Starting phenix.real_space_refine on Thu Feb 13 19:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8m_31804/02_2025/7v8m_31804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8m_31804/02_2025/7v8m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v8m_31804/02_2025/7v8m_31804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8m_31804/02_2025/7v8m_31804.map" model { file = "/net/cci-nas-00/data/ceres_data/7v8m_31804/02_2025/7v8m_31804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8m_31804/02_2025/7v8m_31804.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} 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: 5.47, per 1000 atoms: 0.59 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.13 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: 3.07 Time building geometry restraints manager: 2.62 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.570 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- 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= 0.253 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.002 TRP C 246 HIS 0.020 0.002 HIS E 84 PHE 0.021 0.002 PHE E 285 TYR 0.032 0.002 TYR C 13 ARG 0.006 0.001 ARG D 138 *********************** 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 : 1.098 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: 0.8333 (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: 0.8771 (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: 0.5919 (tptm) REVERT: D 66 VAL cc_start: 0.7039 (t) cc_final: 0.6737 (p) REVERT: D 184 ILE cc_start: 0.7936 (pt) cc_final: 0.7653 (pt) REVERT: E 264 ASP cc_start: 0.8177 (m-30) cc_final: 0.7742 (m-30) REVERT: E 353 GLU cc_start: 0.7546 (tt0) cc_final: 0.5941 (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: 0.4560 (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: 0.1893 time to fit residues: 85.2213 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 : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 87 GLN E 84 HIS E 376 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 = 0.3842 r_free = 0.3842 target = 0.119350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093221 restraints weight = 26637.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096108 restraints weight = 16067.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098151 restraints weight = 11018.651| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9492 Z= 0.212 Angle : 0.656 6.948 12901 Z= 0.338 Chirality : 0.045 0.171 1541 Planarity : 0.005 0.053 1664 Dihedral : 4.791 20.310 1335 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1255 helix: 0.94 (0.22), residues: 571 sheet: -0.38 (0.37), residues: 185 loop : -0.75 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 246 HIS 0.009 0.001 HIS E 84 PHE 0.012 0.001 PHE E 285 TYR 0.017 0.002 TYR D 15 ARG 0.005 0.001 ARG F 193 *********************** 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 303 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 1.056 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: C 29 LEU cc_start: 0.9299 (mt) cc_final: 0.9024 (mt) REVERT: C 88 ASP cc_start: 0.8467 (p0) cc_final: 0.8260 (p0) REVERT: C 211 LEU cc_start: 0.9071 (tp) cc_final: 0.8859 (tp) REVERT: C 323 ILE cc_start: 0.8957 (mt) cc_final: 0.8665 (mt) REVERT: C 351 LEU cc_start: 0.5950 (tp) cc_final: 0.5739 (tp) REVERT: C 368 ILE cc_start: 0.8912 (pt) cc_final: 0.8649 (mm) REVERT: D 66 VAL cc_start: 0.7510 (t) cc_final: 0.7034 (p) REVERT: D 67 ILE cc_start: 0.8056 (tt) cc_final: 0.7797 (tt) REVERT: D 96 HIS cc_start: 0.9028 (p90) cc_final: 0.8750 (p90) REVERT: D 170 ASP cc_start: 0.8033 (t0) cc_final: 