Starting phenix.real_space_refine on Wed Feb 14 13:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8m_31804/02_2024/7v8m_31804.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8m_31804/02_2024/7v8m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8m_31804/02_2024/7v8m_31804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8m_31804/02_2024/7v8m_31804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8m_31804/02_2024/7v8m_31804.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8m_31804/02_2024/7v8m_31804.pdb" } 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 Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F ASP 182": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 - 3.50 Amino acid : False - 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: 3.85 Conformation dependent library (CDL) restraints added in 2.0 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: 1.01 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: 2.67 Time building geometry restraints manager: 4.13 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: 99.14 - 106.11: 227 106.11 - 113.08: 5253 113.08 - 120.06: 3340 120.06 - 127.03: 3985 127.03 - 134.01: 96 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 2.440 nonbonded pdb=" NE2 GLN D 152 " pdb=" O PRO D 172 " model vdw 2.167 2.520 nonbonded pdb=" O SER C 70 " pdb=" NZ LYS C 245 " model vdw 2.167 2.520 nonbonded pdb=" OD1 ASP C 233 " pdb=" N SER C 234 " model vdw 2.184 2.520 nonbonded pdb=" NH2 ARG F 138 " pdb=" O ARG F 142 " model vdw 2.191 2.520 ... (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 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: 0.290 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: 2.140 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 28.410 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 1.064 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: 0.1839 time to fit residues: 82.2941 Evaluate side-chains 245 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 238 GLN D 87 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1381 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= 0.203 Angle : 0.642 7.154 12901 Z= 0.330 Chirality : 0.044 0.168 1541 Planarity : 0.005 0.054 1664 Dihedral : 4.785 19.822 1335 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.21 % Allowed : 5.21 % Favored : 94.58 % 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: 0.07 (0.24), residues: 1255 helix: 0.97 (0.22), residues: 570 sheet: -0.40 (0.37), residues: 184 loop : -0.77 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 246 HIS 0.010 0.001 HIS E 84 PHE 0.012 0.001 PHE E 285 TYR 0.017 0.002 TYR D 15 ARG 0.007 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 305 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 303 time to evaluate : 1.134 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: 0.8684 (mt) cc_final: 0.8345 (mt) REVERT: C 323 ILE cc_start: 0.9050 (mt) cc_final: 0.8763 (mt) REVERT: C 368 ILE cc_start: 0.9246 (pt) cc_final: 0.8633 (mm) REVERT: D 184 ILE cc_start: 0.7899 (pt) cc_final: 0.7634 (pt) REVERT: D 195 GLN cc_start: 0.8858 (mm110) cc_final: 0.8545 (tp-100) REVERT: E 264 ASP cc_start: 0.8196 (m-30) cc_final: 0.7595 (m-30) REVERT: E 353 GLU cc_start: 0.7388 (tt0) cc_final: 0.5840 (tp30) REVERT: F 102 PHE cc_start: 0.7387 (m-10) cc_final: 0.7043 (m-10) REVERT: F 152 GLN cc_start: 0.7482 (mm110) cc_final: 0.6782 (tt0) REVERT: F 201 VAL cc_start: 0.8454 (m) cc_final: 0.8238 (m) REVERT: F 215 GLN cc_start: 0.7739 (mt0) cc_final: 0.7018 (mm110) outliers start: 2 outliers final: 0 residues processed: 304 average time/residue: 0.1775 time to fit residues: 77.5632 Evaluate side-chains 241 