVERT: B 45 MET cc_start: 0.7508 (mmm) cc_final: 0.7272 (mmp) REVERT: B 46 ARG cc_start: 0.6912 (mpp-170) cc_final: 0.6378 (mpp-170) REVERT: B 132 ASN cc_start: 0.7690 (m110) cc_final: 0.7327 (m110) REVERT: B 153 ASP cc_start: 0.7982 (t0) cc_final: 0.7324 (p0) REVERT: B 164 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7471 (m) REVERT: B 170 ASP cc_start: 0.7061 (p0) cc_final: 0.6672 (p0) REVERT: B 205 ASP cc_start: 0.7639 (t0) cc_final: 0.7388 (t0) REVERT: B 219 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7389 (tpp80) REVERT: B 247 ASP cc_start: 0.7830 (t0) cc_final: 0.7205 (t0) REVERT: B 292 PHE cc_start: 0.7151 (m-80) cc_final: 0.6863 (m-80) REVERT: B 298 ASP cc_start: 0.8244 (t0) cc_final: 0.7774 (t0) REVERT: C 48 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: C 51 LYS cc_start: 0.9268 (ptpp) cc_final: 0.8066 (pttm) REVERT: C 52 MET cc_start: 0.8515 (mmp) cc_final: 0.7886 (mmp) REVERT: C 69 MET cc_start: 0.8590 (mtm) cc_final: 0.8174 (mtm) REVERT: C 73 GLU cc_start: 0.8167 (pp20) cc_final: 0.7905 (pp20) REVERT: R 82 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7692 (tt) REVERT: R 113 MET cc_start: 0.8050 (ppp) cc_final: 0.7617 (ppp) REVERT: R 114 TYR cc_start: 0.7783 (m-80) cc_final: 0.6624 (m-80) REVERT: R 182 TYR cc_start: 0.8306 (p90) cc_final: 0.7773 (p90) REVERT: R 183 MET cc_start: 0.6741 (tmm) cc_final: 0.5943 (tmm) REVERT: R 253 LEU cc_start: 0.8563 (mp) cc_final: 0.8343 (mp) REVERT: R 261 TRP cc_start: 0.6725 (t-100) cc_final: 0.6252 (t-100) REVERT: R 265 HIS cc_start: 0.8109 (m-70) cc_final: 0.7284 (m-70) REVERT: R 266 LEU cc_start: 0.8970 (mt) cc_final: 0.8759 (pp) REVERT: R 286 PHE cc_start: 0.8280 (m-80) cc_final: 0.7500 (m-80) REVERT: R 295 THR cc_start: 0.8274 (p) cc_final: 0.6789 (p) REVERT: R 299 TYR cc_start: 0.7858 (m-80) cc_final: 0.7591 (m-80) REVERT: S 6 GLU cc_start: 0.6886 (mp0) cc_final: 0.6479 (mp0) REVERT: S 38 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7346 (ptm160) REVERT: S 93 MET cc_start: 0.7039 (mmm) cc_final: 0.6653 (tmm) REVERT: S 160 ARG cc_start: 0.7366 (mtm110) cc_final: 0.7052 (mtm110) REVERT: S 231 GLN cc_start: 0.6967 (pp30) cc_final: 0.6754 (pp30) outliers start: 51 outliers final: 39 residues processed: 374 average time/residue: 0.3174 time to fit residues: 152.7481 Evaluate side-chains 396 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 352 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 313 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.150869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117707 restraints weight = 17264.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122238 restraints weight = 9096.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125223 restraints weight = 5872.530| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9305 Z= 0.173 Angle : 0.806 10.602 12607 Z= 0.414 Chirality : 0.047 0.198 1422 Planarity : 0.005 0.059 1593 Dihedral : 5.297 24.412 1262 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 5.43 % Allowed : 26.36 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1143 helix: 0.87 (0.28), residues: 373 sheet: -0.60 (0.33), residues: 255 loop : -2.51 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 85 HIS 0.009 0.001 HIS S 35 PHE 0.027 0.002 PHE A 191 TYR 0.021 0.002 TYR R 221 ARG 0.015 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 339) hydrogen bonds : angle 4.95160 ( 969) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.63199 ( 2) covalent geometry : bond 0.00394 ( 9304) covalent geometry : angle 