Starting phenix.real_space_refine on Fri Jul 19 12:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/07_2024/8pok_17793.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/07_2024/8pok_17793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/07_2024/8pok_17793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/07_2024/8pok_17793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/07_2024/8pok_17793.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/07_2024/8pok_17793.cif" } resolution = 3.4 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= 0.064 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 51 5.16 5 C 5082 2.51 5 N 1416 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 220": "OE1" <-> "OE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8042 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2169 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1825 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 461 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.60 Number of scatterers: 8042 At special positions: 0 Unit cell: (80.388, 106.26, 133.98, 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 51 16.00 O 1493 8.00 N 1416 7.00 C 5082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 180 " distance=2.03 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: 2.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 20 through 51 removed outlier: 3.545A pdb=" N ILE A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.655A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 93 through 128 removed outlier: 3.654A pdb=" N ILE A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.580A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 removed outlier: 3.738A pdb=" N ILE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.622A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.663A pdb=" N ARG A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 4.042A pdb=" N LYS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.831A pdb=" N PHE A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.589A pdb=" N GLY A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 9 through 39 removed outlier: 3.562A pdb=" N ASN B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.902A pdb=" N GLN B 222 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 223 " --> pdb=" O TRP B 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 224 " --> pdb=" O ILE B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.691A pdb=" N LYS B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.117A pdb=" N LYS B 286 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 4.011A pdb=" N ALA B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.529A pdb=" N THR B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 329 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.548A pdb=" N ARG B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 376 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 removed outlier: 3.594A pdb=" N LEU C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 13 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 18 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.664A pdb=" N ILE C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 22 Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.622A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.649A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.516A pdb=" N MET B 207 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.516A pdb=" N MET B 207 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N ALA B 229 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 42 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE B 231 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 44 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL B 233 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 46 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 230 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE B 276 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE B 232 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 273 " --> pdb=" O TYR B 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.536A pdb=" N ARG C 54 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 341 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 322 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 68 removed outlier: 6.943A pdb=" N ALA C 78 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N