Starting phenix.real_space_refine on Tue Mar 3 23:39:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8m_31804/03_2026/7v8m_31804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8m_31804/03_2026/7v8m_31804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_2026/7v8m_31804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_2026/7v8m_31804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_2026/7v8m_31804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_2026/7v8m_31804.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5949 2.51 5 N 1629 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9338 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2845 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 374} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1742 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3009 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 394} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 4, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "F" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1742 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.90, per 1000 atoms: 0.20 Number of scatterers: 9338 At special positions: 0 Unit cell: (103.36, 84.32, 152.32, 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 49 16.00 O 1711 8.00 N 1629 7.00 C 5949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 365.4 milliseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 52.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.883A pdb=" N PHE C 8 " --> pdb=" O PRO C 4 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 59 removed outlier: 4.933A pdb=" N SER C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 63 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.584A pdb=" N LEU C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.996A pdb=" N TYR C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 199' Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 249 through 271 removed outlier: 6.663A pdb=" N GLU C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 303 removed outlier: 4.290A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 337 removed outlier: 3.746A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 Processing helix chain 'C' and resid 361 through 390 removed outlier: 3.571A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'D' and resid 48 through 55 removed outlier: 3.958A pdb=" N LEU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 103 through 115 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.811A pdb=" N ILE D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 147 through 161 removed outlier: 3.574A pdb=" N ARG D 151 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 195 removed outlier: 4.371A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 removed outlier: 3.556A pdb=" N ALA D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 16 removed outlier: 4.157A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 59 removed outlier: 3.931A pdb=" N SER E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 119 through 127 removed outlier: 3.973A pdb=" N ARG E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.697A pdb=" N LEU E 179 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 180 " --> pdb=" O HIS E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 180' Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.706A pdb=" N SER E 202 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.531A pdb=" N ASP E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 removed outlier: 3.572A pdb=" N LEU E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 298 removed outlier: 5.712A pdb=" N TYR E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N MET E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'E' and resid 313 through 341 removed outlier: 3.609A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 376 through 404 removed outlier: 4.368A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.500A pdb=" N VAL E 410 " --> pdb=" O ASP E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.588A pdb=" N LYS F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 115 Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 118 through 134 removed outlier: 3.793A pdb=" N ILE F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.531A pdb=" N GLU F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 161 Processing helix chain 'F' and resid 177 through 195 removed outlier: 4.039A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 Processing sheet with id=AA1, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.575A pdb=" N VAL C 130 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 144 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE C 190 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 146 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 147 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLU C 200 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N MET C 201 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL C 113 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL C 203 