Starting phenix.real_space_refine on Sat Apr 6 10:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/04_2024/8pok_17793_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/04_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_17793/04_2024/8pok_17793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/04_2024/8pok_17793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/04_2024/8pok_17793_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pok_17793/04_2024/8pok_17793_updated.pdb" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.02, per 1000 atoms: 0.62 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: 3.01 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... running ksdssp... Secondary structure from input PDB file: 24 helices and 10 sheets defined 34.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 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 58 through 69 removed outlier: 3.721A pdb=" N CYS A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE A 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 64 " --> pdb=" O CYS A 61 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 94 through 127 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 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 138 through 160 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) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 198 through 215 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 217 through 223 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) No H-bonds generated for 'chain 'A' and resid 217 through 223' Processing helix chain 'A' and resid 238 through 265 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 276 through 295 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 10 through 38 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 220 through 223 removed outlier: 3.658A pdb=" N CYS B 223 " --> pdb=" O TRP B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.691A pdb=" N LYS B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 318 through 336 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) Processing helix chain 'B' and resid 358 through 376 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) Processing helix chain 'C' and resid 8 through 30 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) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'D' and resid 5 through 24 removed outlier: 3.915A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 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 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 204 through 209 removed outlier: 7.134A pdb=" N ALA B 229 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU B 46 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 231 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER B 272 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE B 232 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 274 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing sheet with id= B, 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= C, 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: 3.929A pdb=" N HIS C 96 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP C 88 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 94 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing sheet with id= D, 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: 3.868A pdb=" N ARG C 142 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN C 130 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 140 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 151 through 156 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: 3.684A pdb=" N CYS C 171 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C 183 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP C 175 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN C 181 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 225 through 228 removed outlier: 4.022A pdb=" N GLN C 225 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 204 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 234 through 239 removed outlier: 6.935A pdb=" N GLY C 249 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 237 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA C 247 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE C 239 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA C 245 " --> pdb=" O PHE C 239 " (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= H, 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= I, 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= J, first strand: chain 'E' and resid 122 through 124 removed outlier: 4.545A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 51 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 804 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: 2.42 Time building geometry restraints manager: 3.20 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: 169 2.67 - 3.23: 7281 3.23 - 3.79: 10810 3.79 - 4.34: 15024 4.34 - 4.90: 25205 Nonbonded interactions: 58489 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 58484 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: 1.230 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: 5.460 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.580 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- 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= 0.488 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 : 0.955 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: 0.2229 time to fit residues: 78.2950 Evaluate side-chains 213 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 209 