MET C 66 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 76 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP C 68 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 74 " --> pdb=" O TRP C 68 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 85 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 79 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 84 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 97 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 86 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 88 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN C 93 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.722A pdb=" N GLY C 120 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS C 108 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA C 118 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 126 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU C 143 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 128 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 130 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG C 139 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 158 removed outlier: 6.783A pdb=" N SER C 165 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS C 154 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 163 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE C 156 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN C 161 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 162 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS C 171 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR C 184 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU C 173 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 197 removed outlier: 7.118A pdb=" N GLY C 207 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 195 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 205 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 197 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 203 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 204 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.530A pdb=" N ALA C 247 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 255 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 267 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 259 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU C 265 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 281 through 283 removed outlier: 3.611A pdb=" N GLY C 311 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.130A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.531A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 51 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 885 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: 2.06 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1320 1.28 - 1.41: 2069 1.41 - 1.54: 4728 1.54 - 1.68: 7 1.68 - 1.81: 69 Bond restraints: 8193 Sorted by residual: bond pdb=" CA ILE B 193 " pdb=" C ILE B 193 " ideal model delta sigma weight residual 1.524 1.441 0.083 8.60e-03 1.35e+04 9.33e+01 bond pdb=" CA VAL A 182 " pdb=" CB VAL A 182 " ideal model delta sigma weight residual 1.537 1.457 0.080 9.90e-03 1.02e+04 6.49e+01 bond pdb=" C CYS C 238 " pdb=" O CYS C 238 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.26e-02 6.30e+03 5.43e+01 bond pdb=" CA ASP B 317 " pdb=" C ASP B 317 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.13e-02 7.83e+03 4.02e+01 bond pdb=" C TYR A 284 " pdb=" O TYR A 284 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.67e+01 ... (remaining 8188 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.58: 123 105.58 - 112.90: 4377 112.90 - 120.21: 3113 120.21 - 127.53: 3411 127.53 - 134.85: 76 Bond angle restraints: 11100 Sorted by residual: angle pdb=" N TRP A 164 " pdb=" CA TRP A 164 " pdb=" C TRP A 164 " ideal model delta sigma weight residual 112.45 98.26 14.19 1.39e+00 5.18e-01 1.04e+02 angle pdb=" C ILE B 193 " pdb=" CA ILE B 193 " pdb=" CB ILE B 193 " ideal model delta sigma weight residual 113.22 103.03 10.19 1.12e+00 7.97e-01 8.27e+01 angle pdb=" N GLN A 183 " pdb=" CA GLN A 183 " pdb=" C GLN A 183 " ideal model delta sigma weight residual 110.14 122.62 -12.48 1.55e+00 4.16e-01 6.49e+01 angle pdb=" N LEU A 162 " pdb=" CA LEU A 162 " pdb=" C LEU A 162 " ideal model delta sigma weight residual 111.28 100.71 10.57 1.35e+00 5.49e-01 6.13e+01 angle pdb=" N HIS A 161 " pdb=" CA HIS A 161 " pdb=" C HIS A 161 " ideal