Starting phenix.real_space_refine on Thu Mar 13 23:08:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8m_31804/03_2025/7v8m_31804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8m_31804/03_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_31804/03_2025/7v8m_31804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_2025/7v8m_31804.map" model { file = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_2025/7v8m_31804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8m_31804/03_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-5624/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: 5.54, 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: 2.32 Conformation dependent library (CDL) restraints added in 1.3 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: 1.02 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: 2.54 Time building geometry restraints manager: 2.70 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: 0.550 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- 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 : 1.073 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: 0.1861 time to fit residues: 83.7231 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 : 1.174 ------------------------------------------------------------------------------- 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 = 26637.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096118 restraints weight = 16067.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097982 restraints weight = 11006.548| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 1.083 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: 0.9300 (mt) cc_final: 0.9024 (mt) REVERT: C 88 ASP cc_start: 0.8469 (p0) cc_final: 0.8264 (p0) REVERT: C 211 LEU cc_start: 0.9074 (tp) cc_final: 0.8862 (tp) REVERT: C 323 ILE cc_start: 0.8955 (mt) cc_final: 0.8663 (mt) REVERT: C 351 LEU cc_start: 0.6010 (tp) cc_final: 0.5793 (tp) REVERT: C 368 ILE cc_start: 0.8910 (pt) cc_final: 0.8650 (mm) REVERT: D 66 VAL cc_start: 0.7516 (t) cc_final: 0.7033 (p) REVERT: D 67 ILE cc_start: 0.8066 (tt) cc_final: 0.7801 (tt) REVERT: D 96 HIS cc_start: 0.9023 (p90) cc_final: 0.8743 (p90) REVERT: D 170 ASP cc_start: 0.8017 (t0) cc_final: 0.7806 (t0) REVERT: D 191 LEU cc_start: 0.9594 (mm) cc_final: 0.9355 (mm) REVERT: E 264 ASP cc_start: 0.8978 (m-30) cc_final: 0.8608 (m-30) REVERT: E 353 GLU cc_start: 0.8309 (tt0) cc_final: 0.6539 (tp30) REVERT: F 38 MET cc_start: 0.7346 (ttm) cc_final: 0.7139 (ttp) REVERT: F 84 LEU cc_start: 0.9182 (mt) cc_final: 0.8892 (tt) REVERT: F 152 GLN cc_start: 0.7991 (mm110) cc_final: 0.7089 (tt0) REVERT: F 212 MET cc_start: 0.7190 (mpp) cc_final: 0.6711 (mpp) REVERT: F 215 GLN cc_start: 0.7686 (mt0) cc_final: 0.6830 (mm110) REVERT: F 218 MET cc_start: 0.6826 (tpt) cc_final: 0.6571 (tpp) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.1806 time to fit residues: 79.3516 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 : 1.173 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.0050 chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 97 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.120548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094596 restraints weight = 26814.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097506 restraints weight = 15829.