Starting phenix.real_space_refine on Fri Aug 7 08:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukk_64242/08_2026/9ukk_64242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukk_64242/08_2026/9ukk_64242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukk_64242/08_2026/9ukk_64242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukk_64242/08_2026/9ukk_64242.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukk_64242/08_2026/9ukk_64242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukk_64242/08_2026/9ukk_64242.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.037 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 86 5.16 5 C 12509 2.51 5 N 3558 2.21 5 O 3700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19853 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "D" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2433 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain breaks: 1 Chain: "E" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2386 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Chain: "F" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2225 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 2 Chain: "H" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "G" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2072 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain breaks: 1 Chain: "d" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1531 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 10, 'TRANS': 189} Chain: "I" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2119 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain breaks: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.21 Number of scatterers: 19853 At special positions: 0 Unit cell: (117.264, 140.298, 129.828, 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 86 16.00 O 3700 8.00 N 3558 7.00 C 12509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 750.9 milliseconds 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 50.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 152 through 160 removed outlier: 4.193A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.597A pdb=" N ARG A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.557A pdb=" N HIS B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.554A pdb=" N ARG B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.540A pdb=" N GLU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 241 through 262 Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.701A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.813A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.625A pdb=" N TYR C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.964A pdb=" N ILE C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.281A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.773A pdb=" N ARG C 210 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 4.325A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 238 through 262 removed outlier: 3.785A pdb=" N ILE C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 258 " --> pdb=" O MET C 254 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 removed outlier: 4.191A pdb=" N THR C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.805A pdb=" N PHE C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 4.020A pdb=" N ARG C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.343A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR C 310 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 78 through 89 Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.778A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.683A pdb=" N GLU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 226 " --> pdb=" O HIS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 238 through 262 removed outlier: 4.348A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.617A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 298 removed outlier: 3.672A pdb=" N CYS D 298 " --> pdb=" O LEU D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 298' Processing helix chain 'D' and resid 299 through 315 removed outlier: 4.326A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 327 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.598A pdb=" N GLY E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 76 through 88 removed outlier: 3.896A pdb=" N LEU E 88 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.501A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.057A pdb=" N ILE E 154 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 removed outlier: 3.860A pdb=" N MET E 208 " --> pdb=" O ASN E 204 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 204 through 209' Processing helix chain 'E' and resid 221 through 233 removed outlier: 3.532A pdb=" N ASN E 227 " --> pdb=" O ASP E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 