model delta sigma weight residual 110.50 99.69 10.81 1.41e+00 5.03e-01 5.88e+01 ... (remaining 11095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.85: 4434 12.85 - 25.71: 341 25.71 - 38.56: 86 38.56 - 51.41: 26 51.41 - 64.26: 6 Dihedral angle restraints: 4893 sinusoidal: 1916 harmonic: 2977 Sorted by residual: dihedral pdb=" C ASP A 104 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta harmonic sigma weight residual -122.60 -136.63 14.03 0 2.50e+00 1.60e-01 3.15e+01 dihedral pdb=" N VAL A 105 " pdb=" C VAL A 105 " pdb=" CA VAL A 105 " pdb=" CB VAL A 105 " ideal model delta harmonic sigma weight residual 123.40 110.43 12.97 0 2.50e+00 1.60e-01 2.69e+01 dihedral pdb=" C TYR A 284 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.59e+01 ... (remaining 4890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1150 0.100 - 0.200: 95 0.200 - 0.300: 19 0.300 - 0.401: 1 0.401 - 0.501: 2 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA ASP A 104 " pdb=" N ASP A 104 " pdb=" C ASP A 104 " pdb=" CB ASP A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA VAL A 105 " pdb=" N VAL A 105 " pdb=" C VAL A 105 " pdb=" CB VAL A 105 " both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU C 157 " pdb=" N LEU C 157 " pdb=" C LEU C 157 " pdb=" CB LEU C 157 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1264 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 180 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C CYS A 180 " -0.074 2.00e-02 2.50e+03 pdb=" O CYS A 180 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS A 181 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 161 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C HIS A 161 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 161 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 162 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 350 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C THR B 350 " 0.062 2.00e-02 2.50e+03 pdb=" O THR B 350 " -0.024 2.00e-02 2.50e+03 pdb=" N CYS B 351 " -0.021 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 166 2.67 - 3.23: 7268 3.23 - 3.79: 10789 3.79 - 4.34: 14974 4.34 - 4.90: 25200 Nonbonded interactions: 58397 Sorted by model distance: nonbonded pdb=" O GLY C 167 " pdb=" OD1 ASP C 191 " model vdw 2.115 3.040 nonbonded pdb=" OG SER C 166 " pdb=" OD1 ASP C 168 " model vdw 2.181 2.440 nonbonded pdb=" O SER A 65 " pdb=" OG1 THR A 69 " model vdw 2.278 2.440 nonbonded pdb=" O ASP B 317 " pdb=" C PRO B 318 " model vdw 2.373 3.270 nonbonded pdb=" OD1 ASN D 59 " pdb=" N ARG D 62 " model vdw 2.388 2.520 ... (remaining 58392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.160 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.007 0.093 8193 Z= 0.494 Angle : 0.994 14.187 11100 Z= 0.681 Chirality : 0.062 0.501 1267 Planarity : 0.005 0.054 1418 Dihedral : 10.579 64.263 2964 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.46 % Allowed : 7.48 % Favored : 92.06 % Cbeta Deviations : 0.42 % 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: -2.24 (0.25), residues: 1008 helix: -0.60 (0.27), residues: 351 sheet: -0.87 (0.37), residues: 201 loop : -2.50 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.014 0.001 HIS C 147 PHE 0.053 0.002 PHE C 240 TYR 0.017 0.001 TYR A 284 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 0.963 Fit side-chains REVERT: A 81 SER cc_start: 0.9224 (t) cc_final: 0.8913 (p) REVERT: A 100 TYR cc_start: 0.8883 (t80) cc_final: 0.8659 (t80) REVERT: A 119 SER cc_start: 0.8673 (t) cc_final: 0.8207 (p) REVERT: A 131 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7552 (mtt180) REVERT: A 139 VAL cc_start: 0.8666 (t) cc_final: 0.8458 (m) REVERT: B 20 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8162 (mtm180) REVERT: B 38 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7906 (mtp-110) REVERT: B 325 TYR cc_start: 0.8425 (m-80) cc_final: 0.8192 (m-80) REVERT: B 342 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7308 (mmm-85) REVERT: C 22 GLN cc_start: 0.8766 (tt0) cc_final: 0.8428 (tt0) REVERT: C 49 GLN cc_start: 0.8070 (mt0) cc_final: 0.7862 (mt0) REVERT: C 303 ASP cc_start: 0.8604 (t0) cc_final: 0.8197 (t0) REVERT: C 312 VAL cc_start: 0.9034 (m) cc_final: 0.8815 (t) REVERT: E 65 LYS cc_start: 0.8788 (tttm) cc_final: 0.8500 (tttp) outliers start: 4 outliers final: 4 residues processed: 266 average time/residue: 0.2012 time to fit residues: 71.0624 Evaluate side-chains 213 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 