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU C 115 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.575A pdb=" N VAL C 130 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N GLY C 176 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N SER C 170 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N ILE C 178 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER C 168 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N ALA C 169 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 15.110A pdb=" N THR C 98 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 21.581A pdb=" N GLN C 171 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 26.773A pdb=" N ILE C 96 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 33.434A pdb=" N THR C 173 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 38.653A pdb=" N ALA C 94 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 30 removed outlier: 5.903A pdb=" N HIS D 26 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS D 13 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE D 30 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP D 9 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N CYS D 8 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE D 67 " --> pdb=" O CYS D 8 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN D 10 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP D 65 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.376A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASP D 170 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE D 92 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET D 38 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR D 203 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA D 39 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET D 218 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL D 41 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN D 215 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 226 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU D 217 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 249 through 253 removed outlier: 7.366A pdb=" N ILE E 150 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE E 192 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN E 147 " --> pdb=" O PRO E 207 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 204 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 12 removed outlier: 5.642A pdb=" N CYS F 8 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE F 67 " --> pdb=" O CYS F 8 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN F 10 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP F 65 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 89 through 92 removed outlier: 3.726A pdb=" N ASP F 170 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR F 203 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 40 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA F 39 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET F 218 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL F 41 " --> pdb=" O MET F 218 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN F 215 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU F 226 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU F 217 " --> pdb=" O THR F 224 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1527 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: 1.48 Time building geometry restraints manager: 0.84 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: 3137 1.34 - 1.46: 1874 1.46 - 1.58: 4388 1.58 - 1.70: 1 1.70 - 1.82: 92 Bond restraints: 9492 Sorted by residual: bond pdb=" CB PRO C 167 " pdb=" CG PRO C 167 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.53e+00 bond pdb=" C TYR E 397 " pdb=" N PRO E 398 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.75e+00 bond pdb=" CA ARG D 211 " pdb=" C ARG D 211 " ideal model delta sigma weight residual 1.523 1.544 -0.022 1.41e-02 5.03e+03 2.37e+00 bond pdb=" C GLN C 3 " pdb=" N PRO C 4 " ideal model delta sigma weight residual 1.330 1.347 -0.017 1.19e-02 7.06e+03 2.05e+00 bond pdb=" CB PRO C 179 " pdb=" CG PRO C 179 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.04e+00 ... (remaining 9487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12425 1.88 - 3.76: 398 3.76 - 5.65: 59 5.65 - 7.53: 15 7.53 - 9.41: 4 Bond angle restraints: 12901 Sorted by residual: angle pdb=" C HIS D 141 " pdb=" N ARG D 142 " pdb=" CA ARG D 142 " ideal model delta sigma weight residual 120.67 126.60 -5.93 1.34e+00 5.57e-01 1.96e+01 angle pdb=" CA GLU D 171 " pdb=" CB GLU D 171 " pdb=" CG GLU D 171 " ideal model delta sigma weight residual 114.10 122.76 -8.66 2.00e+00 2.50e-01 1.87e+01 angle pdb=" N GLU F 83 " pdb=" CA GLU F 83 " pdb=" CB GLU F 83 " ideal model delta sigma weight residual 110.28 116.08 -5.80 1.55e+00 4.16e-01 1.40e+01 angle pdb=" N VAL E 62 " pdb=" CA VAL E 62 " pdb=" C VAL E 62 " ideal model delta sigma weight residual 113.71 110.40 3.31 9.50e-01 1.11e+00 1.21e+01 angle pdb=" C TYR D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta sigma weight residual 120.44 124.92 -4.48 1.30e+00 