262 removed outlier: 4.253A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 258 " --> pdb=" O MET E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.650A pdb=" N ARG E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.955A pdb=" N ALA E 304 " --> pdb=" O GLU E 300 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 56 through 63 Processing helix chain 'F' and resid 76 through 88 removed outlier: 4.292A pdb=" N HIS F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.558A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 232 Processing helix chain 'F' and resid 241 through 261 Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.561A pdb=" N THR F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 293 removed outlier: 3.660A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 4.099A pdb=" N ALA F 304 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 232 removed outlier: 4.128A pdb=" N ILE H 228 " --> pdb=" O ASN H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 262 removed outlier: 4.035A pdb=" N GLU H 243 " --> pdb=" O ALA H 239 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE H 244 " --> pdb=" O GLU H 240 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 245 " --> pdb=" O GLY H 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN H 246 " --> pdb=" O ARG H 242 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN H 257 " --> pdb=" O ASP H 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA H 258 " --> pdb=" O MET H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 283 removed outlier: 3.762A pdb=" N ALA H 281 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 294 removed outlier: 4.246A pdb=" N LEU H 292 " --> pdb=" O PHE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 313 removed outlier: 3.502A pdb=" N THR H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 4.508A pdb=" N LEU G 334 " --> pdb=" O GLU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 352 removed outlier: 4.135A pdb=" N ARG G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 368 removed outlier: 3.986A pdb=" N VAL G 358 " --> pdb=" O LEU G 354 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY G 359 " --> pdb=" O GLN G 355 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG G 360 " --> pdb=" O GLY G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 428 removed outlier: 3.858A pdb=" N MET G 427 " --> pdb=" O SER G 424 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG G 428 " --> pdb=" O GLY G 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 424 through 428' Processing helix chain 'G' and resid 429 through 444 removed outlier: 4.010A pdb=" N LEU G 442 " --> pdb=" O CYS G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 449 removed outlier: 3.518A pdb=" N CYS G 449 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 474 removed outlier: 3.940A pdb=" N GLU G 470 " --> pdb=" O GLY G 466 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA G 471 " --> pdb=" O GLN G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 511 removed outlier: 3.568A pdb=" N LEU G 506 " --> pdb=" O ARG G 503 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU G 508 " --> pdb=" O ASN G 505 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N MET G 509 " --> pdb=" O LEU G 506 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET G 510 " --> pdb=" O GLY G 507 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 533 removed outlier: 3.594A pdb=" N GLN G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 557 Processing helix chain 'G' and resid 559 through 578 removed outlier: 3.965A pdb=" N LEU G 563 " --> pdb=" O PRO G 559 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 571 " --> pdb=" O LEU G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 620 removed outlier: 3.587A pdb=" N GLU G 613 " --> pdb=" O GLY G 609 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 38 removed outlier: 3.793A pdb=" N GLY d 38 " --> pdb=" O ARG d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 86 removed outlier: 4.359A pdb=" N GLN d 86 " --> pdb=" O MET d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 97 Processing helix chain 'd' and resid 101 through 124 removed outlier: 4.390A pdb=" N ALA d 106 " --> pdb=" O LYS d 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE d 107 " --> pdb=" O GLN d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 143 removed outlier: 4.317A pdb=" N THR d 133 " --> pdb=" O ASP d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 147 Processing helix chain 'd' and resid 155 through 167 removed outlier: 3.963A pdb=" N VAL d 159 " --> pdb=" O LEU d 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER d 160 " --> pdb=" O GLU d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 196 removed outlier: 4.489A pdb=" N ASP d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP d 186 " --> pdb=" O LEU d 182 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA d 193 " --> pdb=" O GLN d 189 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP d 194 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA d 196 " --> pdb=" O SER d 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 197 through 201 removed outlier: 3.742A pdb=" N ASN d 201 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 220 removed outlier: 3.640A pdb=" N ARG d 213 " --> pdb=" O ALA d 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP d 214 " --> pdb=" O ARG d 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 335 removed outlier: 3.556A pdb=" N CYS I 335 " --> pdb=" O THR I 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 332 through 335' Processing helix chain 'I' and resid 340 through 353 removed outlier: 4.280A pdb=" N ARG I 344 " --> pdb=" O LEU I 340 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY I 345 " --> pdb=" O ASP I 341 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU I 347 " --> pdb=" O LEU I 343 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN I 353 " --> pdb=" O LYS I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 372 Processing helix chain 'I' and resid 424 through 428 Processing helix chain 'I' and resid 429 through 450 removed outlier: 4.129A pdb=" N THR I 433 " --> pdb=" O GLY I 429 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 442 " --> pdb=" O CYS I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 474 removed outlier: 4.237A pdb=" N GLU I 470 " --> pdb=" O GLY I 466 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 511 removed outlier: 4.048A pdb=" N GLY I 507 " --> pdb=" O ARG I 504 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU I 508 " --> pdb=" O ASN I 505 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N MET I 509 " --> pdb=" O LEU I 506 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET I 510 " --> pdb=" O GLY I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 533 removed outlier: 3.547A pdb=" N GLY I 533 " --> pdb=" O GLN I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 560 through 576 removed outlier: 4.340A pdb=" N GLU I 564 " --> pdb=" O GLY I 560 " (cutoff:3.500A) Processing helix chain 'I' and resid 606 through 620 removed outlier: 3.606A pdb=" N MET I 611 " --> pdb=" O LEU I 607 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 616 " --> pdb=" O THR I 612 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER I 617 " --> pdb=" O GLU I 613 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 618 " --> pdb=" O GLN I 614 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.626A pdb=" N VAL A 67 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA A 185 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 69 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.395A pdb=" N VAL B 67 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 112 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 3.756A pdb=" N ASP C 141 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU C 138 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR C 184 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE C 140 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA C 185 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 69 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 114 Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB2, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.497A pdb=" N VAL D 67 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA D 185 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 69 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 109 through 114 Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 96 removed outlier: 4.416A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 183 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 71 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 109 through 115 Processing sheet with id=AB7, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AB8, first strand: chain 'F' and resid 92 through 96 removed outlier: 5.874A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 327 through 328 removed outlier: 6.109A pdb=" N GLU G 327 " --> pdb=" O HIS G 489 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL G 491 " --> pdb=" O GLU G 327 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL G 416 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N MET G 542 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR G 418 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE G 544 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL G 420 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU G 581 " --> pdb=" O LYS G 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 43 through 44 removed outlier: 6.906A pdb=" N GLU d 43 " --> pdb=" O ALA d 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 