209 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.0000 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 225 ASN C 41 ASN C 242 ASN C 244 ASN E 3 GLN E 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8193 Z= 0.175 Angle : 0.541 5.739 11100 Z= 0.298 Chirality : 0.042 0.157 1267 Planarity : 0.004 0.039 1418 Dihedral : 5.253 52.532 1128 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.68 % Allowed : 13.23 % Favored : 83.08 % 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: -1.34 (0.26), residues: 1008 helix: 0.50 (0.27), residues: 374 sheet: -0.71 (0.36), residues: 216 loop : -2.31 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.003 0.001 HIS C 188 PHE 0.013 0.001 PHE E 108 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 0.892 Fit side-chains REVERT: A 78 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 81 SER cc_start: 0.9155 (t) cc_final: 0.8899 (p) REVERT: A 204 MET cc_start: 0.8086 (mtp) cc_final: 0.7822 (mtp) REVERT: A 213 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6969 (tptp) REVERT: B 20 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7929 (mtm110) REVERT: B 40 THR cc_start: 0.9195 (m) cc_final: 0.8805 (p) REVERT: B 342 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7278 (mmm-85) REVERT: B 356 GLU cc_start: 0.8146 (mp0) cc_final: 0.7823 (mp0) REVERT: B 366 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7240 (ptm-80) REVERT: C 22 GLN cc_start: 0.8737 (tt0) cc_final: 0.8486 (tt0) REVERT: C 303 ASP cc_start: 0.8561 (t0) cc_final: 0.8081 (t0) REVERT: C 312 VAL cc_start: 0.8904 (m) cc_final: 0.8563 (t) REVERT: E 52 SER cc_start: 0.8971 (m) cc_final: 0.8717 (t) REVERT: E 69 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6876 (p) REVERT: E 80 TYR cc_start: 0.8080 (m-80) cc_final: 0.7814 (m-80) REVERT: E 112 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7393 (m) outliers start: 32 outliers final: 18 residues processed: 227 average time/residue: 0.1868 time to fit residues: 57.5155 Evaluate side-chains 216 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 ASN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8193 Z= 0.195 Angle : 0.537 6.343 11100 Z= 0.291 Chirality : 0.042 0.153 1267 Planarity : 0.003 0.040 1418 Dihedral : 4.716 38.532 1124 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.80 % Allowed : 17.15 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1008 helix: 0.80 (0.27), residues: 375 sheet: -0.49 (0.36), residues: 219 loop : -2.23 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.013 0.001 PHE E 108 TYR 0.011 0.001 TYR A 100 ARG 0.002 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9203 (t) cc_final: 0.8890 (p) REVERT: A 121 ASP cc_start: 0.8422 (t0) cc_final: 0.8134 (t0) REVERT: A 204 MET cc_start: 0.8058 (mtp) cc_final: 0.7771 (mtp) REVERT: B 20 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7838 (mtm110) REVERT: B 38 ARG cc_start: 0.8032 (mtp180) cc_final: 0.7665 (mtt-85) REVERT: B 40 THR cc_start: 0.9180 (m) cc_final: 0.8781 (p) REVERT: B 329 ASP cc_start: 0.7917 (m-30) cc_final: 0.7649 (m-30) REVERT: B 342 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7314 (mmm-85) REVERT: B 356 GLU cc_start: 0.8182 (mp0) cc_final: 0.7793 (mp0) REVERT: B 366 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7285 (ptm-80) REVERT: C 22 GLN cc_start: 0.8691 (tt0) cc_final: 0.8454 (tt0) REVERT: C 175 ASP cc_start: 0.7898 (t0) cc_final: 0.7575 (t0) REVERT: C 180 GLN cc_start: 0.8737 (mp10) cc_final: 0.8508 (mp10) REVERT: C 303 ASP cc_start: 0.8555 (t0) cc_final: 0.8092 (t0) REVERT: C 312 VAL cc_start: 0.8978 (m) cc_final: 0.8637 (t) REVERT: E 52 SER cc_start: 0.8959 (m) cc_final: 0.8738 (t) REVERT: E 69 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6921 (p) REVERT: E 80 TYR cc_start: 0.8088 (m-80) cc_final: 0.7880 (m-80) outliers start: 33 outliers final: 23 residues processed: 211 average time/residue: 0.1822 time to fit residues: 53.3894 Evaluate side-chains 209 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN C 242 ASN C 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8193 Z= 0.212 Angle : 0.536 6.308 11100 Z= 0.289 Chirality : 0.042 0.140 1267 Planarity : 0.003 0.040 1418 Dihedral : 4.577 30.920 1122 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.72 % Allowed : 17.38 % Favored : 77.91 % 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: -0.96 (0.26), residues: 1008 helix: 0.91 (0.28), residues: 375 sheet: -0.44 (0.36), residues: 