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099588 restraints weight = 10784.061| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9492 Z= 0.179 Angle : 0.620 6.504 12901 Z= 0.318 Chirality : 0.044 0.198 1541 Planarity : 0.004 0.050 1664 Dihedral : 4.631 20.047 1335 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1255 helix: 1.13 (0.22), residues: 577 sheet: -0.06 (0.40), residues: 177 loop : -0.63 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 246 HIS 0.008 0.001 HIS D 53 PHE 0.013 0.001 PHE D 91 TYR 0.015 0.001 TYR C 13 ARG 0.007 0.000 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 292 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.095 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: 0.9284 (mt) cc_final: 0.8986 (mt) REVERT: C 291 MET cc_start: 0.8635 (mtt) cc_final: 0.8428 (mtt) REVERT: C 323 ILE cc_start: 0.8972 (mt) cc_final: 0.8625 (mt) REVERT: D 66 VAL cc_start: 0.7520 (t) cc_final: 0.7146 (p) REVERT: D 67 ILE cc_start: 0.8050 (tt) cc_final: 0.7840 (tt) REVERT: D 71 GLN cc_start: 0.8514 (mp10) cc_final: 0.8224 (mp10) REVERT: D 96 HIS cc_start: 0.9000 (p90) cc_final: 0.8455 (p90) REVERT: D 191 LEU cc_start: 0.9676 (mm) cc_final: 0.9427 (mm) REVERT: D 195 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8113 (tp-100) REVERT: E 264 ASP cc_start: 0.8840 (m-30) cc_final: 0.8472 (m-30) REVERT: E 306 ARG cc_start: 0.9268 (tpp80) cc_final: 0.9013 (tpp80) REVERT: E 336 ILE cc_start: 0.9431 (mm) cc_final: 0.9216 (mp) REVERT: E 353 GLU cc_start: 0.8298 (tt0) cc_final: 0.6668 (tp30) REVERT: F 83 GLU cc_start: 0.8090 (pp20) cc_final: 0.7635 (pp20) REVERT: F 84 LEU cc_start: 0.9137 (mt) cc_final: 0.8851 (mt) REVERT: F 95 PHE cc_start: 0.6011 (m-80) cc_final: 0.5532 (m-10) REVERT: F 102 PHE cc_start: 0.8329 (m-10) cc_final: 0.8099 (m-80) REVERT: F 128 GLU cc_start: 0.8937 (mp0) cc_final: 0.8473 (mp0) REVERT: F 131 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8361 (ptpt) REVERT: F 146 LEU cc_start: 0.6945 (mt) cc_final: 0.6698 (tp) REVERT: F 152 GLN cc_start: 0.7922 (mm110) cc_final: 0.7251 (tt0) REVERT: F 215 GLN cc_start: 0.7966 (mt0) cc_final: 0.6861 (mm110) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1780 time to fit residues: 74.8505 Evaluate side-chains 257 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 20.0000 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN F 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.119304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093259 restraints weight = 26530.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096099 restraints weight = 15946.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098048 restraints weight = 10986.850| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2292 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= 0.184 Angle : 0.616 6.416 12901 Z= 0.315 Chirality : 0.044 0.156 1541 Planarity : 0.004 0.049 1664 Dihedral : 4.559 19.952 1335 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: 0.39 (0.24), residues: 1255 helix: 1.15 (0.22), residues: 582 sheet: 0.05 (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 53 PHE 0.013 0.001 PHE D 91 TYR 0.015 0.001 TYR C 13 ARG 0.005 0.001 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 299 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.091 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: 0.9294 (mt) cc_final: 0.9019 (mt) REVERT: C 114 MET cc_start: 0.6877 (ppp) cc_final: 0.6348 (ptm) REVERT: C 226 LEU cc_start: 0.8782 (mp) cc_final: 0.8474 (tp) REVERT: C 323 ILE cc_start: 0.8990 (mt) cc_final: 0.8679 (mt) REVERT: C 351 LEU cc_start: 0.6012 (tp) cc_final: 0.5784 (tp) REVERT: D 66 VAL cc_start: 0.7395 (t) cc_final: 0.7030 (p) REVERT: D 71 GLN cc_start: 0.8488 (mp10) cc_final: 0.8271 (mp10) REVERT: D 96 HIS cc_start: 0.8812 (p90) cc_final: 0.8234 (p90) REVERT: E 264 ASP cc_start: 0.8877 (m-30) cc_final: 0.8594 (m-30) REVERT: E 306 ARG cc_start: 0.9258 (tpp80) cc_final: 