0.7817 (t0) REVERT: D 191 LEU cc_start: 0.9592 (mm) cc_final: 0.9353 (mm) REVERT: E 264 ASP cc_start: 0.8975 (m-30) cc_final: 0.8607 (m-30) REVERT: E 353 GLU cc_start: 0.8295 (tt0) cc_final: 0.6528 (tp30) REVERT: F 38 MET cc_start: 0.7354 (ttm) cc_final: 0.7151 (ttp) REVERT: F 84 LEU cc_start: 0.9183 (mt) cc_final: 0.8895 (tt) REVERT: F 152 GLN cc_start: 0.7986 (mm110) cc_final: 0.7084 (tt0) REVERT: F 212 MET cc_start: 0.7200 (mpp) cc_final: 0.6719 (mpp) REVERT: F 215 GLN cc_start: 0.7688 (mt0) cc_final: 0.6825 (mm110) REVERT: F 218 MET cc_start: 0.6800 (tpt) cc_final: 0.6551 (tpp) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.1788 time to fit residues: 78.0313 Evaluate side-chains 249 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 152 GLN E 376 HIS F 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093718 restraints weight = 26924.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096646 restraints weight = 16061.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098693 restraints weight = 10968.954| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9492 Z= 0.191 Angle : 0.627 6.484 12901 Z= 0.322 Chirality : 0.044 0.194 1541 Planarity : 0.004 0.050 1664 Dihedral : 4.655 19.862 1335 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1255 helix: 1.12 (0.22), residues: 575 sheet: -0.07 (0.40), residues: 177 loop : -0.62 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 246 HIS 0.008 0.001 HIS D 97 PHE 0.012 0.001 PHE D 91 TYR 0.015 0.001 TYR C 13 ARG 0.010 0.001 ARG F 193 *********************** 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 293 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.109 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: C 29 LEU cc_start: 0.9293 (mt) cc_final: 0.9057 (mt) REVERT: C 323 ILE cc_start: 0.8981 (mt) cc_final: 0.8653 (mt) REVERT: C 368 ILE cc_start: 0.8963 (pt) cc_final: 0.8761 (mm) REVERT: D 66 VAL cc_start: 0.7533 (t) cc_final: 0.7163 (p) REVERT: D 67 ILE cc_start: 0.8055 (tt) cc_final: 0.7847 (tt) REVERT: D 71 GLN cc_start: 0.8514 (mp10) cc_final: 0.8220 (mp10) REVERT: D 96 HIS cc_start: 0.9019 (p90) cc_final: 0.8459 (p90) REVERT: D 191 LEU cc_start: 0.9678 (mm) cc_final: 0.9457 (mm) REVERT: E 22 MET cc_start: 0.7435 (tmm) cc_final: 0.7230 (tmm) REVERT: E 264 ASP cc_start: 0.8847 (m-30) cc_final: 0.8482 (m-30) REVERT: E 306 ARG cc_start: 0.9279 (tpp80) cc_final: 0.9013 (tpp80) REVERT: E 336 ILE cc_start: 0.9439 (mm) cc_final: 0.9231 (mp) REVERT: E 353 GLU cc_start: 0.8306 (tt0) cc_final: 0.6670 (tp30) REVERT: F 83 GLU cc_start: 0.8098 (pp20) cc_final: 0.7638 (pp20) REVERT: F 84 LEU cc_start: 0.9135 (mt) cc_final: 0.8850 (mt) REVERT: F 95 PHE cc_start: 0.5845 (m-80) cc_final: 0.5428 (m-10) REVERT: F 102 PHE cc_start: 0.8329 (m-10) cc_final: 0.8087 (m-80) REVERT: F 128 GLU cc_start: 0.8943 (mp0) cc_final: 0.8479 (mp0) REVERT: F 146 LEU cc_start: 0.7010 (mt) cc_final: 0.6758 (tp) REVERT: F 152 GLN cc_start: 0.7931 (mm110) cc_final: 0.7245 (tt0) REVERT: F 168 LEU cc_start: 0.9178 (mp) cc_final: 0.8606 (pp) REVERT: F 215 GLN cc_start: 0.7981 (mt0) cc_final: 0.6857 (mm110) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1889 time to fit residues: 79.8705 Evaluate side-chains 252 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 152 GLN D 186 GLN F 53 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093292 restraints weight = 26574.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096132 restraints weight = 15906.