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 152 GLN D 180 ASN E 84 HIS E 188 HIS E 376 HIS F 123 ASN F 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1830 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= 0.204 Angle : 0.617 6.381 12901 Z= 0.317 Chirality : 0.044 0.197 1541 Planarity : 0.004 0.050 1664 Dihedral : 4.692 18.476 1335 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.21 % Allowed : 4.69 % Favored : 95.10 % 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: 1.14 (0.22), residues: 575 sheet: -0.26 (0.39), residues: 180 loop : -0.82 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 246 HIS 0.009 0.001 HIS D 97 PHE 0.011 0.001 PHE D 95 TYR 0.014 0.002 TYR C 13 ARG 0.007 0.001 ARG F 138 *********************** 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 301 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 1.162 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: 0.8723 (mt) cc_final: 0.8446 (mt) REVERT: C 291 MET cc_start: 0.7973 (mtt) cc_final: 0.7768 (mtt) REVERT: C 323 ILE cc_start: 0.9112 (mt) cc_final: 0.8773 (mt) REVERT: C 368 ILE cc_start: 0.9295 (pt) cc_final: 0.8551 (mm) REVERT: D 195 GLN cc_start: 0.8863 (mm110) cc_final: 0.8548 (tp-100) REVERT: E 264 ASP cc_start: 0.7886 (m-30) cc_final: 0.7428 (m-30) REVERT: E 353 GLU cc_start: 0.7608 (tt0) cc_final: 0.6071 (tp30) REVERT: F 102 PHE cc_start: 0.7367 (m-10) cc_final: 0.7049 (m-10) REVERT: F 152 GLN cc_start: 0.7274 (mm110) cc_final: 0.6859 (tt0) REVERT: F 187 LEU cc_start: 0.8554 (tp) cc_final: 0.8134 (tt) REVERT: F 215 GLN cc_start: 0.7538 (mt0) cc_final: 0.6829 (mm110) outliers start: 2 outliers final: 0 residues processed: 300 average time/residue: 0.1797 time to fit residues: 77.6610 Evaluate side-chains 239 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 0.0170 chunk 118 optimal weight: 0.4980 chunk 106 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 153 GLN C 238 GLN C 294 GLN D 152 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2224 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= 0.159 Angle : 0.618 9.197 12901 Z= 0.312 Chirality : 0.044 0.148 1541 Planarity : 0.004 0.049 1664 Dihedral : 4.561 19.307 1335 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % 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: 1.01 (0.22), residues: 579 sheet: 0.05 (0.41), residues: 169 loop : -0.86 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 246 HIS 0.007 0.001 HIS D 53 PHE 0.010 0.001 PHE D 91 TYR 0.013 0.001 TYR C 13 ARG 0.003 0.000 ARG D 142 *********************** 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 307 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 0.977 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 26 VAL cc_start: 0.9379 (t) cc_final: 0.9107 (p) REVERT: C 29 LEU cc_start: 0.8786 (mt) cc_final: 0.8433 (mt) REVERT: C 114 MET cc_start: 0.7022 (ppp) cc_final: 0.6090 (ptm) REVERT: C 291 MET cc_start: 0.8046 (mtt) cc_final: 0.7711 (mtt) REVERT: C 323 ILE cc_start: 0.9086 (mt) cc_final: 0.8694 (mt) REVERT: C 368 ILE cc_start: 0.9108 (pt) cc_final: 0.8771 (mm) REVERT: D 195 GLN cc_start: 0.8817 (mm110) cc_final: 0.8459 (tp-100) REVERT: E 264 ASP cc_start: 0.7799 (m-30) cc_final: 0.7539 (m-30) REVERT: E 298 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8683 (mmmt) REVERT: E 301 ASP cc_start: 0.6553 (m-30) cc_final: 0.6139 (m-30) REVERT: E 353 GLU cc_start: 0.7794 (tt0) cc_final: 0.6359 (tp30) REVERT: F 102 PHE cc_start: 0.7309 (m-10) cc_final: 0.6973 (m-10) REVERT: F 152 GLN cc_start: 0.6968 (mm110) cc_final: 0.6728 (tt0) REVERT: F 215 GLN cc_start: 0.7526 (mt0) cc_final: 0.7256 (mp10) outliers start: 2 outliers final: 1 residues processed: 306 average time/residue: 0.1773 time