221 loop : -2.26 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.014 0.002 PHE E 108 TYR 0.013 0.001 TYR A 100 ARG 0.006 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9187 (t) cc_final: 0.8840 (p) REVERT: A 121 ASP cc_start: 0.8418 (t0) cc_final: 0.8118 (t0) REVERT: A 204 MET cc_start: 0.8062 (mtp) cc_final: 0.7800 (mtp) REVERT: B 20 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7839 (mtm110) REVERT: B 40 THR cc_start: 0.9141 (m) cc_final: 0.8712 (p) REVERT: B 329 ASP cc_start: 0.7952 (m-30) cc_final: 0.7641 (m-30) REVERT: B 342 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7342 (mmm-85) REVERT: B 356 GLU cc_start: 0.8135 (mp0) cc_final: 0.7748 (mp0) REVERT: B 366 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7298 (ptm-80) REVERT: C 22 GLN cc_start: 0.8670 (tt0) cc_final: 0.8446 (tt0) REVERT: C 54 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7846 (mmt90) REVERT: C 175 ASP cc_start: 0.7914 (t0) cc_final: 0.7544 (t0) REVERT: C 303 ASP cc_start: 0.8524 (t0) cc_final: 0.8025 (t0) REVERT: C 312 VAL cc_start: 0.8966 (m) cc_final: 0.8631 (t) REVERT: E 52 SER cc_start: 0.8963 (m) cc_final: 0.8739 (t) REVERT: E 69 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6925 (p) outliers start: 41 outliers final: 31 residues processed: 213 average time/residue: 0.1812 time to fit residues: 53.1952 Evaluate side-chains 219 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8193 Z= 0.289 Angle : 0.579 6.599 11100 Z= 0.313 Chirality : 0.043 0.186 1267 Planarity : 0.004 0.041 1418 Dihedral : 4.821 36.809 1122 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.52 % Allowed : 17.95 % Favored : 76.52 % 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: -0.98 (0.26), residues: 1008 helix: 0.89 (0.28), residues: 374 sheet: -0.27 (0.37), residues: 215 loop : -2.35 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.015 0.002 PHE A 260 TYR 0.016 0.002 TYR E 95 ARG 0.004 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9201 (t) cc_final: 0.8855 (p) REVERT: A 121 ASP cc_start: 0.8382 (t0) cc_final: 0.8068 (t0) REVERT: A 204 MET cc_start: 0.8084 (mtp) cc_final: 0.7808 (mtp) REVERT: B 20 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7849 (mtm110) REVERT: B 40 THR cc_start: 0.9135 (m) cc_final: 0.8704 (p) REVERT: B 342 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7366 (mmm-85) REVERT: B 356 GLU cc_start: 0.8045 (mp0) cc_final: 0.7633 (mp0) REVERT: B 366 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7228 (ptm-80) REVERT: C 22 GLN cc_start: 0.8685 (tt0) cc_final: 0.8452 (tt0) REVERT: C 54 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.8081 (mmt90) REVERT: C 178 THR cc_start: 0.8116 (m) cc_final: 0.7902 (m) REVERT: C 264 GLN cc_start: 0.8444 (pt0) cc_final: 0.7800 (mt0) REVERT: C 303 ASP cc_start: 0.8537 (t0) cc_final: 0.8030 (t0) REVERT: E 69 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6982 (p) outliers start: 48 outliers final: 40 residues processed: 217 average time/residue: 0.1973 time to fit residues: 58.8621 Evaluate side-chains 227 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.0670 chunk 86 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8193 Z= 0.154 Angle : 0.504 7.738 11100 Z= 0.271 Chirality : 0.041 0.136 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.445 32.812 1122 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.03 % Allowed : 20.14 % Favored : 75.83 % 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: -0.82 (0.27), residues: 1008 helix: 1.08 (0.28), residues: 374 sheet: -0.23 (0.36), residues: 220 loop : -2.32 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.002 0.001 HIS C 147 PHE 0.011 0.001 PHE A 249 TYR 0.014 0.001 TYR A 256 ARG 0.008 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 SER cc_start: 0.9193 (t) cc_final: 0.8840 (p) REVERT: A 121 ASP cc_start: 0.8308 (t0) cc_final: 0.8021 (t0) REVERT: A 204 MET cc_start: 0.8037 (mtp) cc_final: 0.7824 (mtp) REVERT: A 213 LYS cc_start: 0.7828 (ttpt) cc_final: 0.6958 (tptt) REVERT: B 20 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7834 (mtm110) REVERT: B 40 THR cc_start: 0.9071 (m) cc_final: 0.8663 (p) REVERT: B 329 ASP cc_start: 0.7975 (m-30) cc_final: 0.7575 (m-30) REVERT: B 342 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7349 (mmm-85) REVERT: B 356 GLU cc_start: 0.8041 (mp0) cc_final: 0.7637 (mp0) REVERT: B 366 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7253 (ptm-80) REVERT: C 22 GLN cc_start: 0.8635 (tt0) cc_final: 0.8411 (tt0) REVERT: C 54 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.8091 (mmt90) REVERT: C 175 ASP cc_start: 0.8030 (t70) cc_final: 0.7550 (t0) REVERT: C 264 GLN cc_start: 0.8490 (pt0) cc_final: 0.8031 (mt0) REVERT: C 303 ASP cc_start: 0.8488 (t0) cc_final: 0.7994 (t0) REVERT: E 52 SER cc_start: 0.8936 (m) cc_final: 0.8701 (t) REVERT: E 69 THR cc_start: 0.7034 (OUTLIER) cc_final: 0.6767 (p) outliers start: 35 outliers final: 28 residues processed: 208 average time/residue: 0.1720 time to fit residues: 49.8389 Evaluate side-chains 218 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 41 ASN C 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8193 Z= 0.148 Angle : 0.498 6.591 11100 Z= 0.265 Chirality : 0.040 0.136 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.163 23.962 1122 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.49 % Allowed : 20.02 % Favored : 75.49 % 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: -0.71 (0.27), residues: 1008 helix: 1.20 (0.28), residues: 374 sheet: -0.17 (0.36), residues: 221 loop : -2.28 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 220 HIS 0.002 0.001 HIS C 188 PHE 0.012 0.001 PHE A 249 TYR 0.013 0.001 TYR A 100 ARG 0.008 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9186 (t) cc_final: 0.8818 (p) REVERT: A 119 SER cc_start: 0.8356 (t) cc_final: 0.8140 (p) REVERT: A 121 ASP cc_start: 0.8360 (t0) cc_final: 0.8096 (t0) REVERT: A 213 LYS cc_start: 0.7812 (mtpt) cc_final: 0.6962 (tptt) REVERT: B 20 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7816 (mtm110) REVERT: B 21 GLU cc_start: 0.8125 (tt0) cc_final: 0.7775 (mm-30) REVERT: B 38 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7429 (mtt-85) REVERT: B 40 THR cc_start: 0.9043 (m) cc_final: 0.8660 (p) REVERT: B 342 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7335 (mmm-85) REVERT: B 356 GLU cc_start: 0.8014 (mp0) cc_final: 0.7618 (mp0) REVERT: B 366 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7255 (ptm-80) REVERT: C 54 ARG cc_start: 0.8447 (tpp-160) cc_final: 0.8048 (mmt90) REVERT: C 303 ASP cc_start: 0.8491 (t0) cc_final: 0.8014 (t0) REVERT: E 52 SER cc_start: 0.8912 (m) cc_final: 0.8706 (t) REVERT: E 69 THR cc_start: 0.7021 (OUTLIER) cc_final: 0.6749 (p) outliers start: 39 outliers final: 33 residues processed: 205 average time/residue: 0.1765 time to fit residues: 50.3419 Evaluate side-chains 217 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8193 Z= 0.184 Angle : 0.528 7.198 11100 Z= 0.281 Chirality : 0.041 0.137 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.279 27.002 1122 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.60 % Allowed : 20.37 % Favored : 75.03 % 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: -0.75 (0.26), residues: 1008 helix: 1.15 (0.28), residues: 374 sheet: -0.11 (0.36), residues: 220 loop : -2.35 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS C 188 PHE 0.013 0.001 PHE A 249 TYR 0.013 0.001 TYR A 256 ARG 0.007 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9197 (t) cc_final: 0.8827 (p) REVERT: A 119 SER cc_start: 0.8380 (t) cc_final: 0.8178 (p) REVERT: A 121 ASP cc_start: 0.8326 (t0) cc_final: 0.8061 (t0) REVERT: A 213 LYS cc_start: 0.7817 (mtpt) cc_final: 0.6950 (tptt) REVERT: B 20 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7820 (mtm110) REVERT: B 21 GLU cc_start: 0.8130 (tt0) cc_final: 0.7776 (mm-30) REVERT: B 38 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7489 (mtt-85) REVERT: B 40 THR cc_start: 0.9037 (m) cc_final: 0.8647 (p) REVERT: B 342 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7347 (mmm-85) REVERT: B 356 GLU cc_start: 0.7998 (mp0) cc_final: 0.7586 (mp0) REVERT: B 366 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7259 (ptm-80) REVERT: C 47 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7591 (ttp-110) REVERT: C 54 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.8009 (mmt90) REVERT: C 175 ASP cc_start: 0.8074 (t70) cc_final: 0.7556 (t0) REVERT: C 303 ASP cc_start: 0.8480 (t0) cc_final: 0.8020 (t0) REVERT: E 52 SER cc_start: 0.8926 (m) cc_final: 0.8714 (t) REVERT: E 69 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6787 (p) outliers start: 40 outliers final: 35 residues processed: 204 average time/residue: 0.1868 time to fit residues: 53.0932 Evaluate side-chains 218 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.0060 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8193 Z= 0.209 Angle : 0.544 