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098067 restraints weight = 10911.002| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2211 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= 0.191 Angle : 0.615 6.393 12901 Z= 0.315 Chirality : 0.043 0.157 1541 Planarity : 0.004 0.049 1664 Dihedral : 4.582 19.827 1335 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1255 helix: 1.11 (0.22), residues: 582 sheet: 0.04 (0.40), residues: 177 loop : -0.66 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 246 HIS 0.007 0.001 HIS D 97 PHE 0.011 0.001 PHE D 91 TYR 0.016 0.001 TYR C 13 ARG 0.009 0.000 ARG F 193 *********************** 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 297 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9300 (mt) cc_final: 0.9030 (mt) REVERT: C 114 MET cc_start: 0.7054 (ppp) cc_final: 0.6505 (ptm) REVERT: C 226 LEU cc_start: 0.8715 (mp) cc_final: 0.8405 (tp) REVERT: C 323 ILE cc_start: 0.8978 (mt) cc_final: 0.8675 (mt) REVERT: C 351 LEU cc_start: 0.6094 (tp) cc_final: 0.5856 (tp) REVERT: D 66 VAL cc_start: 0.7408 (t) cc_final: 0.7029 (p) REVERT: D 96 HIS cc_start: 0.8859 (p90) cc_final: 0.8285 (p90) REVERT: E 264 ASP cc_start: 0.8885 (m-30) cc_final: 0.8602 (m-30) REVERT: E 306 ARG cc_start: 0.9270 (tpp80) cc_final: 0.9015 (tpp80) REVERT: E 336 ILE cc_start: 0.9423 (mm) cc_final: 0.9167 (mp) REVERT: E 353 GLU cc_start: 0.8300 (tt0) cc_final: 0.6879 (tp30) REVERT: F 83 GLU cc_start: 0.8027 (pp20) cc_final: 0.7567 (pp20) REVERT: F 84 LEU cc_start: 0.9127 (mt) cc_final: 0.8853 (mt) REVERT: F 95 PHE cc_start: 0.5935 (m-80) cc_final: 0.5699 (m-10) REVERT: F 128 GLU cc_start: 0.8961 (mp0) cc_final: 0.8651 (mp0) REVERT: F 146 LEU cc_start: 0.6992 (mt) cc_final: 0.6711 (tp) REVERT: F 152 GLN cc_start: 0.7879 (mm110) cc_final: 0.7190 (tt0) REVERT: F 186 GLN cc_start: 0.9345 (pt0) cc_final: 0.9123 (pp30) REVERT: F 215 GLN cc_start: 0.8246 (mt0) cc_final: 0.7349 (mp10) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1871 time to fit residues: 79.5646 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 : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 0.9980 chunk 45 optimal weight: 0.0040 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 D 107 ASN D 152 GLN E 122 GLN F 21 GLN F 94 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.118247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092237 restraints weight = 26677.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095058 restraints weight = 15860.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097103 restraints weight = 10907.531| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2484 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= 0.198 Angle : 0.623 6.431 12901 Z= 0.318 Chirality : 0.044 0.176 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.556 21.650 1335 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.31 % Allowed : 2.81 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1255 helix: 1.14 (0.22), residues: 581 sheet: 0.01 (0.39), residues: 177 loop : -0.66 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 246 HIS 0.007 0.001 HIS D 97 PHE 0.012 0.001 PHE D 91 TYR 0.018 0.001 TYR C 13 ARG 0.005 0.000 ARG F 193 *********************** 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 298 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 0.838 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: C 29 LEU cc_start: 0.9277 (mt) cc_final: 0.8981 (mt) REVERT: C 373 MET cc_start: 0.8720 (mmm) cc_final: 0.8407 (mmt) REVERT: D 16 GLN cc_start: 0.4363 (OUTLIER) cc_final: 0.3950 (pm20) REVERT: D 96 HIS cc_start: 0.9041 (p90) cc_final: 0.8582 (p90) REVERT: D 129 MET cc_start: 0.8384 (mmp) cc_final: 0.8091 (mmp) REVERT: E 264 ASP cc_start: 0.8915 (m-30) cc_final: 