5.92e-01 1.19e+01 ... (remaining 12896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5205 17.98 - 35.96: 425 35.96 - 53.94: 58 53.94 - 71.92: 20 71.92 - 89.90: 8 Dihedral angle restraints: 5716 sinusoidal: 2123 harmonic: 3593 Sorted by residual: dihedral pdb=" CA ASP E 83 " pdb=" C ASP E 83 " pdb=" N HIS E 84 " pdb=" CA HIS E 84 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLN F 94 " pdb=" C GLN F 94 " pdb=" N PHE F 95 " pdb=" CA PHE F 95 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG F 214 " pdb=" C ARG F 214 " pdb=" N GLN F 215 " pdb=" CA GLN F 215 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 973 0.040 - 0.079: 421 0.079 - 0.119: 115 0.119 - 0.159: 28 0.159 - 0.198: 4 Chirality restraints: 1541 Sorted by residual: chirality pdb=" CA GLU F 171 " pdb=" N GLU F 171 " pdb=" C GLU F 171 " pdb=" CB GLU F 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CB ILE C 67 " pdb=" CA ILE C 67 " pdb=" CG1 ILE C 67 " pdb=" CG2 ILE C 67 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CB ILE E 365 " pdb=" CA ILE E 365 " pdb=" CG1 ILE E 365 " pdb=" CG2 ILE E 365 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 1538 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 163 " 0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO D 164 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 60 " 0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO F 61 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 61 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 61 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 73 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO E 74 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.030 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 106 2.62 - 3.19: 8904 3.19 - 3.76: 14300 3.76 - 4.33: 18633 4.33 - 4.90: 29684 Nonbonded interactions: 71627 Sorted by model distance: nonbonded pdb=" OG1 THR F 103 " pdb=" OE1 GLU F 106 " model vdw 2.046 3.040 nonbonded pdb=" NE2 GLN D 152 " pdb=" O PRO D 172 " model vdw 2.167 3.120 nonbonded pdb=" O SER C 70 " pdb=" NZ LYS C 245 " model vdw 2.167 3.120 nonbonded pdb=" OD1 ASP C 233 " pdb=" N SER C 234 " model vdw 2.184 3.120 nonbonded pdb=" NH2 ARG F 138 " pdb=" O ARG F 142 " model vdw 2.191 3.120 ... (remaining 71622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.004 0.094 9492 Z= 0.179 Angle : 0.809 9.411 12901 Z= 0.439 Chirality : 0.047 0.198 1541 Planarity : 0.006 0.098 1664 Dihedral : 13.856 89.905 3404 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1255 helix: 0.66 (0.22), residues: 557 sheet: -0.48 (0.38), residues: 178 loop : -0.92 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 138 TYR 0.032 0.002 TYR C 13 PHE 0.021 0.002 PHE E 285 TRP 0.023 0.002 TRP C 246 HIS 0.020 0.002 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9492) covalent geometry : angle 0.80893 (12901) hydrogen bonds : bond 0.15228 ( 520) hydrogen bonds : angle 6.92451 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.8630 (mt) cc_final: 0.8332 (mt) REVERT: C 258 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8356 (tm-30) REVERT: C 323 ILE cc_start: 0.9018 (mt) cc_final: 0.8772 (mt) REVERT: C 368 ILE cc_start: 0.9243 (pt) cc_final: 0.8616 (mm) REVERT: C 378 LEU cc_start: 0.9262 (mm) cc_final: 0.9020 (tp) REVERT: D 13 LYS cc_start: 0.6767 (tptm) cc_final: 0.5917 (tptm) REVERT: D 66 VAL cc_start: 0.7039 (t) cc_final: 0.6569 (p) REVERT: D 184 ILE cc_start: 0.7936 (pt) cc_final: 0.7654 (pt) REVERT: E 264 ASP cc_start: 0.8177 (m-30) cc_final: 0.7743 (m-30) REVERT: E 353 GLU cc_start: 0.7546 (tt0) cc_final: 0.5940 (tp30) REVERT: F 102 PHE cc_start: 0.7227 (m-10) cc_final: 0.6866 (m-80) REVERT: F 103 THR cc_start: 0.5011 (p) cc_final: 0.4559 (p) REVERT: F 152 GLN cc_start: 0.7541 (mm110) cc_final: 0.7122 (tt0) REVERT: F 215 GLN cc_start: 0.7438 (mt0) cc_final: 0.7044 (mm110) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.0736 time to fit residues: 33.8925 Evaluate side-chains 245 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0030 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN D 207 GLN E 84 HIS ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094590 restraints weight = 26551.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097524 restraints weight = 15989.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.099596 restraints weight = 10972.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100999 restraints weight = 8315.