to fit residues: 77.5332 Evaluate side-chains 248 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 0.0040 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 0.034 9492 Z= 0.228 Angle : 0.637 6.152 12901 Z= 0.329 Chirality : 0.044 0.171 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.594 18.656 1335 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 1.03 (0.22), residues: 585 sheet: -0.05 (0.39), residues: 179 loop : -0.77 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 246 HIS 0.006 0.001 HIS D 97 PHE 0.017 0.002 PHE C 184 TYR 0.011 0.002 TYR E 260 ARG 0.006 0.001 ARG E 125 *********************** 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 292 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.158 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: 0.8896 (mt) cc_final: 0.8585 (mt) REVERT: C 291 MET cc_start: 0.7938 (mtt) cc_final: 0.7479 (mtt) REVERT: C 368 ILE cc_start: 0.9179 (pt) cc_final: 0.8805 (mm) REVERT: C 373 MET cc_start: 0.8112 (mmm) cc_final: 0.7566 (mmt) REVERT: E 264 ASP cc_start: 0.7788 (m-30) cc_final: 0.7378 (m-30) REVERT: E 272 MET cc_start: 0.8467 (mtm) cc_final: 0.8206 (mtp) REVERT: E 298 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8826 (mmmt) REVERT: E 301 ASP cc_start: 0.6609 (m-30) cc_final: 0.6345 (m-30) REVERT: E 353 GLU cc_start: 0.7714 (tt0) cc_final: 0.6489 (tp30) REVERT: F 102 PHE cc_start: 0.7319 (m-10) cc_final: 0.7043 (m-10) REVERT: F 215 GLN cc_start: 0.7519 (mt0) cc_final: 0.7259 (mp10) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1789 time to fit residues: 75.2029 Evaluate side-chains 244 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 114 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 107 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9492 Z= 0.176 Angle : 0.613 6.494 12901 Z= 0.311 Chirality : 0.044 0.184 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.525 21.708 1335 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 587 sheet: 0.07 (0.40), residues: 173 loop : -0.75 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 246 HIS 0.008 0.001 HIS E 84 PHE 0.011 0.001 PHE C 184 TYR 0.019 0.001 TYR C 13 ARG 0.003 0.000 ARG D 151 *********************** 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 311 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 0.988 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 26 VAL cc_start: 0.9409 (t) cc_final: 0.9180 (p) REVERT: C 29 LEU cc_start: 0.8814 (mt) cc_final: 0.8447 (mt) REVERT: C 291 MET cc_start: 0.8162 (mtt) cc_final: 0.7740 (mtt) REVERT: C 293 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8106 (mmmm) REVERT: C 296 GLU cc_start: 0.7302 (tt0) cc_final: 0.6955 (tt0) REVERT: C 368 ILE cc_start: 0.9133 (pt) cc_final: 0.8829 (mm) REVERT: C 373 MET cc_start: 0.8010 (mmm) cc_final: 0.7689 (mmt) REVERT: E 264 ASP cc_start: 0.7882 (m-30) cc_final: 0.7621 (m-30) REVERT: E 298 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8794 (mmmt) REVERT: E 301 ASP cc_start: 0.6582 (m-30) cc_final: 0.6140 (m-30) REVERT: E 353 GLU cc_start: 0.7627 (tt0) cc_final: 0.6465 (tp30) REVERT: F 102 PHE cc_start: 0.7233 (m-10) cc_final: 0.6946 (m-10) REVERT: F 152 GLN cc_start: 0.7299 (mm110) cc_final: 0.6797 (tt0) REVERT: F 215 GLN cc_start: 0.7455 (mt0) cc_final: 0.7206 (mp10) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.1814 time to fit residues: 80.9906 Evaluate side-chains 251 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 0.0020 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2928 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= 0.169 Angle : 0.632 7.498 12901 Z= 0.319 Chirality : 0.044 0.148 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.439 20.191 