0.80610 (12605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 345 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: A 53 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6929 (mpp) REVERT: A 245 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6325 (mm-30) REVERT: A 248 LYS cc_start: 0.8486 (mtmm) cc_final: 0.7906 (mtmm) REVERT: A 287 TYR cc_start: 0.8515 (m-80) cc_final: 0.7815 (m-80) REVERT: A 290 TYR cc_start: 0.6978 (t80) cc_final: 0.5884 (t80) REVERT: A 304 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: A 313 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7000 (tpt90) REVERT: A 317 LYS cc_start: 0.8132 (mttt) cc_final: 0.7752 (mttp) REVERT: A 343 ILE cc_start: 0.8508 (tp) cc_final: 0.7778 (tp) REVERT: A 347 ASN cc_start: 0.8254 (m110) cc_final: 0.7761 (m-40) REVERT: A 350 ASP cc_start: 0.7701 (m-30) cc_final: 0.7361 (m-30) REVERT: B 22 ARG cc_start: 0.7626 (tpm170) cc_final: 0.7401 (tpm170) REVERT: B 45 MET cc_start: 0.7274 (mmm) cc_final: 0.7068 (mmp) REVERT: B 46 ARG cc_start: 0.7005 (mpp-170) cc_final: 0.6346 (mpp-170) REVERT: B 89 LYS cc_start: 0.8600 (mttm) cc_final: 0.8097 (mttp) REVERT: B 132 ASN cc_start: 0.7705 (m110) cc_final: 0.7320 (m110) REVERT: B 153 ASP cc_start: 0.7898 (t0) cc_final: 0.7331 (p0) REVERT: B 164 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7539 (m) REVERT: B 170 ASP cc_start: 0.7011 (p0) cc_final: 0.6623 (p0) REVERT: B 219 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.7372 (tpp80) REVERT: B 247 ASP cc_start: 0.7877 (t0) cc_final: 0.7249 (t0) REVERT: B 284 LEU cc_start: 0.8804 (mp) cc_final: 0.8589 (mm) REVERT: B 292 PHE cc_start: 0.7145 (m-80) cc_final: 0.6590 (m-80) REVERT: B 298 ASP cc_start: 0.8261 (t0) cc_final: 0.7779 (t0) REVERT: C 48 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: C 51 LYS cc_start: 0.9297 (ptpp) cc_final: 0.8070 (pttm) REVERT: C 52 MET cc_start: 0.8592 (mmp) cc_final: 0.7942 (mmp) REVERT: C 69 MET cc_start: 0.8658 (mtm) cc_final: 0.8219 (mtm) REVERT: D 20 ARG cc_start: 0.7826 (tmm-80) cc_final: 0.7336 (tmm-80) REVERT: R 82 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7752 (tt) REVERT: R 114 TYR cc_start: 0.7838 (m-80) cc_final: 0.7262 (m-80) REVERT: R 182 TYR cc_start: 0.8339 (p90) cc_final: 0.7737 (p90) REVERT: R 183 MET cc_start: 0.6773 (tmm) cc_final: 0.5961 (tmm) REVERT: R 261 TRP cc_start: 0.6802 (t-100) cc_final: 0.6245 (t-100) REVERT: R 265 HIS cc_start: 0.8232 (m-70) cc_final: 0.7356 (m-70) REVERT: R 286 PHE cc_start: 0.8311 (m-80) cc_final: 0.7515 (m-80) REVERT: R 295 THR cc_start: 0.8287 (p) cc_final: 0.6845 (p) REVERT: R 299 TYR cc_start: 0.7957 (m-80) cc_final: 0.7596 (m-80) REVERT: S 6 GLU cc_start: 0.6954 (mp0) cc_final: 0.6480 (mp0) REVERT: S 34 MET cc_start: 0.7467 (ptp) cc_final: 0.7263 (ptm) REVERT: S 93 MET cc_start: 0.7107 (mmm) cc_final: 0.6723 (tmm) REVERT: S 160 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7168 (mtm110) REVERT: S 231 GLN cc_start: 0.6998 (pp30) cc_final: 0.6732 (pp30) outliers start: 54 outliers final: 41 residues processed: 369 average time/residue: 0.3643 time to fit residues: 174.3172 Evaluate side-chains 382 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 335 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 313 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 35 HIS Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.152649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120950 restraints weight = 16984.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125324 restraints weight = 8968.