0.9008 (tpp80) REVERT: E 336 ILE cc_start: 0.9422 (mm) cc_final: 0.9161 (mp) REVERT: E 353 GLU cc_start: 0.8287 (tt0) cc_final: 0.6881 (tp30) REVERT: F 84 LEU cc_start: 0.9123 (mt) cc_final: 0.8913 (mt) REVERT: F 95 PHE cc_start: 0.6181 (m-80) cc_final: 0.5935 (m-10) REVERT: F 128 GLU cc_start: 0.8959 (mp0) cc_final: 0.8637 (mp0) REVERT: F 146 LEU cc_start: 0.6965 (mt) cc_final: 0.6702 (tp) REVERT: F 152 GLN cc_start: 0.7843 (mm110) cc_final: 0.7179 (tt0) REVERT: F 168 LEU cc_start: 0.9101 (mp) cc_final: 0.8575 (pp) REVERT: F 212 MET cc_start: 0.7405 (mpp) cc_final: 0.6446 (mpp) REVERT: F 215 GLN cc_start: 0.8216 (mt0) cc_final: 0.7341 (mp10) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1811 time to fit residues: 77.5848 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 : 1.036 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 16 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN D 107 ASN D 152 GLN E 122 GLN F 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.121821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095781 restraints weight = 26494.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098663 restraints weight = 15732.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100746 restraints weight = 10806.875| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9492 Z= 0.161 Angle : 0.621 6.786 12901 Z= 0.314 Chirality : 0.044 0.184 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.446 21.600 1335 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.21 % Allowed : 2.40 % 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 (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: 0.42 (0.24), residues: 1255 helix: 1.20 (0.22), residues: 581 sheet: 0.11 (0.40), residues: 167 loop : -0.69 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.009 0.001 HIS E 84 PHE 0.011 0.001 PHE D 91 TYR 0.018 0.001 TYR C 13 ARG 0.004 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 315 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 1.075 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: 0.9208 (mt) cc_final: 0.8925 (mt) REVERT: C 125 LEU cc_start: 0.8512 (pp) cc_final: 0.8232 (pt) REVERT: C 184 PHE cc_start: 0.7914 (m-80) cc_final: 0.7156 (m-80) REVERT: C 226 LEU cc_start: 0.8688 (mp) cc_final: 0.8341 (tp) REVERT: C 262 MET cc_start: 0.8132 (tpp) cc_final: 0.7714 (tpp) REVERT: C 351 LEU cc_start: 0.5987 (tp) cc_final: 0.5751 (tp) REVERT: C 373 MET cc_start: 0.8608 (mmm) cc_final: 0.8271 (mmt) REVERT: D 16 GLN cc_start: 0.4094 (OUTLIER) cc_final: 0.3637 (pm20) REVERT: D 66 VAL cc_start: 0.7304 (t) cc_final: 0.6915 (p) REVERT: D 94 GLN cc_start: 0.5575 (pt0) cc_final: 0.5109 (pp30) REVERT: D 96 HIS cc_start: 0.8837 (p90) cc_final: 0.8313 (p90) REVERT: D 210 LYS cc_start: 0.9346 (mttp) cc_final: 0.9145 (mttp) REVERT: E 272 MET cc_start: 0.8525 (mtp) cc_final: 0.7766 (ttm) REVERT: E 306 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8969 (tpp80) REVERT: E 353 GLU cc_start: 0.8243 (tt0) cc_final: 0.6796 (tp30) REVERT: F 83 GLU cc_start: 0.8045 (pp20) cc_final: 0.7668 (pp20) REVERT: F 84 LEU cc_start: 0.9054 (mt) cc_final: 0.8762 (mt) REVERT: F 87 GLN cc_start: 0.9137 (tt0) cc_final: 0.8912 (tt0) REVERT: F 91 PHE cc_start: 0.6055 (t80) cc_final: 0.5812 (t80) REVERT: F 128 GLU cc_start: 0.8951 (mp0) cc_final: 0.8593 (mp0) REVERT: F 129 MET cc_start: 0.8353 (mmm) cc_final: 0.7717 (mmm) REVERT: F 146 LEU cc_start: 0.7039 (mt) cc_final: 0.6816 (tp) REVERT: F 152 GLN cc_start: 0.7904 (mm110) cc_final: 0.7312 (tt0) REVERT: F 168 LEU cc_start: 0.9077 (mp) cc_final: 0.8410 (tt) REVERT: F 170 ASP cc_start: 0.7816 (t0) cc_final: 0.7056 (t0) REVERT: F 215 GLN cc_start: 0.8283 (mt0) cc_final: 0.7578 (mp10) outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.1789 time to fit residues: 80.9726 Evaluate side-chains 256 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 7.9990 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090074 restraints weight = 27027.