1335 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: 1.08 (0.22), residues: 588 sheet: -0.02 (0.39), residues: 167 loop : -0.77 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 246 HIS 0.009 0.001 HIS D 97 PHE 0.011 0.001 PHE D 91 TYR 0.020 0.001 TYR C 13 ARG 0.003 0.000 ARG D 151 *********************** 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 fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.9411 (t) cc_final: 0.9171 (p) REVERT: C 29 LEU cc_start: 0.8797 (mt) cc_final: 0.8430 (mt) REVERT: C 114 MET cc_start: 0.7859 (ppp) cc_final: 0.6283 (ptm) REVERT: C 293 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8116 (mmmm) REVERT: C 296 GLU cc_start: 0.7500 (tt0) cc_final: 0.7227 (tt0) REVERT: C 368 ILE cc_start: 0.9150 (pt) cc_final: 0.8839 (mm) REVERT: C 373 MET cc_start: 0.8019 (mmm) cc_final: 0.7586 (mmt) REVERT: D 94 GLN cc_start: 0.6284 (pp30) cc_final: 0.5995 (pp30) REVERT: E 264 ASP cc_start: 0.7797 (m-30) cc_final: 0.7567 (m-30) REVERT: E 298 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8782 (mmmt) REVERT: E 353 GLU cc_start: 0.7603 (tt0) cc_final: 0.6449 (tp30) REVERT: F 152 GLN cc_start: 0.7286 (mm110) cc_final: 0.6762 (tt0) REVERT: F 215 GLN cc_start: 0.7421 (mt0) cc_final: 0.7181 (mp10) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1862 time to fit residues: 80.9073 Evaluate side-chains 242 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3116 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= 0.180 Angle : 0.639 7.199 12901 Z= 0.322 Chirality : 0.044 0.144 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.449 21.385 1335 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 1.11 (0.22), residues: 588 sheet: -0.03 (0.39), residues: 169 loop : -0.72 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 246 HIS 0.008 0.001 HIS D 97 PHE 0.011 0.001 PHE C 184 TYR 0.022 0.001 TYR C 13 ARG 0.002 0.000 ARG D 151 *********************** 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 292 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.9407 (t) cc_final: 0.9190 (p) REVERT: C 29 LEU cc_start: 0.8806 (mt) cc_final: 0.8461 (mt) REVERT: C 48 MET cc_start: 0.8896 (mtp) cc_final: 0.8580 (mtp) REVERT: C 291 MET cc_start: 0.7872 (mtt) cc_final: 0.7635 (mtt) REVERT: C 293 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8074 (mmmm) REVERT: C 296 GLU cc_start: 0.7619 (tt0) cc_final: 0.7284 (tt0) REVERT: C 368 ILE cc_start: 0.9154 (pt) cc_final: 0.8850 (mm) REVERT: C 373 MET cc_start: 0.7959 (mmm) cc_final: 0.7616 (mmt) REVERT: D 94 GLN cc_start: 0.6044 (pp30) cc_final: 0.5798 (pp30) REVERT: D 142 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.6852 (tpp80) REVERT: E 264 ASP cc_start: 0.7819 (m-30) cc_final: 0.7561 (m-30) REVERT: E 298 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8816 (mmmt) REVERT: E 353 GLU cc_start: 0.7709 (tt0) cc_final: 0.6473 (tp30) REVERT: F 152 GLN cc_start: 0.7334 (mm110) cc_final: 0.6733 (tt0) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1796 time to fit residues: 75.7814 Evaluate side-chains 246 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- 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 D 180 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9492 Z= 0.170 Angle : 0.662 9.104 12901 Z= 0.328 Chirality : 0.044 0.142 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.465 21.214 1335 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: 0.35 (0.24), residues: 1255 helix: 1.10 (0.22), residues: 588 sheet: 0.03 (0.40), residues: 169 loop : -0.68 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.005 0.001 HIS D 53 PHE 0.012 0.001 PHE C 184 TYR 0.023 0.001 TYR C 13 ARG 0.002 0.000 ARG D 151 *********************** 