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102052 restraints weight = 6783.057| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9492 Z= 0.129 Angle : 0.648 7.080 12901 Z= 0.332 Chirality : 0.045 0.171 1541 Planarity : 0.005 0.054 1664 Dihedral : 4.753 20.227 1335 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1255 helix: 0.93 (0.22), residues: 571 sheet: -0.35 (0.38), residues: 178 loop : -0.74 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 138 TYR 0.016 0.001 TYR D 15 PHE 0.012 0.001 PHE E 285 TRP 0.020 0.001 TRP C 246 HIS 0.010 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9492) covalent geometry : angle 0.64754 (12901) hydrogen bonds : bond 0.04377 ( 520) hydrogen bonds : angle 5.20875 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9294 (mt) cc_final: 0.9018 (mt) REVERT: C 211 LEU cc_start: 0.9039 (tp) cc_final: 0.8837 (tp) REVERT: C 258 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 323 ILE cc_start: 0.8799 (mt) cc_final: 0.8528 (mt) REVERT: C 351 LEU cc_start: 0.5757 (tp) cc_final: 0.5520 (tp) REVERT: C 368 ILE cc_start: 0.8928 (pt) cc_final: 0.8692 (mm) REVERT: D 66 VAL cc_start: 0.7456 (t) cc_final: 0.7010 (p) REVERT: D 67 ILE cc_start: 0.8004 (tt) cc_final: 0.7776 (tt) REVERT: D 96 HIS cc_start: 0.8975 (p90) cc_final: 0.8714 (p90) REVERT: D 170 ASP cc_start: 0.7945 (t0) cc_final: 0.7733 (t0) REVERT: D 191 LEU cc_start: 0.9634 (mm) cc_final: 0.9399 (mm) REVERT: D 195 GLN cc_start: 0.8643 (mm110) cc_final: 0.7976 (tp-100) REVERT: E 29 ILE cc_start: 0.9216 (mm) cc_final: 0.8983 (mm) REVERT: E 264 ASP cc_start: 0.8980 (m-30) cc_final: 0.8668 (m-30) REVERT: E 350 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8111 (tm-30) REVERT: E 353 GLU cc_start: 0.8247 (tt0) cc_final: 0.6560 (tp30) REVERT: F 38 MET cc_start: 0.7291 (ttm) cc_final: 0.7042 (ttp) REVERT: F 84 LEU cc_start: 0.9181 (mt) cc_final: 0.8888 (tt) REVERT: F 152 GLN cc_start: 0.7954 (mm110) cc_final: 0.7138 (tt0) REVERT: F 212 MET cc_start: 0.7156 (mpp) cc_final: 0.6666 (mpp) REVERT: F 215 GLN cc_start: 0.7713 (mt0) cc_final: 0.6851 (mm110) REVERT: F 218 MET cc_start: 0.6598 (tpt) cc_final: 0.6367 (tpp) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 0.0690 time to fit residues: 31.4844 Evaluate side-chains 244 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 0.0470 chunk 78 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 294 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN E 188 HIS F 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.120545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094435 restraints weight = 26681.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097379 restraints weight = 15933.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099414 restraints weight = 10879.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100898 restraints weight = 8214.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101764 restraints weight = 6692.027| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9492 Z= 0.123 Angle : 0.617 6.480 12901 Z= 0.316 Chirality : 0.044 0.198 1541 Planarity : 0.004 0.049 1664 Dihedral : 4.600 20.175 1335 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1255 helix: 1.10 (0.22), residues: 574 sheet: -0.11 (0.40), residues: 177 loop : -0.70 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 138 TYR 0.014 0.001 TYR C 13 PHE 0.012 0.001 PHE D 91 TRP 0.018 0.001 TRP C 246 HIS 0.009 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9492) covalent geometry : angle 0.61737 (12901) hydrogen bonds : bond 0.03917 ( 520) hydrogen bonds : angle 4.78952 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.351 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: C 29 LEU cc_start: 0.9258 (mt) cc_final: 0.8964 (mt) REVERT: C 323 ILE cc_start: 0.8968 (mt) cc_final: 0.8644 (mt) REVERT: D 66 VAL cc_start: 0.7532 (t) cc_final: 0.7115 (p) REVERT: D 96 HIS cc_start: 0.8947 (p90) cc_final: 0.8420 (p90) REVERT: D 187 LEU cc_start: 0.9491 (tt) cc_final: 0.9203 (mt) REVERT: D 195 GLN cc_start: 0.8705 (mm110) cc_final: 0.8128 (tp-100) REVERT: E 29 ILE cc_start: 0.9196 (mm) cc_final: 0.8961 (mm) REVERT: E 97 TYR cc_start: 0.7972 (p90) cc_final: 0.7769 (p90) REVERT: E 264 ASP cc_start: 0.8851 (m-30) cc_final: 0.8538 (m-30) REVERT: E 298 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8714 (mmmt) REVERT: E 306 ARG cc_start: 0.9261 (tpp80) cc_final: 0.9023 (tpp80) REVERT: E 336 ILE cc_start: 0.9401 (mm) cc_final: 0.9178 (mp) REVERT: E 353 GLU cc_start: 0.8232 (tt0) cc_final: 0.6798 (tp30) REVERT: F 38 MET cc_start: 0.7694 (ttm) cc_final: 0.7460 (tpp) REVERT: F 83 GLU cc_start: 0.8037 (pp20) cc_final: 0.7610 (pp20) REVERT: F 84 LEU cc_start: 0.9100 (mt) cc_final: 0.8838 (mt) REVERT: F 87 GLN cc_start: 0.9068 (tt0) cc_final: 0.8863 (tt0) REVERT: F 128 GLU cc_start: 0.8945 (mp0) cc_final: 0.8558 (mp0) REVERT: F 146 LEU cc_start: 0.6881 (mt) cc_final: 0.6658 (tp) REVERT: F 152 GLN cc_start: 0.7898 (mm110) cc_final: 0.7233 (tt0) REVERT: F 215 GLN cc_start: 0.7982 (mt0) cc_final: 0.6860 (mm110) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.0707 time to fit residues: 31.9268 Evaluate side-chains 251 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN D 152 GLN D 207 GLN F 10 ASN F 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.120920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094832 restraints weight = 26714.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097730 restraints weight = 15960.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.099676 restraints weight = 10953.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101217 restraints weight = 8316.