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092903 restraints weight = 16403.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094880 restraints weight = 11350.531| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9492 Z= 0.265 Angle : 0.664 6.370 12901 Z= 0.344 Chirality : 0.045 0.161 1541 Planarity : 0.005 0.049 1664 Dihedral : 4.611 22.320 1335 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 0.39 (0.24), residues: 1255 helix: 1.18 (0.22), residues: 584 sheet: -0.05 (0.39), residues: 174 loop : -0.66 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 254 HIS 0.009 0.001 HIS D 97 PHE 0.012 0.002 PHE E 319 TYR 0.019 0.002 TYR C 13 ARG 0.005 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 294 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.063 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 305 LEU cc_start: 0.9380 (mm) cc_final: 0.9150 (mm) REVERT: C 351 LEU cc_start: 0.6115 (tp) cc_final: 0.5901 (tp) REVERT: D 66 VAL cc_start: 0.7392 (t) cc_final: 0.7024 (t) REVERT: D 96 HIS cc_start: 0.9041 (p90) cc_final: 0.8440 (p90) REVERT: E 264 ASP cc_start: 0.8950 (m-30) cc_final: 0.8611 (m-30) REVERT: E 306 ARG cc_start: 0.9322 (tpp80) cc_final: 0.9057 (tpp80) REVERT: E 336 ILE cc_start: 0.9410 (mm) cc_final: 0.9161 (mp) REVERT: E 353 GLU cc_start: 0.8389 (tt0) cc_final: 0.6880 (tp30) REVERT: E 389 LEU cc_start: 0.9168 (tp) cc_final: 0.8957 (tp) REVERT: F 87 GLN cc_start: 0.9185 (tt0) cc_final: 0.8939 (tt0) REVERT: F 125 ARG cc_start: 0.8433 (tpt170) cc_final: 0.8050 (tpt-90) REVERT: F 129 MET cc_start: 0.8268 (mmm) cc_final: 0.7390 (mmm) REVERT: F 146 LEU cc_start: 0.7333 (mt) cc_final: 0.6936 (tp) REVERT: F 207 GLN cc_start: 0.8523 (tp40) cc_final: 0.7822 (pt0) REVERT: F 212 MET cc_start: 0.7488 (mpp) cc_final: 0.6626 (mpp) REVERT: F 215 GLN cc_start: 0.8627 (mt0) cc_final: 0.7717 (mp10) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1913 time to fit residues: 80.2371 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 : 1.085 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN 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 = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092770 restraints weight = 26881.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095701 restraints weight = 16101.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097756 restraints weight = 11102.265| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2981 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= 0.182 Angle : 0.650 7.837 12901 Z= 0.330 Chirality : 0.045 0.154 1541 Planarity : 0.004 0.046 1664 Dihedral : 4.500 23.144 1335 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.38 (0.24), residues: 1255 helix: 1.17 (0.22), residues: 589 sheet: -0.12 (0.38), residues: 179 loop : -0.64 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 246 HIS 0.004 0.001 HIS D 97 PHE 0.010 0.001 PHE D 95 TYR 0.015 0.001 TYR C 13 ARG 0.003 0.000 ARG F 138 *********************** 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: 0 poor density : 300 time to evaluate : 1.071 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: 0.9182 (mt) cc_final: 0.8871 (mt) REVERT: C 201 MET cc_start: 0.8030 (ppp) cc_final: 0.7780 (ppp) REVERT: C 248 ASP cc_start: 0.8033 (p0) cc_final: 0.7560 (p0) REVERT: C 305 LEU cc_start: 0.9313 (mm) cc_final: 0.9106 (mm) REVERT: D 67 ILE cc_start: 0.8171 (tt) cc_final: 0.7950 (tt) REVERT: D 94 GLN cc_start: 0.6169 (pt0) cc_final: 0.5921 (pt0) REVERT: D 96 HIS cc_start: 0.8931 (p90) cc_final: 0.8394 (p90) REVERT: E 264 ASP cc_start: 0.8893 (m-30) cc_final: 0.8621 (m-30) REVERT: E 306 ARG cc_start: 0.9252 (tpp80) cc_final: 0.8961 (tpp80) REVERT: E 353 GLU cc_start: 0.8303 (tt0) cc_final: 0.6907 (tp30) REVERT: F 83 GLU cc_start: 0.8024 (pp20) cc_final: 0.7676 (pp20) REVERT: F 84 LEU cc_start: 0.9115 (mt) cc_final: 0.8866 (mt) REVERT: F 87 GLN cc_start: 0.9104 (tt0) cc_final: 0.8855 (tt0) REVERT: F 125 ARG cc_start: 0.8347 (tpt170) cc_final: 0.7846 (tpt-90) REVERT: F 128 GLU cc_start: 0.9001 (mp0) cc_final: 0.8699 (mp0) REVERT: F 129 MET cc_start: 0.8272 (mmm) cc_final: 0.7364 (mmm) REVERT: F 146 LEU cc_start: 0.7235 (mt) cc_final: 0.6884 (tp) REVERT: F 152 GLN cc_start: 0.8043 (mm110) cc_final: 0.7138 (tt0) REVERT: F 207 GLN cc_start: 0.8457 (tp40) cc_final: 0.7779 (pt0) REVERT: F 212 MET cc_start: 0.7580 (mpp) cc_final: 0.6663 (mpp) REVERT: F 215 GLN cc_start: 0.8484 (mt0) cc_final: 0.7576 (mp10) REVERT: F 218 MET cc_start: 0.6629 (tpp) cc_final: 0.6401 (tpp) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1801 time to fit residues: 77.1740 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 : 1.032 ------------------------------------------------------------------------------- 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: 0.0670 chunk 6 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 102 optimal weight: 0.0470 chunk 76 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 GLN E 77 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 = 0.3868 r_free = 0.3868 target = 0.120917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.095013 restraints weight = 26814.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097968 restraints weight = 16020.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.099859 restraints weight = 11004.832| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3168 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= 0.173 Angle : 0.676 8.697 12901 Z= 0.339 Chirality : 0.045 0.153 1541 Planarity : 0.004 0.044 1664 Dihedral : 4.474 23.826 1335 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: 0.44 (0.24), residues: 1255 helix: 1.15 (0.22), residues: 588 sheet: 0.06 (0.39), residues: 174 loop : -0.59 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 246 HIS 0.005 0.001 HIS D 53 PHE 0.011 0.001 PHE D 91 TYR 0.024 0.001 TYR D 15 ARG 0.006 0.000 ARG F 193 *********************** 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 303 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.066 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: 0.9127 (mt) cc_final: 0.8797 (mt) REVERT: C 48 MET cc_start: 0.8878 (mtp) cc_final: 0.8613 (mtm) REVERT: C 201 MET cc_start: 0.7954 (ppp) cc_final: 0.7753 (ppp) REVERT: C 373 MET cc_start: 0.8600 (mmm) cc_final: 0.8396 (mmt) REVERT: D 66 VAL cc_start: 0.7334 (t) cc_final: 0.6984 (t) REVERT: D 71 GLN cc_start: 0.8792 (mp10) cc_final: 0.8566 (mp10) REVERT: D 89 LEU cc_start: 0.8359 (tt) cc_final: 0.7928 (mm) REVERT: D 94 GLN cc_start: 0.5906 (pt0) cc_final: 0.5411 (pp30) REVERT: D 96 HIS cc_start: 0.8882 (p90) cc_final: 0.8492 (p90) REVERT: D 152 GLN cc_start: 0.9494 (tt0) cc_final: 0.9034 (pt0) REVERT: E 264 ASP cc_start: 0.8834 (m-30) cc_final: 0.8624 (m-30) REVERT: E 272 MET cc_start: 0.8511 (mtp) cc_final: 0.7830 (ttm) REVERT: E 306 ARG cc_start: 0.9268 (tpp80) cc_final: 0.8982 (tpp80) REVERT: E 353 GLU cc_start: 0.8260 (tt0) cc_final: 0.6855 (tp30) REVERT: F 83 GLU cc_start: 