6.897 11100 Z= 0.290 Chirality : 0.041 0.152 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.363 28.361 1122 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.06 % Allowed : 20.14 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.26), residues: 1008 helix: 1.10 (0.28), residues: 374 sheet: -0.14 (0.36), residues: 220 loop : -2.35 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS C 147 PHE 0.013 0.001 PHE A 249 TYR 0.015 0.001 TYR A 256 ARG 0.007 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 0.969 Fit side-chains REVERT: A 81 SER cc_start: 0.9203 (t) cc_final: 0.8836 (p) REVERT: A 121 ASP cc_start: 0.8304 (t0) cc_final: 0.8028 (t0) REVERT: B 20 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7834 (mtm110) REVERT: B 38 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7506 (mtt-85) REVERT: B 40 THR cc_start: 0.9047 (m) cc_final: 0.8654 (p) REVERT: B 329 ASP cc_start: 0.7985 (m-30) cc_final: 0.7551 (m-30) REVERT: B 342 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7373 (mmm-85) REVERT: B 356 GLU cc_start: 0.7947 (mp0) cc_final: 0.7505 (mp0) REVERT: B 366 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7265 (ptm-80) REVERT: C 54 ARG cc_start: 0.8408 (tpp-160) cc_final: 0.8018 (mmt90) REVERT: C 175 ASP cc_start: 0.8075 (t70) cc_final: 0.7571 (t0) REVERT: C 303 ASP cc_start: 0.8493 (t0) cc_final: 0.8021 (t0) REVERT: E 52 SER cc_start: 0.8936 (m) cc_final: 0.8730 (t) REVERT: E 69 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6771 (p) outliers start: 44 outliers final: 37 residues processed: 204 average time/residue: 0.1867 time to fit residues: 52.0007 Evaluate side-chains 209 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS C 41 ASN C 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8193 Z= 0.155 Angle : 0.513 5.732 11100 Z= 0.275 Chirality : 0.040 0.147 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.243 26.384 1122 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.14 % Allowed : 20.83 % Favored : 75.03 % 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: -0.71 (0.26), residues: 1008 helix: 1.18 (0.28), residues: 374 sheet: -0.12 (0.36), residues: 220 loop : -2.30 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 220 HIS 0.003 0.001 HIS C 316 PHE 0.011 0.001 PHE A 249 TYR 0.013 0.001 TYR A 256 ARG 0.007 0.000 ARG B 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 0.832 Fit side-chains REVERT: A 81 SER cc_start: 0.9175 (t) cc_final: 0.8797 (p) REVERT: A 121 ASP cc_start: 0.8312 (t0) cc_final: 0.8061 (t0) REVERT: A 213 LYS cc_start: 0.7789 (mtpt) cc_final: 0.6942 (tptt) REVERT: B 20 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7756 (mtm180) REVERT: B 38 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7476 (mtt-85) REVERT: B 40 THR cc_start: 0.9031 (m) cc_final: 0.8648 (p) REVERT: B 342 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7281 (mmm-85) REVERT: B 366 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7269 (ptm-80) REVERT: C 54 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.7982 (mmt90) REVERT: C 303 ASP cc_start: 0.8469 (t0) cc_final: 0.8001 (t0) REVERT: E 52 SER cc_start: 0.8900 (m) cc_final: 0.8687 (t) REVERT: E 69 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6697 (p) outliers start: 36 outliers final: 33 residues processed: 195 average time/residue: 0.1769 time to fit residues: 47.7430 Evaluate side-chains 204 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0000 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS B 225 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.167690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.127914 restraints weight = 9732.261| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.60 r_work: 0.3059 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8193 Z= 0.168 Angle : 0.519 5.755 11100 Z= 0.278 Chirality : 0.041 0.144 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.216 27.263 1122 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.14 % Allowed : 21.40 % Favored : 74.45 % 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: -0.70 (0.26), residues: 1008 helix: 1.21 (0.28), residues: 374 sheet: -0.14 (0.36), residues: 222 loop : -2.30 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.005 0.001 HIS B 343 PHE 0.012 0.001 PHE A 249 TYR 0.014 0.001 TYR A 256 ARG 0.007 0.000 ARG B 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.18 seconds wall clock time: 38 minutes 20.68 seconds (2300.68 seconds total)