0.8664 (m-30) REVERT: E 272 MET cc_start: 0.8701 (mtp) cc_final: 0.7896 (ttm) REVERT: E 306 ARG cc_start: 0.9264 (tpp80) cc_final: 0.8991 (tpp80) REVERT: E 353 GLU cc_start: 0.8333 (tt0) cc_final: 0.6865 (tp30) REVERT: F 84 LEU cc_start: 0.9083 (mt) cc_final: 0.8869 (mt) REVERT: F 87 GLN cc_start: 0.9152 (tt0) cc_final: 0.8804 (tt0) REVERT: F 146 LEU cc_start: 0.7071 (mt) cc_final: 0.6750 (tp) REVERT: F 152 GLN cc_start: 0.7830 (mm110) cc_final: 0.7198 (tt0) REVERT: F 207 GLN cc_start: 0.8538 (tp40) cc_final: 0.7882 (pt0) REVERT: F 215 GLN cc_start: 0.8307 (mt0) cc_final: 0.7443 (mp10) outliers start: 3 outliers final: 0 residues processed: 298 average time/residue: 0.1802 time to fit residues: 77.0516 Evaluate side-chains 241 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 87 GLN E 376 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.116810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090775 restraints weight = 26874.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093606 restraints weight = 16149.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095539 restraints weight = 11151.372| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9492 Z= 0.230 Angle : 0.658 6.211 12901 Z= 0.340 Chirality : 0.045 0.195 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.658 22.713 1335 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1255 helix: 1.05 (0.22), residues: 588 sheet: -0.08 (0.39), residues: 177 loop : -0.71 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 246 HIS 0.008 0.001 HIS D 97 PHE 0.012 0.001 PHE D 91 TYR 0.021 0.002 TYR D 15 ARG 0.004 0.000 ARG F 138 *********************** 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 : 1.164 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: 0.9267 (mt) cc_final: 0.8975 (mt) REVERT: C 48 MET cc_start: 0.9500 (mtp) cc_final: 0.8919 (mtp) REVERT: C 305 LEU cc_start: 0.9395 (mm) cc_final: 0.9123 (mm) REVERT: D 62 THR cc_start: 0.8627 (p) cc_final: 0.8357 (p) REVERT: D 67 ILE cc_start: 0.8254 (tt) cc_final: 0.7978 (tt) REVERT: D 96 HIS cc_start: 0.9029 (p90) cc_final: 0.8450 (p90) REVERT: D 190 GLU cc_start: 0.8359 (pm20) cc_final: 0.8119 (pm20) REVERT: E 264 ASP cc_start: 0.8933 (m-30) cc_final: 0.8728 (m-30) REVERT: E 306 ARG cc_start: 0.9320 (tpp80) cc_final: 0.9051 (tpp80) REVERT: E 353 GLU cc_start: 0.8388 (tt0) cc_final: 0.6869 (tp30) REVERT: F 83 GLU cc_start: 0.8085 (pp20) cc_final: 0.7782 (pp20) REVERT: F 87 GLN cc_start: 0.9115 (tt0) cc_final: 0.8843 (tt0) REVERT: F 125 ARG cc_start: 0.8471 (tpt170) cc_final: 0.8152 (tpt-90) REVERT: F 128 GLU cc_start: 0.8988 (mp0) cc_final: 0.8661 (mp0) REVERT: F 146 LEU cc_start: 0.7218 (mt) cc_final: 0.6791 (tp) REVERT: F 152 GLN cc_start: 0.7898 (mm110) cc_final: 0.7289 (tt0) REVERT: F 168 LEU cc_start: 0.9086 (mp) cc_final: 0.8584 (pp) REVERT: F 170 ASP cc_start: 0.8262 (t0) cc_final: 0.8021 (t0) REVERT: F 207 GLN cc_start: 0.8539 (tp40) cc_final: 0.7831 (pt0) REVERT: F 215 GLN cc_start: 0.8452 (mt0) cc_final: 0.7608 (mp10) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1930 time to fit residues: 81.5782 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 : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.118388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092439 restraints weight = 26830.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095265 restraints weight = 16074.