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 E 3 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8193 Z= 0.196 Angle : 0.552 6.320 11100 Z= 0.303 Chirality : 0.042 0.153 1267 Planarity : 0.004 0.037 1418 Dihedral : 5.340 52.679 1128 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.14 % Allowed : 12.89 % Favored : 82.97 % 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: -1.49 (0.25), residues: 1008 helix: 0.40 (0.27), residues: 353 sheet: -0.74 (0.36), residues: 210 loop : -2.28 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 220 HIS 0.004 0.001 HIS C 96 PHE 0.015 0.002 PHE E 108 TYR 0.009 0.001 TYR E 95 ARG 0.003 0.000 ARG C 142 *********************** 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 245 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 0.896 Fit side-chains REVERT: A 121 ASP cc_start: 0.8428 (t0) cc_final: 0.8007 (t0) REVERT: A 131 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7516 (mtt180) REVERT: A 204 MET cc_start: 0.8099 (mtp) cc_final: 0.7832 (mtp) REVERT: A 213 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7070 (tptt) REVERT: B 20 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7948 (mtm110) REVERT: B 38 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7686 (mtt90) REVERT: B 40 THR cc_start: 0.9261 (m) cc_final: 0.8840 (p) REVERT: B 342 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7303 (mmm-85) REVERT: B 356 GLU cc_start: 0.8081 (mp0) cc_final: 0.7800 (mp0) REVERT: B 366 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7220 (ptm-80) REVERT: C 22 GLN cc_start: 0.8749 (tt0) cc_final: 0.8501 (tt0) REVERT: C 303 ASP cc_start: 0.8562 (t0) cc_final: 0.8226 (t70) REVERT: C 312 VAL cc_start: 0.8946 (m) cc_final: 0.8612 (t) REVERT: E 52 SER cc_start: 0.8990 (m) cc_final: 0.8754 (t) REVERT: E 69 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6895 (p) REVERT: E 80 TYR cc_start: 0.8124 (m-80) cc_final: 0.7917 (m-80) REVERT: E 83 MET cc_start: 0.6952 (mtt) cc_final: 0.6746 (mtp) REVERT: E 112 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7480 (m) outliers start: 36 outliers final: 22 residues processed: 224 average time/residue: 0.1996 time to fit residues: 60.7298 Evaluate side-chains 216 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 99 ILE 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 36 VAL 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 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: 1.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8193 Z= 0.280 Angle : 0.592 7.358 11100 Z= 0.320 Chirality : 0.043 0.148 1267 Planarity : 0.004 0.040 1418 Dihedral : 5.179 43.837 1124 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.72 % Allowed : 15.65 % Favored : 79.63 % 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: -1.43 (0.25), residues: 1008 helix: 0.45 (0.28), residues: 354 sheet: -0.48 (0.37), residues: 201 loop : -2.37 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.005 0.001 HIS C 147 PHE 0.016 0.002 PHE A 260 TYR 0.015 0.002 TYR E 95 ARG 0.005 0.000 ARG C 54 *********************** 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 240 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 0.951 Fit side-chains REVERT: A 78 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 121 ASP cc_start: 0.8422 (t0) cc_final: 0.8062 (t0) REVERT: A 131 ARG cc_start: 0.7838 (mtm180) cc_final: 0.7525 (mtt180) REVERT: A 204 MET cc_start: 0.8081 (mtp) cc_final: 0.7788 (mtp) REVERT: B 20 ARG cc_start: 0.8170 (mtm180) cc_final: 0.7861 (mtm110) REVERT: B 38 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7779 (mtt-85) REVERT: B 40 THR cc_start: 0.9271 (m) cc_final: 0.8811 (p) REVERT: B 202 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8073 (mmtp) REVERT: B 342 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7356 (mmm-85) REVERT: B 356 GLU cc_start: 0.8119 (mp0) cc_final: 0.7798 (mp0) REVERT: B 366 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7219 (ptm-80) REVERT: C 22 GLN cc_start: 0.8705 (tt0) cc_final: 0.8459 (tt0) REVERT: C 157 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7771 (mp) REVERT: C 175 ASP cc_start: 0.8053 (t0) cc_final: 0.7442 (t70) REVERT: C 180 GLN cc_start: 0.8659 (mp10) cc_final: 0.8434 (mp10) REVERT: C 303 ASP cc_start: 0.8568 (t0) cc_final: 0.8157 (t70) REVERT: E 52 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8770 (t) REVERT: E 69 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6938 (p) outliers start: 41 outliers final: 30 residues processed: 223 average time/residue: 0.1937 time to fit residues: 58.8302 Evaluate side-chains 224 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 36 VAL 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 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 157 LEU 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 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 7 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 ASN C 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8193 Z= 0.233 Angle : 0.551 6.324 11100 Z= 0.297 Chirality : 0.042 0.166 1267 Planarity : 0.004 0.041 1418 Dihedral : 4.925 39.069 1122 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 5.06 % Allowed : 17.03 % 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: -1.36 (0.26), residues: 1008 helix: 0.65 (0.28), residues: 348 sheet: -0.37 (0.38), residues: 201 loop : -2.46 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.004 0.001 HIS C 147 PHE 0.013 0.002 PHE A 249 TYR 0.014 0.001 TYR A 256 ARG 0.005 0.000 ARG C 54 *********************** 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 243 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 