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 301 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.121 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 26 VAL cc_start: 0.9399 (t) cc_final: 0.9195 (p) REVERT: C 29 LEU cc_start: 0.8909 (mt) cc_final: 0.8496 (mt) REVERT: C 262 MET cc_start: 0.8082 (tpp) cc_final: 0.6868 (tpp) REVERT: C 293 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8066 (mmmm) REVERT: C 296 GLU cc_start: 0.7622 (tt0) cc_final: 0.7266 (tt0) REVERT: C 368 ILE cc_start: 0.9241 (pt) cc_final: 0.8837 (mm) REVERT: C 373 MET cc_start: 0.7923 (mmm) cc_final: 0.7441 (mmt) REVERT: D 94 GLN cc_start: 0.6097 (pp30) cc_final: 0.5828 (pp30) REVERT: E 272 MET cc_start: 0.8362 (mtp) cc_final: 0.7703 (ttm) REVERT: E 298 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8793 (mmmt) REVERT: E 350 GLU cc_start: 0.6657 (pp20) cc_final: 0.6433 (tm-30) REVERT: E 353 GLU cc_start: 0.7548 (tt0) cc_final: 0.6384 (tp30) REVERT: F 152 GLN cc_start: 0.7129 (mm110) cc_final: 0.6603 (tt0) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1815 time to fit residues: 78.2425 Evaluate side-chains 249 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3415 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= 0.181 Angle : 0.662 7.917 12901 Z= 0.330 Chirality : 0.044 0.148 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.434 21.316 1335 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: 0.35 (0.24), residues: 1255 helix: 1.13 (0.22), residues: 589 sheet: -0.10 (0.39), residues: 170 loop : -0.65 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.004 0.001 HIS D 97 PHE 0.014 0.001 PHE D 91 TYR 0.024 0.001 TYR C 13 ARG 0.003 0.000 ARG D 142 ********************** 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 295 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.9407 (t) cc_final: 0.9187 (p) REVERT: C 29 LEU cc_start: 0.8901 (mt) cc_final: 0.8421 (mt) REVERT: C 262 MET cc_start: 0.8057 (tpp) cc_final: 0.6861 (tpp) REVERT: C 368 ILE cc_start: 0.9249 (pt) cc_final: 0.8882 (mm) REVERT: C 373 MET cc_start: 0.7888 (mmm) cc_final: 0.7537 (mmt) REVERT: D 94 GLN cc_start: 0.6132 (pp30) cc_final: 0.5828 (pp30) REVERT: E 298 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8821 (mmmt) REVERT: E 353 GLU cc_start: 0.7536 (tt0) cc_final: 0.5873 (tp30) REVERT: F 152 GLN cc_start: 0.7211 (mm110) cc_final: 0.6604 (tt0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1749 time to fit residues: 74.4883 Evaluate side-chains 246 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 0.4980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 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 = 0.3861 r_free = 0.3861 target = 0.119921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094597 restraints weight = 26294.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097494 restraints weight = 15816.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099470 restraints weight = 10855.534| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3516 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= 0.185 Angle : 0.654 7.178 12901 Z= 0.329 Chirality : 0.045 0.153 1541 Planarity : 0.004 0.048 1664 Dihedral : 4.388 21.153 1335 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % 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: 0.33 (0.24), residues: 1255 helix: 1.08 (0.22), residues: 593 sheet: -0.14 (0.39), residues: 170 loop : -0.63 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.004 0.001 HIS D 53 PHE 0.014 0.001 PHE C 184 TYR 0.024 0.001 TYR C 13 ARG 0.005 0.000 ARG F 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.62 seconds wall clock time: 40 minutes 3.41 seconds (2403.41 seconds total)