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102137 restraints weight = 6805.410| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9492 Z= 0.118 Angle : 0.614 6.521 12901 Z= 0.313 Chirality : 0.043 0.153 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.488 19.867 1335 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1255 helix: 1.13 (0.22), residues: 582 sheet: 0.02 (0.40), residues: 173 loop : -0.73 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.017 0.001 TYR C 13 PHE 0.010 0.001 PHE D 91 TRP 0.017 0.001 TRP C 246 HIS 0.007 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9492) covalent geometry : angle 0.61426 (12901) hydrogen bonds : bond 0.03738 ( 520) hydrogen bonds : angle 4.70951 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9191 (mt) cc_final: 0.8917 (mt) REVERT: C 48 MET cc_start: 0.9467 (mtp) cc_final: 0.8782 (mtp) REVERT: C 184 PHE cc_start: 0.7975 (m-80) cc_final: 0.7320 (m-80) REVERT: C 226 LEU cc_start: 0.8668 (mp) cc_final: 0.8348 (tp) REVERT: C 323 ILE cc_start: 0.8957 (mt) cc_final: 0.8639 (mt) REVERT: C 351 LEU cc_start: 0.5904 (tp) cc_final: 0.5678 (tp) REVERT: D 16 GLN cc_start: 0.4154 (OUTLIER) cc_final: 0.3794 (pm20) REVERT: D 71 GLN cc_start: 0.8742 (mp10) cc_final: 0.8506 (mp10) REVERT: E 264 ASP cc_start: 0.8810 (m-30) cc_final: 0.8596 (m-30) REVERT: E 298 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8722 (mmmt) REVERT: E 306 ARG cc_start: 0.9259 (tpp80) cc_final: 0.9020 (tpp80) REVERT: E 353 GLU cc_start: 0.8204 (tt0) cc_final: 0.6767 (tp30) REVERT: F 128 GLU cc_start: 0.8986 (mp0) cc_final: 0.8602 (mp0) REVERT: F 129 MET cc_start: 0.8355 (mmm) cc_final: 0.7737 (mmm) REVERT: F 131 LYS cc_start: 0.8375 (ptpp) cc_final: 0.8119 (ptpt) REVERT: F 146 LEU cc_start: 0.7014 (mt) cc_final: 0.6725 (tp) REVERT: F 152 GLN cc_start: 0.7849 (mm110) cc_final: 0.7286 (tt0) REVERT: F 168 LEU cc_start: 0.9109 (mp) cc_final: 0.8696 (tt) REVERT: F 215 GLN cc_start: 0.8205 (mt0) cc_final: 0.6901 (mm110) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.0713 time to fit residues: 32.4506 Evaluate side-chains 253 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 GLN E 122 GLN E 376 HIS F 21 GLN F 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.120650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094620 restraints weight = 26869.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097494 restraints weight = 16255.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099559 restraints weight = 11170.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100804 restraints weight = 8472.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.101809 restraints weight = 7012.871| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9492 Z= 0.119 Angle : 0.614 6.539 12901 Z= 0.312 Chirality : 0.044 0.176 1541 Planarity : 0.004 0.047 1664 Dihedral : 4.457 22.746 1335 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.24), residues: 1255 helix: 1.21 (0.22), residues: 583 sheet: 0.06 (0.39), residues: 177 loop : -0.62 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 151 TYR 0.020 0.001 TYR D 15 PHE 0.009 0.001 PHE D 91 TRP 0.017 0.001 TRP C 246 HIS 0.008 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9492) covalent geometry : angle 0.61356 (12901) hydrogen bonds : bond 0.03747 ( 520) hydrogen bonds : angle 4.61293 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.336 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: C 29 LEU cc_start: 0.9154 (mt) cc_final: 0.8862 (mt) REVERT: C 114 MET cc_start: 0.6769 (ppp) cc_final: 0.6084 (ptm) REVERT: C 184 PHE cc_start: 0.7959 (m-80) cc_final: 0.7278 (m-80) REVERT: C 226 LEU cc_start: 0.8646 (mp) cc_final: 0.8369 (tp) REVERT: C 263 GLU cc_start: 0.8633 (pp20) cc_final: 0.8424 (pp20) REVERT: C 351 LEU cc_start: 0.5907 (tp) cc_final: 0.5696 (tp) REVERT: C 373 MET cc_start: 0.8530 (mmm) cc_final: 0.8164 (mmt) REVERT: D 62 THR cc_start: 0.8758 (p) cc_final: 0.8392 (p) REVERT: D 67 ILE cc_start: 0.8205 (tt) cc_final: 0.7899 (tt) REVERT: D 94 GLN cc_start: 0.5684 (pt0) cc_final: 0.5173 (pp30) REVERT: D 96 HIS cc_start: 0.8726 (p-80) cc_final: 0.8246 (p-80) REVERT: D 210 LYS cc_start: 0.9376 (mttp) cc_final: 0.9161 (mttp) REVERT: E 298 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8790 (mmmt) REVERT: E 306 ARG cc_start: 0.9237 (tpp80) cc_final: 0.8999 (tpp80) REVERT: E 353 GLU cc_start: 0.8157 (tt0) cc_final: 0.6751 (tp30) REVERT: F 129 MET cc_start: 0.8256 (mmm) cc_final: 0.7667 (mmm) REVERT: F 141 HIS cc_start: 0.5987 (m90) cc_final: 0.5701 (m-70) REVERT: F 146 LEU cc_start: 0.7066 (mt) cc_final: 0.6839 (tp) REVERT: F 152 GLN cc_start: 0.7799 (mm110) cc_final: 0.7244 (tt0) REVERT: F 215 GLN cc_start: 0.8266 (mt0) cc_final: 0.7415 (mp10) outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.0681 time to fit residues: 30.5584 Evaluate side-chains 253 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.0980 chunk 58 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN E 376 HIS F 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.117061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091085 restraints weight = 26812.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093848 restraints weight = 16213.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095788 restraints weight = 11265.