0.957 Fit side-chains REVERT: A 121 ASP cc_start: 0.8466 (t0) cc_final: 0.8083 (t0) REVERT: A 131 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7628 (mtt180) REVERT: A 204 MET cc_start: 0.8057 (mtp) cc_final: 0.7838 (mtp) REVERT: B 20 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7821 (mtm110) REVERT: B 40 THR cc_start: 0.9254 (m) cc_final: 0.8791 (p) REVERT: B 202 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7996 (mmtp) REVERT: B 342 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7355 (mmm-85) REVERT: B 356 GLU cc_start: 0.7946 (mp0) cc_final: 0.7670 (mp0) REVERT: B 366 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7231 (ptm-80) REVERT: C 22 GLN cc_start: 0.8697 (tt0) cc_final: 0.8458 (tt0) REVERT: C 54 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.7994 (mmt90) REVERT: C 157 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7581 (mp) REVERT: C 175 ASP cc_start: 0.8040 (t0) cc_final: 0.7709 (t0) REVERT: C 180 GLN cc_start: 0.8683 (mp10) cc_final: 0.8470 (mp10) REVERT: C 303 ASP cc_start: 0.8550 (t0) cc_final: 0.8133 (t70) REVERT: D 47 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: E 52 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8744 (t) REVERT: E 69 THR cc_start: 0.7142 (OUTLIER) cc_final: 0.6893 (p) outliers start: 44 outliers final: 33 residues processed: 223 average time/residue: 0.2086 time to fit residues: 62.8848 Evaluate side-chains 230 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 207 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 36 VAL 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 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 157 LEU 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 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 47 GLU 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 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=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: 0.7980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 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 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2989 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= 0.273 Angle : 0.581 7.146 11100 Z= 0.311 Chirality : 0.043 0.172 1267 Planarity : 0.004 0.042 1418 Dihedral : 4.981 39.104 1122 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 5.64 % Allowed : 17.49 % Favored : 76.87 % 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: -1.39 (0.26), residues: 1008 helix: 0.59 (0.28), residues: 353 sheet: -0.35 (0.38), residues: 201 loop : -2.50 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.004 0.001 HIS C 147 PHE 0.015 0.002 PHE A 260 TYR 0.016 0.001 TYR A 256 ARG 0.008 0.000 ARG B 266 *********************** 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 244 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 121 ASP cc_start: 0.8414 (t0) cc_final: 0.8046 (t0) REVERT: A 131 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7586 (mtt180) REVERT: B 20 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7903 (mtm110) REVERT: B 40 THR cc_start: 0.9239 (m) cc_final: 0.8758 (p) REVERT: B 202 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7932 (mmtp) REVERT: B 342 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7399 (mmm-85) REVERT: B 356 GLU cc_start: 0.7899 (mp0) cc_final: 0.7607 (mp0) REVERT: B 366 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7527 (ttp80) REVERT: C 22 GLN cc_start: 0.8701 (tt0) cc_final: 0.8462 (tt0) REVERT: C 54 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8084 (mmt90) REVERT: C 157 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7612 (mp) REVERT: C 175 ASP cc_start: 0.8029 (t0) cc_final: 0.7688 (t0) REVERT: C 180 GLN cc_start: 0.8759 (mp10) cc_final: 0.8550 (mp10) REVERT: C 303 ASP cc_start: 0.8539 (t0) cc_final: 0.8111 (t70) REVERT: D 47 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: E 69 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6879 (p) outliers start: 49 outliers final: 38 residues processed: 223 average time/residue: 0.1851 time to fit residues: 56.5721 Evaluate side-chains 235 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 193 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 102 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 186 GLU 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 36 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 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 157 LEU 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 26 ASP Chi-restraints excluded: chain D residue 47 GLU 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 Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 ASN C 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3190 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 : 0.504 5.554 11100 Z= 0.270 Chirality : 0.041 0.164 1267 Planarity : 0.003 0.044 1418 Dihedral : 4.472 30.115 1122 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.37 % Allowed : 18.76 % Favored : 76.87 % 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: -1.11 (0.26), residues: 1008 helix: 0.91 (0.28), residues: 351 sheet: -0.20 (0.38), residues: 203 loop : -2.41 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.003 0.001 HIS C 96 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 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 233 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 0.881 Fit side-chains REVERT: A 78 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 121 ASP cc_start: 0.8437 (t0) cc_final: 0.8098 (t0) REVERT: A 131 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7629 (mtt180) REVERT: A 213 LYS cc_start: 0.7815 (mtpt) cc_final: 0.6960 (tptt) REVERT: A 294 TYR cc_start: 0.8212 (m-80) cc_final: 0.7912 (m-80) REVERT: B 20 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7737 (mtm180) REVERT: B 40 THR cc_start: 0.9209 (m) cc_final: 0.8733 (p) REVERT: B 329 ASP cc_start: 0.7972 (m-30) cc_final: 0.7604 (m-30) REVERT: B 342 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7354 (mmm-85) REVERT: B 356 GLU cc_start: 0.7867 (mp0) cc_final: 0.7570 (mp0) REVERT: B 366 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7255 (ptm-80) REVERT: C 22 GLN cc_start: 0.8645 (tt0) cc_final: 0.8429 (tt0) REVERT: C 54 ARG cc_start: 0.8223 (mmt-90) cc_final: 0.7951 (mmt90) REVERT: C 157 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7421 (mp) REVERT: C 180 GLN cc_start: 0.8716 (mp10) cc_final: 0.8513 (mp10) REVERT: C 303 ASP cc_start: 0.8489 (t0) cc_final: 0.7984 (t0) outliers start: 38 outliers final: 29 residues processed: 218 average time/residue: 0.1802 time to fit residues: 53.8637 Evaluate side-chains 224 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 275 LEU Chi-restraints excluded: chain B residue 9 THR 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 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 157 LEU Chi-restraints excluded: chain C residue 182 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 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 112 SER Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8193 Z= 0.148 Angle : 0.509 7.174 11100 Z= 0.269 Chirality : 0.041 0.133 1267 Planarity : 0.003 0.044 1418 Dihedral : 4.280 27.081 1122 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.60 % Allowed : 19.33 % Favored : 76.06 % 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: -0.99 (0.26), residues: 1008 helix: 1.02 (0.29), residues: 351 sheet: -0.05 (0.39), residues: 195 loop : -2.36 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 220 HIS 0.003 0.001 HIS C 188 PHE 0.012 0.001 PHE A 249 TYR 0.013 0.001 TYR A 256 ARG 0.006 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 226 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 121 ASP cc_start: 0.8334 (t0) cc_final: 0.8049 (t0) REVERT: A 131 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7634 (mtt180) REVERT: A 213 LYS cc_start: 0.7778 (mtpt) cc_final: 0.6936 (tptt) REVERT: B 20 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7737 (mtm180) REVERT: B 40 THR cc_start: 0.9185 (m) cc_final: 0.8702 (p) REVERT: B 329 ASP cc_start: 0.7982 (m-30) cc_final: 0.7561 (m-30) REVERT: B 342 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7357 (mmm-85) REVERT: B 344 TYR cc_start: 0.9078 (m-80) cc_final: 0.8798 (m-80) REVERT: B 356 GLU cc_start: 0.7841 (mp0) cc_final: 0.7507 (mp0) REVERT: B 366 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7204 (ptm-80) REVERT: C 54 ARG cc_start: 0.8231 (mmt-90) cc_final: 0.7938 (mmt90) REVERT: C 157 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7374 (mp) REVERT: C 303 ASP cc_start: 0.8477 (t0) cc_final: 0.7995 (t0) REVERT: E 69 THR cc_start: 0.6979 (OUTLIER) cc_final: 0.6699 (p) outliers start: 40 outliers final: 29 residues processed: 210 average time/residue: 0.1924 time to fit residues: 55.5202 Evaluate side-chains 216 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 210 VAL Chi-restraints excluded: chain B residue 234 VAL 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 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 157 LEU 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 316 HIS Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU 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 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.0000 chunk 91 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS C 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8193 Z= 0.132 Angle : 0.495 6.569 11100 Z= 0.262 Chirality : 0.040 0.133 1267 Planarity : 0.003 0.044 1418 Dihedral : 4.059 22.299 1122 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.80 % Allowed : 20.94 % Favored : 75.26 % 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: -0.88 (0.26), residues: 1008 helix: 1.11 (0.28), residues: 352 sheet: 0.04 (0.38), residues: 209 loop : -2.38 (0.26), residues: 447 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 0.011 0.001 PHE A 249 TYR 0.012 0.001 TYR A 256 ARG 0.006 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: 33 poor density : 189 time to evaluate : 0.965 Fit side-chains REVERT: A 78 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8210 (tt) REVERT: A 121 ASP cc_start: 0.8352 (t0) cc_final: 0.8075 (t0) REVERT: A 131 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7621 (mtt180) REVERT: A 143 ILE cc_start: 0.8336 (tt) cc_final: 0.8125 (mt) REVERT: A 213 LYS cc_start: 0.7722 (mtpt) cc_final: 0.6919 (tptt) REVERT: B 20 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7721 (mtm180) REVERT: B 40 THR cc_start: 0.9170 (m) cc_final: 0.8694 (p) REVERT: B 329 ASP cc_start: 0.7977 (m-30) cc_final: 0.7541 (m-30) REVERT: B 342 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7289 (mmm-85) REVERT: B 344 TYR cc_start: 0.9065 (m-80) cc_final: 0.8796 (m-80) REVERT: B 356 GLU cc_start: 0.7792 (mp0) cc_final: 0.7455 (mp0) REVERT: B 366 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7184 (ptm-80) REVERT: C 267 MET cc_start: 0.8026 (tpp) cc_final: 0.7790 (mmt) REVERT: C 303 ASP cc_start: 0.8453 (t0) cc_final: 0.7978 (t0) REVERT: E 69 THR cc_start: 0.6911 (OUTLIER) cc_final: 0.6630 (p) outliers start: 33 outliers final: 28 residues processed: 206 average time/residue: 0.1973 time to fit residues: 55.2809 Evaluate