327 through 330 removed outlier: 3.731A pdb=" N GLU I 327 " --> pdb=" O LEU I 487 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR I 415 " --> pdb=" O LYS I 452 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLU I 454 " --> pdb=" O THR I 415 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL I 417 " --> pdb=" O GLU I 454 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LEU I 456 " --> pdb=" O VAL I 417 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU I 419 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE I 458 " --> pdb=" O LEU I 419 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU I 421 " --> pdb=" O PHE I 458 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR I 460 " --> pdb=" O LEU I 421 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL I 416 " --> pdb=" O ILE I 540 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N MET I 542 " --> pdb=" O VAL I 416 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR I 418 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE I 544 " --> pdb=" O THR I 418 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL I 420 " --> pdb=" O ILE I 544 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE I 587 " --> pdb=" O SER I 545 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA I 584 " --> pdb=" O VAL I 599 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE I 601 " --> pdb=" O ALA I 584 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY I 586 " --> pdb=" O ILE I 601 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2439 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6781 1.34 - 1.46: 2769 1.46 - 1.57: 10525 1.57 - 1.69: 1 1.69 - 1.81: 153 Bond restraints: 20229 Sorted by residual: bond pdb=" N ILE G 601 " pdb=" CA ILE G 601 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N VAL G 602 " pdb=" CA VAL G 602 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.07e-02 8.73e+03 1.11e+01 bond pdb=" N ASP G 603 " pdb=" CA ASP G 603 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.43e+00 bond pdb=" N ASN D 10 " pdb=" CA ASN D 10 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" N SER A 212 " pdb=" CA SER A 212 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.17e-02 7.31e+03 6.22e+00 ... (remaining 20224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 26897 1.82 - 3.65: 469 3.65 - 5.47: 62 5.47 - 7.29: 17 7.29 - 9.12: 4 Bond angle restraints: 27449 Sorted by residual: angle pdb=" N VAL G 602 " pdb=" CA VAL G 602 " pdb=" C VAL G 602 " ideal model delta sigma weight residual 113.10 106.15 6.95 9.70e-01 1.06e+00 5.14e+01 angle pdb=" N ALA H 289 " pdb=" CA ALA H 289 " pdb=" C ALA H 289 " ideal model delta sigma weight residual 113.12 106.20 6.92 1.25e+00 6.40e-01 3.06e+01 angle pdb=" N ASN D 10 " pdb=" CA ASN D 10 " pdb=" C ASN D 10 " ideal model delta sigma weight residual 112.26 106.66 5.60 1.32e+00 5.74e-01 1.80e+01 angle pdb=" CA PRO F 270 " pdb=" N PRO F 270 " pdb=" CD PRO F 270 " ideal model delta sigma weight residual 112.00 106.39 5.61 1.40e+00 5.10e-01 1.61e+01 angle pdb=" CA ASP G 603 " pdb=" CB ASP G 603 " pdb=" CG ASP G 603 " ideal model delta sigma weight residual 112.60 115.67 -3.07 1.00e+00 1.00e+00 9.45e+00 ... (remaining 27444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10889 17.87 - 35.74: 1050 35.74 - 53.62: 186 53.62 - 71.49: 30 71.49 - 89.36: 16 Dihedral angle restraints: 12171 sinusoidal: 4875 harmonic: 7296 Sorted by residual: dihedral pdb=" CA MET C 29 " pdb=" C MET C 29 " pdb=" N VAL C 30 " pdb=" CA VAL C 30 " ideal model delta harmonic sigma weight residual -180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU F 159 " pdb=" C GLU F 159 " pdb=" N SER F 160 " pdb=" CA SER F 160 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR D 165 " pdb=" C THR D 165 " pdb=" N LEU D 166 " pdb=" CA LEU D 166 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 12168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2340 0.046 - 0.091: 608 0.091 - 0.137: 148 0.137 - 0.183: 10 0.183 - 0.229: 2 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CA VAL G 602 " pdb=" N VAL G 602 " pdb=" C VAL G 602 " pdb=" CB VAL G 602 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB THR B 165 " pdb=" CA THR B 165 " pdb=" OG1 THR B 165 " pdb=" CG2 THR B 165 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB VAL G 602 " pdb=" CA VAL G 602 " pdb=" CG1 VAL G 602 " pdb=" CG2 VAL G 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 3105 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 269 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F 270 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 270 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 270 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " 0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 129 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 