0.7997 (pp20) cc_final: 0.7608 (pp20) REVERT: F 84 LEU cc_start: 0.9103 (mt) cc_final: 0.8843 (mt) REVERT: F 87 GLN cc_start: 0.9006 (tt0) cc_final: 0.8759 (tt0) REVERT: F 125 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7831 (tpt-90) REVERT: F 128 GLU cc_start: 0.8988 (mp0) cc_final: 0.8498 (mp0) REVERT: F 129 MET cc_start: 0.8255 (mmm) cc_final: 0.7282 (mmm) REVERT: F 131 LYS cc_start: 0.8577 (pttm) cc_final: 0.8159 (tptp) REVERT: F 146 LEU cc_start: 0.7290 (mt) cc_final: 0.6927 (tp) REVERT: F 152 GLN cc_start: 0.8105 (mm110) cc_final: 0.7305 (tt0) REVERT: F 207 GLN cc_start: 0.8570 (tp40) cc_final: 0.7912 (pt0) REVERT: F 212 MET cc_start: 0.7517 (mpp) cc_final: 0.6829 (mpp) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1778 time to fit residues: 77.7617 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 : 1.115 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.117522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091900 restraints weight = 26563.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094778 restraints weight = 16065.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096799 restraints weight = 11018.934| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3264 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= 0.228 Angle : 0.686 9.425 12901 Z= 0.348 Chirality : 0.045 0.147 1541 Planarity : 0.004 0.045 1664 Dihedral : 4.525 23.772 1335 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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 (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: 0.42 (0.24), residues: 1255 helix: 1.15 (0.22), residues: 589 sheet: -0.12 (0.37), residues: 184 loop : -0.56 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 246 HIS 0.004 0.001 HIS D 53 PHE 0.013 0.001 PHE D 91 TYR 0.021 0.001 TYR C 13 ARG 0.004 0.000 ARG F 138 *********************** 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 295 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.053 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: 0.9178 (mt) cc_final: 0.8881 (mt) REVERT: C 201 MET cc_start: 0.8025 (ppp) cc_final: 0.7737 (ppp) REVERT: C 262 MET cc_start: 0.8166 (tpp) cc_final: 0.7249 (tpp) REVERT: C 263 GLU cc_start: 0.8533 (pp20) cc_final: 0.8313 (pp20) REVERT: C 373 MET cc_start: 0.8672 (mmm) cc_final: 0.8408 (mmt) REVERT: D 66 VAL cc_start: 0.7299 (t) cc_final: 0.6904 (t) REVERT: D 71 GLN cc_start: 0.8785 (mp10) cc_final: 0.8498 (mp10) REVERT: D 89 LEU cc_start: 0.8136 (tt) cc_final: 0.7558 (mm) REVERT: D 94 GLN cc_start: 0.6079 (pt0) cc_final: 0.5553 (pp30) REVERT: D 96 HIS cc_start: 0.8851 (p90) cc_final: 0.8404 (p90) REVERT: E 306 ARG cc_start: 0.9316 (tpp80) cc_final: 0.9002 (tpp80) REVERT: E 353 GLU cc_start: 0.8320 (tt0) cc_final: 0.6912 (tp30) REVERT: F 83 GLU cc_start: 0.8050 (pp20) cc_final: 0.7688 (pp20) REVERT: F 84 LEU cc_start: 0.9118 (mt) cc_final: 0.8851 (mt) REVERT: F 87 GLN cc_start: 0.9133 (tt0) cc_final: 0.8872 (tt0) REVERT: F 125 ARG cc_start: 0.8429 (tpt170) cc_final: 0.8155 (tpt-90) REVERT: F 129 MET cc_start: 0.8250 (mmm) cc_final: 0.7409 (mmm) REVERT: F 131 LYS cc_start: 0.8613 (pttm) cc_final: 0.8131 (tptp) REVERT: F 146 LEU cc_start: 0.7305 (mt) cc_final: 0.6925 (tp) REVERT: F 152 GLN cc_start: 0.8121 (mm110) cc_final: 0.7272 (tt0) REVERT: F 207 GLN cc_start: 0.8545 (tp40) cc_final: 0.7833 (pt0) REVERT: F 212 MET cc_start: 0.7596 (mpp) cc_final: 0.6908 (mpp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1841 time to fit residues: 78.3199 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 : 1.262 ------------------------------------------------------------------------------- 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: 9.