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097217 restraints weight = 8594.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098019 restraints weight = 7041.545| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9492 Z= 0.161 Angle : 0.649 6.594 12901 Z= 0.336 Chirality : 0.044 0.166 1541 Planarity : 0.004 0.047 1664 Dihedral : 4.557 22.761 1335 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1255 helix: 1.13 (0.22), residues: 590 sheet: -0.07 (0.38), residues: 183 loop : -0.60 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 193 TYR 0.018 0.002 TYR C 13 PHE 0.011 0.001 PHE D 91 TRP 0.021 0.002 TRP C 246 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9492) covalent geometry : angle 0.64883 (12901) hydrogen bonds : bond 0.04108 ( 520) hydrogen bonds : angle 4.76832 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9254 (mt) cc_final: 0.8931 (mt) REVERT: C 114 MET cc_start: 0.7012 (ppp) cc_final: 0.6418 (ptm) REVERT: C 258 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 305 LEU cc_start: 0.9309 (mm) cc_final: 0.9088 (mm) REVERT: D 75 LYS cc_start: 0.8104 (pttm) cc_final: 0.7783 (pttp) REVERT: D 96 HIS cc_start: 0.8700 (p-80) cc_final: 0.8309 (p-80) REVERT: E 264 ASP cc_start: 0.8864 (m-30) cc_final: 0.8590 (m-30) REVERT: E 272 MET cc_start: 0.8766 (mtp) cc_final: 0.8102 (ttm) REVERT: E 306 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8993 (tpp80) REVERT: E 353 GLU cc_start: 0.8234 (tt0) cc_final: 0.6798 (tp30) REVERT: F 83 GLU cc_start: 0.8039 (pp20) cc_final: 0.7596 (pp20) REVERT: F 84 LEU cc_start: 0.9063 (mt) cc_final: 0.8849 (mt) REVERT: F 128 GLU cc_start: 0.9070 (mp0) cc_final: 0.8766 (mp0) REVERT: F 129 MET cc_start: 0.8211 (mmm) cc_final: 0.7714 (mmm) REVERT: F 146 LEU cc_start: 0.7234 (mt) cc_final: 0.6948 (tp) REVERT: F 152 GLN cc_start: 0.7885 (mm110) cc_final: 0.7274 (tt0) REVERT: F 207 GLN cc_start: 0.8450 (tp40) cc_final: 0.7768 (pt0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.0699 time to fit residues: 30.7652 Evaluate side-chains 240 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN D 107 ASN D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091708 restraints weight = 26786.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094474 restraints weight = 16255.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096455 restraints weight = 11264.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097805 restraints weight = 8610.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098633 restraints weight = 7079.267| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9492 Z= 0.135 Angle : 0.652 7.372 12901 Z= 0.331 Chirality : 0.044 0.149 1541 Planarity : 0.004 0.046 1664 Dihedral : 4.547 23.341 1335 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1255 helix: 1.17 (0.22), residues: 589 sheet: -0.09 (0.38), residues: 180 loop : -0.59 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.023 0.001 TYR D 15 PHE 0.013 0.001 PHE D 95 TRP 0.021 0.001 TRP C 246 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9492) covalent geometry : angle 0.65152 (12901) hydrogen bonds : bond 0.03993 ( 520) hydrogen bonds : angle 4.61621 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9169 (mt) cc_final: 0.8855 (mt) REVERT: C 201 MET cc_start: 0.8002 (ppp) cc_final: 0.7741 (ppp) REVERT: C 258 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8426 (tm-30) REVERT: C 262 MET cc_start: 0.8055 (tpp) cc_final: 0.7378 (tpp) REVERT: C 305 LEU cc_start: 0.9293 (mm) cc_final: 0.9089 (mm) REVERT: D 75 LYS cc_start: 0.8128 (pttm) cc_final: 0.7813 (pttp) REVERT: D 89 LEU cc_start: 0.8419 (tt) cc_final: 0.7987 (mm) REVERT: D 96 HIS cc_start: 0.8610 (p-80) cc_final: 0.8281 (p-80) REVERT: E 264 ASP cc_start: 0.8788 (m-30) cc_final: 0.8551 (m-30) REVERT: E 298 LYS cc_start: 0.9165 (mmmm) cc_final: 0.8893 (mmmt) REVERT: E 306 ARG cc_start: 0.9261 (tpp80) cc_final: 0.8976 (tpp80) REVERT: E 353 GLU cc_start: 0.8286 (tt0) cc_final: 0.6743 (tp30) REVERT: F 87 GLN cc_start: 0.9090 (tt0) cc_final: 0.8868 (tt0) REVERT: F 125 ARG cc_start: 0.8364 (tpt170) cc_final: 0.7879 (tpt-90) REVERT: F 128 GLU cc_start: 0.8805 (mp0) cc_final: 0.8315 (mp0) REVERT: F 129 MET cc_start: 0.8237 (mmm) cc_final: 0.7400 (mmm) REVERT: F 131 LYS cc_start: 0.8590 (pttm) cc_final: 0.8155 (tptp) REVERT: F 146 LEU cc_start: 0.7263 (mt) cc_final: 0.6936 (tp) REVERT: F 152 GLN cc_start: 0.7875 (mm110) cc_final: 0.7302 (tt0) REVERT: F 168 LEU cc_start: 0.9000 (mp) cc_final: 0.8525 (pp) REVERT: F 207 GLN cc_start: 0.8480 (tp40) cc_final: 0.7816 (pt0) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.0706 time to fit residues: 31.3633 Evaluate side-chains 243 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN F 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092716 restraints weight = 26746.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095591 restraints weight = 16104.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.097615 restraints weight = 11129.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098888 restraints weight = 8463.