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128218 restraints weight = 5763.356| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9305 Z= 0.154 Angle : 0.828 11.160 12607 Z= 0.421 Chirality : 0.047 0.218 1422 Planarity : 0.005 0.063 1593 Dihedral : 5.197 23.040 1262 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.13 % Allowed : 27.57 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.25), residues: 1143 helix: 0.79 (0.28), residues: 373 sheet: -0.41 (0.33), residues: 245 loop : -2.48 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 279 HIS 0.006 0.001 HIS S 35 PHE 0.030 0.002 PHE R 312 TYR 0.035 0.001 TYR R 221 ARG 0.015 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 339) hydrogen bonds : angle 4.81846 ( 969) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.57502 ( 2) covalent geometry : bond 0.00356 ( 9304) covalent geometry : angle 0.82787 (12605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: A 53 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6876 (mpp) REVERT: A 245 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6252 (mm-30) REVERT: A 248 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7878 (mtmm) REVERT: A 287 TYR cc_start: 0.8443 (m-80) cc_final: 0.7767 (m-80) REVERT: A 290 TYR cc_start: 0.6902 (t80) cc_final: 0.5812 (t80) REVERT: A 304 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: A 313 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7032 (tpt90) REVERT: A 317 LYS cc_start: 0.8036 (mttt) cc_final: 0.7672 (mttp) REVERT: A 322 HIS cc_start: 0.7814 (t-90) cc_final: 0.7440 (t-90) REVERT: A 343 ILE cc_start: 0.8532 (tp) cc_final: 0.7800 (tp) REVERT: A 347 ASN cc_start: 0.8209 (m110) cc_final: 0.7718 (m-40) REVERT: A 348 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7608 (mm) REVERT: A 350 ASP cc_start: 0.7672 (m-30) cc_final: 0.7321 (m-30) REVERT: B 22 ARG cc_start: 0.7587 (tpm170) cc_final: 0.7353 (tpm170) REVERT: B 46 ARG cc_start: 0.7021 (mpp-170) cc_final: 0.6358 (mpp-170) REVERT: B 89 LYS cc_start: 0.8466 (mttm) cc_final: 0.7953 (mttp) REVERT: B 132 ASN cc_start: 0.7662 (m110) cc_final: 0.7328 (m110) REVERT: B 153 ASP cc_start: 0.7879 (t0) cc_final: 0.7139 (p0) REVERT: B 164 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7494 (m) REVERT: B 170 ASP cc_start: 0.7033 (p0) cc_final: 0.6661 (p0) REVERT: B 205 ASP cc_start: 0.7623 (t0) cc_final: 0.7378 (t0) REVERT: B 247 ASP cc_start: 0.7836 (t0) cc_final: 0.7202 (t0) REVERT: B 256 ARG cc_start: 0.7798 (mpp80) cc_final: 0.7587 (mtt180) REVERT: B 292 PHE cc_start: 0.7128 (m-80) cc_final: 0.6643 (m-80) REVERT: B 298 ASP cc_start: 0.8294 (t0) cc_final: 0.7837 (t0) REVERT: B 301 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7307 (mmtm) REVERT: C 48 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: C 51 LYS cc_start: 0.9274 (ptpp) cc_final: 0.8060 (pttm) REVERT: C 52 MET cc_start: 0.8527 (mmp) cc_final: 0.7897 (mmp) REVERT: C 69 MET cc_start: 0.8583 (mtm) cc_final: 0.8247 (mtm) REVERT: D 20 ARG cc_start: 0.7837 (tmm-80) cc_final: 0.7352 (tmm-80) REVERT: R 82 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7715 (tt) REVERT: R 114 TYR cc_start: 0.7768 (m-80) cc_final: 0.7118 (m-80) REVERT: R 182 TYR cc_start: 0.8356 (p90) cc_final: 0.7767 (p90) REVERT: R 183 MET cc_start: 0.6735 (tmm) cc_final: 0.5911 (tmm) REVERT: R 261 TRP cc_start: 0.6701 (t-100) cc_final: 0.6198 (t-100) REVERT: R 265 HIS cc_start: 0.7989 (m-70) cc_final: 0.7126 (m-70) REVERT: R 266 LEU cc_start: 0.8924 (mt) cc_final: 0.8705 (pp) REVERT: R 286 PHE