side-chains 219 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 36 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 234 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 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 291 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU 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 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8193 Z= 0.168 Angle : 0.524 6.266 11100 Z= 0.278 Chirality : 0.041 0.136 1267 Planarity : 0.003 0.044 1418 Dihedral : 4.163 25.848 1122 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.03 % Allowed : 21.06 % Favored : 74.91 % 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: -0.88 (0.26), residues: 1008 helix: 1.12 (0.29), residues: 352 sheet: -0.00 (0.38), residues: 211 loop : -2.39 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 220 HIS 0.006 0.001 HIS B 343 PHE 0.012 0.001 PHE A 249 TYR 0.018 0.001 TYR A 256 ARG 0.006 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: 35 poor density : 187 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8243 (tt) REVERT: A 121 ASP cc_start: 0.8312 (t0) cc_final: 0.8037 (t0) REVERT: A 131 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7632 (mtt180) REVERT: A 185 ASN cc_start: 0.8876 (p0) cc_final: 0.8410 (p0) REVERT: A 213 LYS cc_start: 0.7755 (mtpt) cc_final: 0.6941 (tptt) REVERT: B 20 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7715 (mtm180) REVERT: B 40 THR cc_start: 0.9189 (m) cc_final: 0.8698 (p) REVERT: B 329 ASP cc_start: 0.7984 (m-30) cc_final: 0.7547 (m-30) REVERT: B 342 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7327 (mmm-85) REVERT: B 344 TYR cc_start: 0.9068 (m-80) cc_final: 0.8806 (m-80) REVERT: B 356 GLU cc_start: 0.7810 (mp0) cc_final: 0.7466 (mp0) REVERT: B 366 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7198 (ptm-80) REVERT: C 303 ASP cc_start: 0.8471 (t0) cc_final: 0.7988 (t0) REVERT: E 69 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6674 (p) outliers start: 35 outliers final: 30 residues processed: 205 average time/residue: 0.1848 time to fit residues: 51.9869 Evaluate side-chains 218 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 36 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 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 52 THR 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 279 THR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU 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 79 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8193 Z= 0.208 Angle : 0.560 7.555 11100 Z= 0.296 Chirality : 0.042 0.139 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.372 27.362 1122 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.26 % Allowed : 20.71 % 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: -0.96 (0.26), residues: 1008 helix: 1.07 (0.29), residues: 351 sheet: -0.08 (0.40), residues: 197 loop : -2.35 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 87 HIS 0.006 0.001 HIS B 343 PHE 0.013 0.001 PHE A 249 TYR 0.015 0.001 TYR A 256 ARG 0.005 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 225 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 121 ASP cc_start: 0.8265 (t0) cc_final: 0.7964 (t0) REVERT: A 131 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7614 (mtt180) REVERT: A 213 LYS cc_start: 0.7803 (mtpt) cc_final: 0.6869 (mmtt) REVERT: B 20 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7740 (mtm180) REVERT: B 40 THR cc_start: 0.9208 (m) cc_final: 0.8724 (p) REVERT: B 342 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7350 (mmm-85) REVERT: B 344 TYR cc_start: 0.9065 (m-80) cc_final: 0.8791 (m-80) REVERT: B 356 GLU cc_start: 0.7834 (mp0) cc_final: 0.7458 (mp0) REVERT: B 366 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7250 (ptm-80) REVERT: C 47 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7548 (ttp-110) REVERT: C 54 ARG cc_start: 0.8209 (mmt-90) cc_final: 0.7896 (mmt90) REVERT: C 303 ASP cc_start: 0.8481 (t0) cc_final: 0.8017 (t0) REVERT: E 69 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6765 (p) outliers start: 37 outliers final: 32 residues processed: 207 average time/residue: 0.2066 time to fit residues: 58.4892 Evaluate side-chains 218 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 36 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 234 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 50 MET Chi-restraints excluded: chain C residue 52 THR 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 291 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU 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 79 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN C 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.167595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.128085 restraints weight = 9682.356| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.68 r_work: 0.3035 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8193 Z= 0.167 Angle : 0.536 8.255 11100 Z= 0.283 Chirality : 0.041 0.138 1267 Planarity : 0.003 0.044 1418 Dihedral : 4.223 26.835 1122 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.91 % Allowed : 21.75 % Favored : 74.34 % 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: -0.92 (0.26), residues: 1008 helix: 1.14 (0.29), residues: 351 sheet: -0.11 (0.39), residues: 205 loop : -2.37 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 220 HIS 0.005 0.001 HIS B 343 PHE 0.012 0.001 PHE A 249 TYR 0.013 0.001 TYR A 256 ARG 0.005 0.000 ARG B 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.30 seconds wall clock time: 40 minutes 41.24 seconds (2441.24 seconds total)