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097356 restraints weight = 11059.484| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3031 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= 0.183 Angle : 0.676 8.471 12901 Z= 0.339 Chirality : 0.045 0.157 1541 Planarity : 0.004 0.047 1664 Dihedral : 4.577 23.391 1335 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1255 helix: 1.10 (0.22), residues: 588 sheet: -0.05 (0.38), residues: 173 loop : -0.70 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 246 HIS 0.004 0.001 HIS D 53 PHE 0.010 0.001 PHE D 95 TYR 0.022 0.001 TYR C 13 ARG 0.006 0.000 ARG F 193 *********************** 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 301 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.079 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: C 29 LEU cc_start: 0.9217 (mt) cc_final: 0.8904 (mt) REVERT: C 201 MET cc_start: 0.8026 (ppp) cc_final: 0.7784 (ppp) REVERT: C 248 ASP cc_start: 0.7696 (p0) cc_final: 0.7351 (p0) REVERT: C 305 LEU cc_start: 0.9305 (mm) cc_final: 0.9052 (mm) REVERT: D 71 GLN cc_start: 0.8778 (mp10) cc_final: 0.8492 (mp10) REVERT: D 89 LEU cc_start: 0.8407 (tt) cc_final: 0.7977 (mm) REVERT: D 96 HIS cc_start: 0.8905 (p90) cc_final: 0.8519 (p90) REVERT: E 306 ARG cc_start: 0.9261 (tpp80) cc_final: 0.8975 (tpp80) REVERT: E 353 GLU cc_start: 0.8306 (tt0) cc_final: 0.6897 (tp30) REVERT: F 83 GLU cc_start: 0.8023 (pp20) cc_final: 0.7658 (pp20) REVERT: F 84 LEU cc_start: 0.9109 (mt) cc_final: 0.8868 (mt) REVERT: F 87 GLN cc_start: 0.9009 (tt0) cc_final: 0.8763 (tt0) REVERT: F 125 ARG cc_start: 0.8475 (tpt170) cc_final: 0.8233 (tpt-90) REVERT: F 128 GLU cc_start: 0.8884 (mp0) cc_final: 0.8453 (mp0) REVERT: F 146 LEU cc_start: 0.7359 (mt) cc_final: 0.6918 (tp) REVERT: F 152 GLN cc_start: 0.7920 (mm110) cc_final: 0.7291 (tt0) REVERT: F 207 GLN cc_start: 0.8527 (tp40) cc_final: 0.7814 (pt0) REVERT: F 218 MET cc_start: 0.6704 (tpp) cc_final: 0.6407 (tpp) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1805 time to fit residues: 78.3740 Evaluate side-chains 241 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 87 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089676 restraints weight = 26899.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.092479 restraints weight = 16352.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094452 restraints weight = 11341.382| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9492 Z= 0.238 Angle : 0.705 7.735 12901 Z= 0.360 Chirality : 0.046 0.170 1541 Planarity : 0.004 0.045 1664 Dihedral : 4.643 23.366 1335 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1255 helix: 1.00 (0.22), residues: 588 sheet: -0.19 (0.38), residues: 173 loop : -0.69 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 246 HIS 0.005 0.001 HIS D 97 PHE 0.013 0.001 PHE D 91 TYR 0.024 0.002 TYR C 13 ARG 0.004 0.000 ARG F 138 *********************** 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 291 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.073 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: 0.9236 (mt) cc_final: 0.8917 (mt) REVERT: C 201 MET cc_start: 0.8014 (ppp) cc_final: 0.7733 (ppp) REVERT: C 262 MET cc_start: 0.8074 (tpp) cc_final: 0.7472 (tpp) REVERT: C 263 GLU cc_start: 0.8744 (pp20) cc_final: 0.8362 (pp20) REVERT: C 296 GLU cc_start: 0.7855 (tt0) cc_final: 0.7634 (tt0) REVERT: C 305 LEU cc_start: 0.9334 (mm) cc_final: 0.9079 (mm) REVERT: D 67 ILE cc_start: 0.8526 (tt) cc_final: 0.8276 (tt) REVERT: D 89 LEU cc_start: 0.8146 (tt) cc_final: 0.7575 (mm) REVERT: D 94 GLN cc_start: 0.6097 (pt0) cc_final: 0.5434 (pp30) REVERT: D 96 HIS cc_start: 0.9039 (p90) cc_final: 0.8446 (p90) REVERT: E 272 MET cc_start: 0.8745 (mtp) cc_final: 0.7907 (ttm) REVERT: E 306 ARG cc_start: 0.9335 (tpp80) cc_final: 0.9013 (tpp80) REVERT: E 353 GLU cc_start: 0.8332 (tt0) cc_final: 0.6923 (tp30) REVERT: E 389 LEU cc_start: 0.9172 (tp) cc_final: 0.8962 (tp) REVERT: F 83 GLU cc_start: 0.8047 (pp20) cc_final: 0.7691 (pp20) REVERT: F 84 LEU cc_start: 0.9121 (mt) cc_final: 0.8873 (mt) REVERT: F 87 GLN cc_start: 0.9087 (tt0) cc_final: 0.8827 (tt0) REVERT: F 125 ARG cc_start: 0.8592 (tpt170) cc_final: 0.8257 (tpt-90) REVERT: F 128 GLU cc_start: 0.9005 (mp0) cc_final: 0.8684 (mp0) REVERT: F 131 LYS cc_start: 0.8555 (pttt) cc_final: 0.8211 (tptp) REVERT: F 146 LEU cc_start: 0.6914 (mt) cc_final: 0.6596 (tp) REVERT: F 152 GLN cc_start: 0.7968 (mm110) cc_final: 0.7313 (tt0) REVERT: F 168 LEU cc_start: 0.8997 (mp) cc_final: 0.8548 (pp) REVERT: F 207 GLN cc_start: 0.8534 (tp40) cc_final: 0.7815 (pt0) REVERT: F 212 MET cc_start: 0.7587 (mpp) cc_final: 0.6768 (mpp) REVERT: F 215 GLN cc_start: 0.8496 (mt0) cc_final: 0.7573 (mp10) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1875 time to fit residues: 78.6019 Evaluate side-chains 239 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089162 restraints weight = 26422.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091894 restraints weight = 16168.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093803 restraints weight = 11235.368| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9492 Z= 0.251 Angle : 0.719 8.155 12901 Z= 0.367 Chirality : 0.046 0.149 1541 Planarity : 0.004 0.045 1664 Dihedral : 4.783 23.908 1335 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1255 helix: 1.04 (0.21), residues: 590 sheet: -0.38 (0.37), residues: 179 loop : -0.78 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 246 HIS 0.004 0.001 HIS D 97 PHE 0.011 0.001 PHE E 319 TYR 0.023 0.002 TYR C 13 ARG 0.008 0.000 ARG F 193 *********************** 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 290 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.061 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 201 MET cc_start: 0.8088 (ppp) cc_final: 0.7821 (ppp) REVERT: C 258 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 262 MET cc_start: 0.8121 (tpp) cc_final: 0.7502 (tpp) REVERT: C 263 GLU cc_start: 0.8675 (pp20) cc_final: 0.8388 (pp20) REVERT: C 305 LEU cc_start: 0.9379 (mm) cc_final: 0.9103 (mm) REVERT: D 67 ILE cc_start: 0.8561 (tt) cc_final: 0.8293 (tt) REVERT: D 75 LYS cc_start: 0.8047 (pttm) cc_final: 0.7802 (pttm) REVERT: D 89 LEU cc_start: 0.8163 (tt) cc_final: 0.7607 (mm) REVERT: D 94 GLN cc_start: 0.6026 (pt0) cc_final: 0.5383 (pp30) REVERT: D 96 HIS cc_start: 0.8986 (p90) cc_final: 0.8538 (p90) REVERT: E 264 ASP cc_start: 0.8862 (m-30) cc_final: 0.8575 (m-30) REVERT: E 272 MET cc_start: 0.8784 (mtp) cc_final: 0.7922 (ttm) REVERT: E 306 ARG cc_start: 0.9327 (tpp80) cc_final: 0.8977 (tpp80) REVERT: E 353 GLU cc_start: 0.8310 (tt0) cc_final: 0.6574 (tp30) REVERT: E 389 LEU cc_start: 0.9177 (tp) cc_final: 0.8961 (tp) REVERT: F 83 GLU cc_start: 0.8026 (pp20) cc_final: 0.7632 (pp20) REVERT: F 84 LEU cc_start: 0.9109 (mt) cc_final: 0.8879 (mt) REVERT: F 87 GLN cc_start: 0.9099 (tt0) cc_final: 0.8839 (tt0) REVERT: F 125 ARG cc_start: 0.8625 (tpt170) cc_final: 0.8226 (tpt-90) REVERT: F 128 GLU cc_start: 0.8921 (mp0) cc_final: 0.8593 (mp0) REVERT: F 131 LYS cc_start: 0.8573 (pttt) cc_final: 0.8213 (tptp) REVERT: F 152 GLN cc_start: 0.8033 (mm110) cc_final: 0.7314 (tt0) REVERT: F 168 LEU cc_start: 0.9005 (mp) cc_final: 0.8529 (pp) REVERT: F 195 GLN cc_start: 0.8846 (pm20) cc_final: 0.8501 (pm20) REVERT: F 207 GLN cc_start: 0.8514 (tp40) cc_final: 0.7794 (pt0) REVERT: F 212 MET cc_start: 0.7667 (mpp) cc_final: 0.6870 (mpp) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1844 time to fit residues: 76.7082 Evaluate side-chains 238 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 87 GLN D 204 HIS E 376 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.119413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093489 restraints weight = 26516.