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099921 restraints weight = 6994.681| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9492 Z= 0.127 Angle : 0.660 7.346 12901 Z= 0.335 Chirality : 0.044 0.146 1541 Planarity : 0.004 0.045 1664 Dihedral : 4.487 23.746 1335 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1255 helix: 1.10 (0.22), residues: 589 sheet: -0.04 (0.38), residues: 178 loop : -0.59 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.020 0.001 TYR C 13 PHE 0.012 0.001 PHE D 95 TRP 0.019 0.001 TRP C 246 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9492) covalent geometry : angle 0.66003 (12901) hydrogen bonds : bond 0.03958 ( 520) hydrogen bonds : angle 4.63348 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9153 (mt) cc_final: 0.8837 (mt) REVERT: C 148 GLU cc_start: 0.7483 (pm20) cc_final: 0.7253 (pm20) REVERT: C 201 MET cc_start: 0.7983 (ppp) cc_final: 0.7717 (ppp) REVERT: C 258 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8436 (tm-30) REVERT: C 262 MET cc_start: 0.8001 (tpp) cc_final: 0.7247 (tpp) REVERT: C 305 LEU cc_start: 0.9293 (mm) cc_final: 0.9091 (mm) REVERT: C 373 MET cc_start: 0.8638 (mmm) cc_final: 0.8409 (mmt) REVERT: D 67 ILE cc_start: 0.8473 (tt) cc_final: 0.8227 (tt) REVERT: D 89 LEU cc_start: 0.8102 (tt) cc_final: 0.7587 (mm) REVERT: D 96 HIS cc_start: 0.8578 (p-80) cc_final: 0.8200 (p-80) REVERT: D 205 ASP cc_start: 0.6574 (p0) cc_final: 0.6130 (p0) REVERT: D 207 GLN cc_start: 0.8194 (tp-100) cc_final: 0.6931 (mp10) REVERT: E 264 ASP cc_start: 0.8798 (m-30) cc_final: 0.8581 (m-30) REVERT: E 298 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8931 (mmmt) REVERT: E 306 ARG cc_start: 0.9335 (tpp80) cc_final: 0.8976 (tpp80) REVERT: E 353 GLU cc_start: 0.8198 (tt0) cc_final: 0.6448 (tp30) REVERT: F 83 GLU cc_start: 0.8116 (pp20) cc_final: 0.7762 (pp20) REVERT: F 87 GLN cc_start: 0.9106 (tt0) cc_final: 0.8884 (tt0) REVERT: F 125 ARG cc_start: 0.8492 (tpt170) cc_final: 0.7998 (tpt-90) REVERT: F 128 GLU cc_start: 0.8966 (mp0) cc_final: 0.8559 (mp0) REVERT: F 131 LYS cc_start: 0.8599 (pttm) cc_final: 0.8162 (tptp) REVERT: F 146 LEU cc_start: 0.7370 (mt) cc_final: 0.6948 (tp) REVERT: F 152 GLN cc_start: 0.7950 (mm110) cc_final: 0.7318 (tt0) REVERT: F 168 LEU cc_start: 0.9004 (mp) cc_final: 0.8516 (pp) REVERT: F 171 GLU cc_start: 0.6913 (mp0) cc_final: 0.6570 (mp0) REVERT: F 195 GLN cc_start: 0.7760 (pm20) cc_final: 0.7534 (pm20) REVERT: F 207 GLN cc_start: 0.8553 (tp40) cc_final: 0.7880 (pt0) REVERT: F 218 MET cc_start: 0.7128 (tpp) cc_final: 0.6920 (tpp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.0691 time to fit residues: 30.3280 Evaluate side-chains 253 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 0.0030 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 115 optimal weight: 0.0970 chunk 116 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.120229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094479 restraints weight = 26405.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097387 restraints weight = 15735.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099398 restraints weight = 10844.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100655 restraints weight = 8252.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101731 restraints weight = 6849.559| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9492 Z= 0.122 Angle : 0.666 7.522 12901 Z= 0.334 Chirality : 0.045 0.144 1541 Planarity : 0.004 0.045 1664 Dihedral : 4.454 24.538 1335 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1255 helix: 1.12 (0.22), residues: 588 sheet: -0.04 (0.38), residues: 178 loop : -0.64 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 250 TYR 0.022 0.001 TYR D 15 PHE 0.012 0.001 PHE F 95 TRP 0.019 0.001 TRP C 246 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9492) covalent geometry : angle 0.66626 (12901) hydrogen bonds : bond 0.03800 ( 520) hydrogen bonds : angle 4.58319 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9175 (mt) cc_final: 0.8814 (mt) REVERT: C 148 GLU cc_start: 0.7536 (pm20) cc_final: 0.7299 (pm20) REVERT: C 201 MET cc_start: 0.7936 (ppp) cc_final: 0.7735 (ppp) REVERT: C 226 LEU cc_start: 0.8697 (mp) cc_final: 0.8416 (tp) REVERT: C 258 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8354 (tm-30) REVERT: C 262 MET cc_start: 0.7909 (tpp) cc_final: 0.7158 (tpp) REVERT: C 305 LEU cc_start: 0.9282 (mm) cc_final: 0.9071 (mm) REVERT: C 373 MET cc_start: 0.8530 (mmm) cc_final: 0.8186 (mmt) REVERT: D 67 ILE cc_start: 0.8490 (tt) cc_final: 0.8212 (tt) REVERT: D 89 LEU cc_start: 0.8093 (tt) cc_final: 0.7566 (mm) REVERT: D 94 GLN cc_start: 0.6062 (pt0) cc_final: 0.5613 (pp30) REVERT: D 96 HIS cc_start: 0.8467 (p-80) cc_final: 0.8138 (p-80) REVERT: D 190 GLU cc_start: 0.8044 (pm20) cc_final: 0.7784 (pm20) REVERT: D 195 GLN cc_start: 0.8411 (mm110) cc_final: 0.8040 (tp-100) REVERT: D 205 ASP cc_start: 0.6524 (p0) cc_final: 0.6122 (p0) REVERT: D 207 GLN cc_start: 0.8174 (tp-100) cc_final: 0.6972 (mp10) REVERT: D 218 MET cc_start: 0.7367 (mmm) cc_final: 0.7093 (tpp) REVERT: E 298 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8823 (mmmm) REVERT: E 306 ARG cc_start: 0.9322 (tpp80) cc_final: 0.8997 (tpp80) REVERT: E 353 GLU cc_start: 0.8168 (tt0) cc_final: 0.6444 (tp30) REVERT: F 83 GLU cc_start: 0.8094 (pp20) cc_final: 0.7710 (pp20) REVERT: F 125 ARG cc_start: 0.8436 (tpt170) cc_final: 0.7753 (tpt-90) REVERT: F 128 GLU cc_start: 0.8922 (mp0) cc_final: 0.8589 (mp0) REVERT: F 129 MET cc_start: 0.8255 (mmm) cc_final: 0.7177 (mmm) REVERT: F 152 GLN cc_start: 0.7925 (mm110) cc_final: 0.7374 (tt0) REVERT: F 168 LEU cc_start: 0.9071 (mp) cc_final: 0.8540 (pp) REVERT: F 195 GLN cc_start: 0.7768 (pm20) cc_final: 0.7505 (pm20) REVERT: F 207 GLN cc_start: 0.8506 (tp40) cc_final: 0.7871 (pt0) REVERT: F 212 MET cc_start: 0.7629 (mpp) cc_final: 0.6995 (mpp) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.0714 time to fit residues: 32.7442 Evaluate side-chains 261 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.0980 chunk 122 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN F 53 HIS F 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.119835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093978 restraints weight = 26514.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096881 restraints weight = 15930.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098900 restraints weight = 10915.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100160 restraints weight = 8289.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101216 restraints weight = 6864.919| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9492 Z= 0.126 Angle : 0.669 7.531 12901 Z= 0.336 Chirality : 0.045 0.143 1541 Planarity : 0.004 0.044 1664 Dihedral : 4.438 24.454 1335 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1255 helix: 1.08 (0.22), residues: 589 sheet: -0.08 (0.37), residues: 178 loop : -0.66 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 222 TYR 0.029 0.001 TYR C 13 PHE 0.017 0.001 PHE D 91 TRP 0.017 0.001 TRP C 246 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9492) covalent geometry : angle 0.66871 (12901) hydrogen bonds : bond 0.03762 ( 520) hydrogen bonds : angle 4.56328 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9167 (mt) cc_final: 0.8821 (mt) REVERT: C 54 GLU cc_start: 0.8749 (tt0) cc_final: 0.8410 (tt0) REVERT: C 148 GLU cc_start: 0.7542 (pm20) cc_final: 0.7321 (pm20) REVERT: C 226 LEU cc_start: 0.8689 (mp) cc_final: 0.8445 (tp) REVERT: C 262 MET cc_start: 0.7954 (tpp) cc_final: 0.7163 (tpp) REVERT: C 305 LEU cc_start: 0.9269 (mm) cc_final: 0.9025 (mm) REVERT: C 373 MET cc_start: 0.8584 (mmm) cc_final: 0.8343 (mmt) REVERT: C 384 SER cc_start: 0.9532 (m) cc_final: 0.9239 (p) REVERT: D 67 ILE cc_start: 0.8484 (tt) cc_final: 0.8202 (tt) REVERT: D 94 GLN cc_start: 0.6066 (pt0) cc_final: 0.5564 (pp30) REVERT: D 190 GLU cc_start: 0.7971 (pm20) cc_final: 0.7722 (pm20) REVERT: D 195 GLN cc_start: 0.8438 (mm110) cc_final: 0.8039 (tp-100) REVERT: E 264 ASP cc_start: 0.8744 (m-30) cc_final: 0.8530 (m-30) REVERT: E 298 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8839 (mmmt) REVERT: E 306 ARG cc_start: 0.9323 (tpp80) cc_final: 0.8998 (tpp80) REVERT: E 353 GLU cc_start: 0.8204 (tt0) cc_final: 0.6424 (tp30) REVERT: F 83 GLU cc_start: 0.8057 (pp20) cc_final: 0.7705 (pp20) REVERT: F 94 GLN cc_start: 0.7648 (mm110) cc_final: 0.7327 (mm-40) REVERT: F 125 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7708 (tpt-90) REVERT: F 128 GLU cc_start: 0.8902 (mp0) cc_final: 0.8614 (mp0) REVERT: F 129 MET cc_start: 0.8217 (mmm) cc_final: 0.7148 (mmm) REVERT: F 131 LYS cc_start: 0.8360 (pttt) cc_final: 0.8083 (ptpp) REVERT: F 152 GLN cc_start: 0.7897 (mm110) cc_final: 0.7323 (tt0) REVERT: F 195 GLN cc_start: 0.7761 (pm20) cc_final: 0.7523 (pm20) REVERT: F 207 GLN cc_start: 0.8482 (tp40) cc_final: 0.7858 (pt0) REVERT: F 212 MET cc_start: 0.7583 (mpp) cc_final: 0.6968 (mpp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.0720 time to fit residues: 32.3815 Evaluate side-chains 260 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN F 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094420 restraints weight = 26311.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.097363 restraints weight = 15996.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099231 restraints weight = 10998.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100795 restraints weight = 8453.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101742 restraints weight = 6886.152| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9492 Z= 0.122 Angle : 0.683 9.921 12901 Z= 0.337 Chirality : 0.046 0.362 1541 Planarity : 0.004 0.044 1664 Dihedral : 4.425 24.559 1335 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1255 helix: 1.13 (0.22), residues: 590 sheet: -0.03 (0.37), residues: 178 loop : -0.63 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 151 TYR 0.030 0.001 TYR C 13 PHE 0.009 0.001 PHE F 102 TRP 0.017 0.001 TRP C 246 HIS 0.008 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9492) covalent geometry : angle 0.68259 (12901) hydrogen bonds : bond 0.03720 ( 520) hydrogen bonds : angle 4.51104 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.46 seconds wall clock time: 26 minutes 33.10 seconds (1593.10 seconds total)