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.118618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092843 restraints weight = 26572.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095753 restraints weight = 16050.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097802 restraints weight = 11064.139| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3393 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= 0.193 Angle : 0.695 8.997 12901 Z= 0.346 Chirality : 0.045 0.142 1541 Planarity : 0.004 0.044 1664 Dihedral : 4.512 24.499 1335 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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 (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: 0.41 (0.24), residues: 1255 helix: 1.14 (0.22), residues: 590 sheet: -0.06 (0.38), residues: 179 loop : -0.60 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 246 HIS 0.008 0.001 HIS D 97 PHE 0.010 0.001 PHE D 68 TYR 0.024 0.001 TYR C 13 ARG 0.004 0.000 ARG F 138 ********************** 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 294 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.142 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: 0.9136 (mt) cc_final: 0.8820 (mt) REVERT: C 48 MET cc_start: 0.9329 (ttp) cc_final: 0.8949 (mtp) REVERT: C 258 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 66 VAL cc_start: 0.7302 (t) cc_final: 0.6897 (t) REVERT: D 71 GLN cc_start: 0.8797 (mp10) cc_final: 0.8548 (mp10) REVERT: D 89 LEU cc_start: 0.8432 (tt) cc_final: 0.7919 (mm) REVERT: D 94 GLN cc_start: 0.5945 (pt0) cc_final: 0.5470 (pp30) REVERT: D 96 HIS cc_start: 0.8782 (p90) cc_final: 0.8385 (p90) REVERT: D 218 MET cc_start: 0.7428 (mmm) cc_final: 0.7179 (tpp) REVERT: E 272 MET cc_start: 0.8588 (mtp) cc_final: 0.7939 (ttm) REVERT: E 306 ARG cc_start: 0.9310 (tpp80) cc_final: 0.8972 (tpp80) REVERT: E 353 GLU cc_start: 0.8262 (tt0) cc_final: 0.6891 (tp30) REVERT: F 83 GLU cc_start: 0.8019 (pp20) cc_final: 0.7624 (pp20) REVERT: F 84 LEU cc_start: 0.9111 (mt) cc_final: 0.8855 (mt) REVERT: F 87 GLN cc_start: 0.9092 (tt0) cc_final: 0.8828 (tt0) REVERT: F 125 ARG cc_start: 0.8314 (tpt170) cc_final: 0.8082 (tpt-90) REVERT: F 128 GLU cc_start: 0.8804 (mp0) cc_final: 0.8405 (mp0) REVERT: F 146 LEU cc_start: 0.7059 (mt) cc_final: 0.6779 (tp) REVERT: F 152 GLN cc_start: 0.8123 (mm110) cc_final: 0.7303 (tt0) REVERT: F 207 GLN cc_start: 0.8577 (tp40) cc_final: 0.7924 (pt0) REVERT: F 212 MET cc_start: 0.7646 (mpp) cc_final: 0.6993 (mpp) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2084 time to fit residues: 88.8021 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 : 1.100 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093726 restraints weight = 26645.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096638 restraints weight = 16014.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098712 restraints weight = 10969.917| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3474 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 : 0.685 8.434 12901 Z= 0.340 Chirality : 0.045 0.154 1541 Planarity : 0.004 0.044 1664 Dihedral : 4.464 24.558 1335 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.39 (0.24), residues: 1255 helix: 1.13 (0.21), residues: 593 sheet: -0.16 (0.38), residues: 179 loop : -0.57 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 254 HIS 0.007 0.001 HIS D 97 PHE 0.012 0.001 PHE D 91 TYR 0.024 0.001 TYR C 13 ARG 0.004 0.000 ARG F 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3004.18 seconds wall clock time: 53 minutes 6.94 seconds (3186.94 seconds total)