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096381 restraints weight = 16049.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098366 restraints weight = 11120.420| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9492 Z= 0.184 Angle : 0.717 8.042 12901 Z= 0.355 Chirality : 0.046 0.148 1541 Planarity : 0.004 0.047 1664 Dihedral : 4.632 24.603 1335 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.10 % Allowed : 0.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1255 helix: 1.06 (0.21), residues: 588 sheet: -0.12 (0.38), residues: 169 loop : -0.77 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 246 HIS 0.004 0.001 HIS D 53 PHE 0.008 0.001 PHE D 91 TYR 0.026 0.002 TYR C 13 ARG 0.012 0.000 ARG F 193 ********************** 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 297 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.9129 (mt) cc_final: 0.8800 (mt) REVERT: C 262 MET cc_start: 0.7871 (tpp) cc_final: 0.7362 (tpp) REVERT: C 263 GLU cc_start: 0.8590 (pp20) cc_final: 0.8172 (pp20) REVERT: C 305 LEU cc_start: 0.9232 (mm) cc_final: 0.9014 (mm) REVERT: D 40 ILE cc_start: 0.8750 (tp) cc_final: 0.8358 (mm) REVERT: D 67 ILE cc_start: 0.8528 (tt) cc_final: 0.8214 (tt) REVERT: D 89 LEU cc_start: 0.8440 (tt) cc_final: 0.7897 (mm) REVERT: D 94 GLN cc_start: 0.6096 (pt0) cc_final: 0.5552 (pp30) REVERT: D 96 HIS cc_start: 0.8869 (p90) cc_final: 0.8511 (p90) REVERT: D 218 MET cc_start: 0.7409 (mmm) cc_final: 0.7098 (tpp) REVERT: E 306 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8912 (tpp80) REVERT: E 353 GLU cc_start: 0.8243 (tt0) cc_final: 0.6507 (tp30) REVERT: F 83 GLU cc_start: 0.7943 (pp20) cc_final: 0.7549 (pp20) REVERT: F 84 LEU cc_start: 0.9101 (mt) cc_final: 0.8889 (mt) REVERT: F 87 GLN cc_start: 0.9021 (tt0) cc_final: 0.8757 (tt0) REVERT: F 125 ARG cc_start: 0.8527 (tpt170) cc_final: 0.8159 (tpt-90) REVERT: F 128 GLU cc_start: 0.8855 (mp0) cc_final: 0.8631 (mp0) REVERT: F 152 GLN cc_start: 0.7881 (mm110) cc_final: 0.7347 (tt0) REVERT: F 168 LEU cc_start: 0.8954 (mp) cc_final: 0.8396 (pp) REVERT: F 195 GLN cc_start: 0.8845 (pm20) cc_final: 0.8617 (pm20) REVERT: F 207 GLN cc_start: 0.8507 (tp40) cc_final: 0.7743 (pt0) REVERT: F 212 MET cc_start: 0.7703 (mpp) cc_final: 0.7129 (mpp) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.1869 time to fit residues: 79.2858 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 : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.119375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093893 restraints weight = 26136.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096728 restraints weight = 15736.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098799 restraints weight = 10871.779| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9492 Z= 0.181 Angle : 0.706 8.922 12901 Z= 0.350 Chirality : 0.046 0.232 1541 Planarity : 0.004 0.046 1664 Dihedral : 4.579 24.689 1335 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1255 helix: 1.06 (0.21), residues: 591 sheet: -0.16 (0.37), residues: 174 loop : -0.70 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 246 HIS 0.009 0.001 HIS D 97 PHE 0.017 0.001 PHE F 68 TYR 0.025 0.001 TYR C 13 ARG 0.003 0.000 ARG D 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.69 seconds wall clock time: 53 minutes 1.31 seconds (3181.31 seconds total)