cc_start: 0.8312 (m-80) cc_final: 0.7504 (m-80) REVERT: R 295 THR cc_start: 0.8188 (p) cc_final: 0.6762 (p) REVERT: R 299 TYR cc_start: 0.7853 (m-80) cc_final: 0.7495 (m-80) REVERT: S 6 GLU cc_start: 0.6818 (mp0) cc_final: 0.6376 (mp0) REVERT: S 93 MET cc_start: 0.7054 (mmm) cc_final: 0.6733 (tmm) REVERT: S 160 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7117 (mtm110) outliers start: 51 outliers final: 41 residues processed: 357 average time/residue: 0.2866 time to fit residues: 132.8305 Evaluate side-chains 380 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 332 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 313 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 35 HIS Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.0170 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.153779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122048 restraints weight = 17040.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126468 restraints weight = 8981.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129427 restraints weight = 5749.369| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9305 Z= 0.149 Angle : 0.847 11.570 12607 Z= 0.431 Chirality : 0.047 0.227 1422 Planarity : 0.005 0.066 1593 Dihedral : 5.105 23.447 1262 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.73 % Allowed : 28.87 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.24), residues: 1143 helix: 0.68 (0.28), residues: 377 sheet: -0.30 (0.33), residues: 242 loop : -2.42 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 85 HIS 0.005 0.001 HIS S 35 PHE 0.029 0.002 PHE R 312 TYR 0.041 0.001 TYR R 221 ARG 0.016 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 339) hydrogen bonds : angle 4.79797 ( 969) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.58037 ( 2) covalent geometry : bond 0.00343 ( 9304) covalent geometry : angle 0.84699 (12605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6944 (m-30) REVERT: A 32 ARG cc_start: 0.7568 (ptp90) cc_final: 0.7002 (ptp90) REVERT: A 53 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6881 (mpp) REVERT: A 245 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6220 (mm-30) REVERT: A 248 LYS cc_start: 0.8471 (mtmm) cc_final: 0.7873 (mtmm) REVERT: A 270 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6276 (pptt) REVERT: A 287 TYR cc_start: 0.8421 (m-80) cc_final: 0.7747 (m-80) REVERT: A 290 TYR cc_start: 0.6908 (t80) cc_final: 0.5813 (t80) REVERT: A 304 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: A 317 LYS cc_start: 0.7948 (mttt) cc_final: 0.7642 (mttm) REVERT: A 322 HIS cc_start: 0.7827 (t-90) cc_final: 0.7474 (t-90) REVERT: A 341 ASP cc_start: 0.8022 (t0) cc_final: 0.7820 (t0) REVERT: A 343 ILE cc_start: 0.8519 (tp) cc_final: 0.7795 (tp) REVERT: A 347 ASN cc_start: 0.8254 (m110) cc_final: 0.7723 (m-40) REVERT: A 348 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7589 (mm) REVERT: A 350 ASP cc_start: 0.7618 (m-30) cc_final: 0.7283 (m-30) REVERT: B 22 ARG cc_start: 0.7579 (tpm170) cc_final: 0.7337 (tpm170) REVERT: B 46 ARG cc_start: 0.6853 (mpp-170) cc_final: 0.6522 (mpp-170) REVERT: B 89 LYS cc_start: 0.8493 (mttm) cc_final: 0.8003 (mttp) REVERT: B 132 ASN cc_start: 0.7647 (m110) cc_final: 0.7304 (m110) REVERT: B 153 ASP cc_start: 0.7958 (t0) cc_final: 0.7209 (p0) REVERT: B 164 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7508 (m) REVERT: B 170 ASP cc_start: 0.7040 (p0) cc_final: 0.6661 (p0) REVERT: B 205 ASP cc_start: 0.7614 (t0) cc_final: 0.7352 (t0) REVERT: B 247 ASP cc_start: 0.7816 (t0) cc_final: 0.7180 (t0) REVERT: B 253 PHE cc_start: 0.8165 (m-80) cc_final: 0.7774 (m-80) REVERT: B 256 ARG cc_start: 0.7785 (mpp80) cc_final: 0.7582 (mtt180) REVERT: B 284 LEU cc_start: 0.8573 (mm) cc_final: 0.8348 (mp) REVERT: B 292 PHE cc_start: 0.7151 (m-80) cc_final: 0.6705 (m-80) REVERT: B 298 ASP cc_start: 0.8506 (t0) cc_final: 0.7925 (t0) REVERT: B 300 LEU cc_start: 0.9143 (mm) cc_final: 0.8880 (mm) REVERT: B 301 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7277 (mmtm) REVERT: C 48 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: C 51 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8008 (pttm) REVERT: C 52 MET cc_start: 0.8506 (mmp) cc_final: 0.7880 (mmp) REVERT: C 69 MET cc_start: 0.8564 (mtm) cc_final: 0.8265 (mtm) REVERT: D 20 ARG cc_start: 0.7812 (tmm-80) cc_final: 0.7181 (tmm-80) REVERT: D 24 PRO cc_start: 0.5364 (Cg_exo) cc_final: 0.4663 (Cg_endo) REVERT: R 82 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7728 (tt) REVERT: R 114 TYR cc_start: 0.7767 (m-80) cc_final: 0.7094 (m-80) REVERT: R 182 TYR cc_start: 0.8380 (p90) cc_final: 0.7770 (p90) REVERT: R 183 MET cc_start: 0.6703 (tmm) cc_final: 0.5885 (tmm) REVERT: R 261 TRP cc_start: 0.6697 (t-100) cc_final: 0.6208 (t-100) REVERT: R 265 HIS cc_start: 0.7978 (m-70) cc_final: 0.7109 (m-70) REVERT: R 266 LEU cc_start: 0.8927 (mt) cc_final: 0.8699 (pp) REVERT: R 286 PHE cc_start: 0.8218 (m-80) cc_final: 0.7431 (m-80) REVERT: R 295 THR cc_start: 0.8161 (p) cc_final: 0.6794 (p) REVERT: R 299 TYR cc_start: 0.7808 (m-80) cc_final: 0.7426 (m-80) REVERT: S 6 GLU cc_start: 0.6780 (mp0) cc_final: 0.6375 (mp0) REVERT: S 38 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7404 (ptm160) REVERT: S 93 MET cc_start: 0.7040 (mmm) cc_final: 0.6712 (tmm) REVERT: S 160 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7141 (mtm110) REVERT: S 231 GLN cc_start: 0.6933 (pp30) cc_final: 0.6566 (tm-30) outliers start: 47 outliers final: 36 residues processed: 359 average time/residue: 0.3018 time to fit residues: 139.6406 Evaluate side-chains 379 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 335 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 313 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 35 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 103 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.153064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121590 restraints weight = 17007.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125980 restraints weight = 8979.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128844 restraints weight = 5762.648| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9305 Z= 0.156 Angle : 0.866 12.068 12607 Z= 0.440 Chirality : 0.047 0.236 1422 Planarity : 0.005 0.067 1593 Dihedral : 5.128 24.903 1262 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.43 % Allowed : 28.77 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1143 helix: 0.93 (0.28), residues: 365 sheet: -0.42 (0.33), residues: 249 loop : -2.39 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 279 HIS 0.006 0.001 HIS S 35 PHE 0.029 0.002 PHE R 312 TYR 0.033 0.001 TYR R 221 ARG 0.016 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 339) hydrogen bonds : angle 4.81965 ( 969) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.55798 ( 2) covalent geometry : bond 0.00358 ( 9304) covalent geometry : angle 0.86622 (12605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5175.57 seconds wall clock time: 98 minutes 16.99 seconds (5896.99 seconds total)