40 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO E 41 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.035 5.00e-02 4.00e+02 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 305 2.63 - 3.20: 18731 3.20 - 3.77: 31022 3.77 - 4.33: 41248 4.33 - 4.90: 63659 Nonbonded interactions: 154965 Sorted by model distance: nonbonded pdb=" O ARG B 210 " pdb=" NH1 ARG B 210 " model vdw 2.063 3.120 nonbonded pdb=" NH2 ARG C 51 " pdb=" OE1 GLN C 52 " model vdw 2.188 3.120 nonbonded pdb=" O GLU E 302 " pdb=" OG1 THR E 305 " model vdw 2.197 3.040 nonbonded pdb=" O GLY B 76 " pdb=" OG1 THR B 79 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASN E 218 " pdb=" N TYR E 219 " model vdw 2.212 3.120 ... (remaining 154960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 10 through 111 or resid 126 through 188 or resid 205 throu \ gh 317)) selection = (chain 'C' and (resid 10 through 111 or resid 126 through 317)) selection = (chain 'D' and (resid 10 through 111 or resid 126 through 317)) selection = (chain 'E' and (resid 10 through 111 or resid 126 through 188 or resid 205 throu \ gh 317)) selection = (chain 'F' and resid 10 through 317) } ncs_group { reference = chain 'G' selection = (chain 'I' and (resid 317 through 369 or resid 412 through 620)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.410 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 : 0.003 0.093 20229 Z= 0.170 Angle : 0.596 9.115 27449 Z= 0.334 Chirality : 0.043 0.229 3108 Planarity : 0.005 0.104 3597 Dihedral : 14.443 89.359 7435 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 0.33 % Allowed : 0.47 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2470 helix: 0.02 (0.16), residues: 1033 sheet: -0.48 (0.30), residues: 314 loop : -1.16 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 303 TYR 0.016 0.001 TYR F 132 PHE 0.027 0.001 PHE D 22 TRP 0.021 0.002 TRP F 130 HIS 0.004 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (20229) covalent geometry : angle 0.59589 / 0.33 (27449) hydrogen bonds : bond 0.23197 / 15.33 ( 848) hydrogen bonds : angle 7.61152 / 5.41 ( 2439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 507 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9138 (mt) cc_final: 0.8781 (mt) REVERT: A 61 PHE cc_start: 0.7886 (m-80) cc_final: 0.7667 (m-80) REVERT: A 68 MET cc_start: 0.5080 (tpt) cc_final: 0.4085 (tpt) REVERT: A 207 GLN cc_start: 0.8363 (tt0) cc_final: 0.8062 (tt0) REVERT: A 208 MET cc_start: 0.7818 (mpp) cc_final: 0.7342 (mpp) REVERT: B 10 ASN cc_start: 0.7385 (t0) cc_final: 0.6958 (t0) REVERT: B 25 ASP cc_start: 0.8063 (t0) cc_final: 0.7622 (t0) REVERT: B 135 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 217 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7234 (tp) REVERT: B 290 PHE cc_start: 0.8109 (t80) cc_final: 0.7558 (t80) REVERT: C 95 VAL cc_start: 0.9025 (p) cc_final: 0.8754 (m) REVERT: C 186 ASN cc_start: 0.7695 (m110) cc_final: 0.7465 (m110) REVERT: C 220 LEU cc_start: 0.8192 (tp) cc_final: 0.7819 (tp) REVERT: C 229 VAL cc_start: 0.9137 (m) cc_final: 0.8916 (p) REVERT: C 235 HIS cc_start: 0.5976 (p-80) cc_final: 0.5759 (p-80) REVERT: C 254 MET cc_start: 0.7035 (ttp) cc_final: 0.6732 (ttp) REVERT: C 288 PHE cc_start: 0.7314 (t80) cc_final: 0.6860 (t80) REVERT: D 29 MET cc_start: 0.7117 (mmm) cc_final: 0.6909 (mmm) REVERT: D 47 TYR cc_start: 0.7355 (t80) cc_final: 0.7145 (t80) REVERT: D 50 ASP cc_start: 0.8091 (t0) cc_final: 0.7888 (t0) REVERT: D 84 VAL cc_start: 0.7934 (p) cc_final: 0.7657 (t) REVERT: D 119 GLN cc_start: 0.7884 (pm20) cc_final: 0.7610 (pm20) REVERT: D 224 ASN cc_start: 0.8572 (m110) cc_final: 0.8236 (m110) REVERT: D 238 ASN cc_start: 0.9221 (p0) cc_final: 0.8804 (p0) REVERT: D 246 ASN cc_start: 0.8658 (m110) cc_final: 0.8305 (m110) REVERT: D 248 MET cc_start: 0.8678 (mmt) cc_final: 0.8293 (tpp) REVERT: D 278 GLU cc_start: 0.7689 (tp30) cc_final: 0.7474 (tp30) REVERT: D 294 PHE cc_start: 0.8195 (t80) cc_final: 0.7742 (t80) REVERT: E 28 MET cc_start: 0.6923 (ptp) cc_final: 0.6393 (ptp) REVERT: E 29 MET cc_start: 0.5904 (tpt) cc_final: 0.5594 (tpt) REVERT: E 44 ASP cc_start: 0.8670 (t0) cc_final: 0.8444 (t0) REVERT: E 144 ASP cc_start: 0.7463 (p0) cc_final: 0.7256 (p0) REVERT: E 179 PHE cc_start: 0.8189 (t80) cc_final: 0.7891 (t80) REVERT: E 181 LEU cc_start: 0.8639 (tt) cc_final: 0.8384 (tt) REVERT: E 248 MET cc_start: 0.7673 (mtm) cc_final: 0.7300 (mtm) REVERT: E 254 MET cc_start: 0.7578 (ppp) cc_final: 0.6967 (ppp) REVERT: E 274 ILE cc_start: 0.7897 (mt) cc_final: 0.7634 (mt) REVERT: E 291 ARG cc_start: 0.7560 (ttm110) cc_final: 0.6960 (ttm110) REVERT: E 296 ASN cc_start: 0.8563 (m110) cc_final: 0.8155 (m110) REVERT: E 309 PHE cc_start: 0.8494 (m-80) cc_final: 0.8226 (m-80) REVERT: F 47 TYR cc_start: 0.8138 (t80) cc_final: 0.7903 (t80) REVERT: F 128 LEU cc_start: 0.8206 (mt) cc_final: 0.7940 (mt) REVERT: F 155 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7717 (tm-30) REVERT: F 208 MET cc_start: 0.5935 (ptp) cc_final: 0.5713 (ptp) REVERT: F 290 PHE cc_start: 0.6768 (t80) cc_final: 0.6550 (t80) REVERT: H 254 MET cc_start: 0.7372 (tpt) cc_final: 0.6871 (tpt) REVERT: H 290 PHE cc_start: 0.7617 (t80) cc_final: 0.7057 (t80) REVERT: G 421 LEU cc_start: 0.8443 (mt) cc_final: 0.8239 (mt) REVERT: G 526 TRP cc_start: 0.8360 (t60) cc_final: 0.8100 (t60) REVERT: G 543 MET cc_start: 0.6192 (mmp) cc_final: 0.5962 (mmp) REVERT: G 563 LEU cc_start: 0.8650 (mt) cc_final: 0.8449 (mt) REVERT: G 605 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6978 (mm-30) REVERT: G 611 MET cc_start: 0.7409 (ptp) cc_final: 0.7023 (ptp) REVERT: I 370 MET cc_start: 0.8019 (mmp) cc_final: 0.7725 (mmp) outliers start: 7 outliers final: 0 residues processed: 510 average time/residue: 0.1339 time to fit residues: 101.6935 Evaluate side-chains 494 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 491 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN B 207 GLN C 135 ASN C 176 HIS C 224 ASN D 261 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 ASN G 528 HIS G 614 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.218418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158878 restraints weight = 37599.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165046 restraints weight = 22320.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169195 restraints weight = 15296.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.172008 restraints weight = 11646.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173914 restraints weight = 9617.454| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20229 Z= 0.140 Angle : 0.562 8.034 27449 Z= 0.301 Chirality : 0.042 0.150 3108 Planarity : 0.005 0.061 3597 Dihedral : 4.458 18.082 2769 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.24 % Allowed : 5.49 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2470 helix: 0.07 (0.16), residues: 1083 sheet: -0.49 (0.30), residues: 319 loop : -1.24 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 303 TYR 0.017 0.001 TYR B 143 PHE 0.019 0.002 PHE A 61 TRP 0.024 0.002 TRP F 130 HIS 0.006 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (20229) covalent geometry : angle 0.56208 / 0.30 (27449) hydrogen bonds : bond 0.04446 / 2.98 ( 848) hydrogen bonds : angle 5.76387 / 4.10 ( 2439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 536 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9118 (mt) cc_final: 0.8702 (mt) REVERT: A 65 ARG cc_start: 0.7233 (mmm160) cc_final: 0.6963 (mmm-85) REVERT: A 143 TYR cc_start: 0.8229 (t80) cc_final: 0.7565 (t80) REVERT: A 182 PHE cc_start: 0.6196 (m-10) cc_final: 0.5725 (m-10) REVERT: A 208 MET cc_start: 0.7839 (mpp) cc_final: 0.7315 (mpp) REVERT: B 25 ASP cc_start: 0.8001 (t0) cc_final: 0.7614 (t0) REVERT: B 135 ASN cc_start: 0.8180 (p0) cc_final: 0.7840 (p0) REVERT: B 217 LEU cc_start: 0.7596 (tp) cc_final: 0.7035 (tp) REVERT: B 248 MET cc_start: 0.7085 (mmp) cc_final: 0.6387 (mmp) REVERT: B 279 ASN cc_start: 0.8365 (m110) cc_final: 0.8142 (m110) REVERT: B 290 PHE cc_start: 0.7947 (t80) cc_final: 0.7572 (t80) REVERT: C 30 VAL cc_start: 0.8178 (t) cc_final: 0.7891 (t) REVERT: C 254 MET cc_start: 0.7238 (ttp) cc_final: 0.6958 (ttp) REVERT: C 257 GLN cc_start: 0.8426 (tp-100) cc_final: 0.7898 (tp-100) REVERT: C 288 PHE cc_start: 0.7365 (t80) cc_final: 0.7019 (t80) REVERT: D 22 PHE cc_start: 0.8533 (m-80) cc_final: 0.8248 (m-10) REVERT: D 29 MET cc_start: 0.7129 (mmm) cc_final: 0.6901 (mmm) REVERT: D 40 VAL cc_start: 0.8707 (t) cc_final: 0.8307 (m) REVERT: D 96 ASN cc_start: 0.7670 (m-40) cc_final: 0.7449 (m-40) REVERT: D 181 LEU cc_start: 0.8247 (tp) cc_final: 0.8042 (tp) REVERT: D 220 LEU cc_start: 0.7212 (tp) cc_final: 0.6941 (tp) REVERT: D 224 ASN cc_start: 0.8746 (m110) cc_final: 0.8283 (m110) REVERT: D 225 GLU cc_start: 0.7087 (mp0) cc_final: 0.6492 (mp0) REVERT: D 238 ASN cc_start: 0.9152 (p0) cc_final: 0.8762 (p0) REVERT: D 246 ASN cc_start: 0.8749 (m110) cc_final: 0.8403 (m110) REVERT: D 248 MET cc_start: 0.8611 (mmt) cc_final: 0.8330 (tpp) REVERT: D 263 ASP cc_start: 0.7059 (m-30) cc_final: 0.6816 (m-30) REVERT: D 268 MET cc_start: 0.7490 (tpp) cc_final: 0.6908 (tpp) REVERT: D 278 GLU cc_start: 0.7639 (tp30) cc_final: 0.7331 (tp30) REVERT: D 294 PHE cc_start: 0.8164 (t80) cc_final: 0.7685 (t80) REVERT: D 302 GLU cc_start: 0.8292 (pm20) cc_final: 0.8079 (pm20) REVERT: E 28 MET cc_start: 0.7083 (ptp) cc_final: 0.6488 (ptp) REVERT: E 29 MET cc_start: 0.6151 (tpt) cc_final: 0.5805 (tpt) REVERT: E 44 ASP cc_start: 0.8684 (t0) cc_final: 0.8397 (t0) REVERT: E 48 LEU cc_start: 0.8147 (tt) cc_final: 0.7899 (tt) REVERT: E 227 ASN cc_start: 0.8623 (m110) cc_final: 0.8350 (m110) REVERT: E 247 LYS cc_start: 0.8300 (ptmt) cc_final: 0.8069 (ptmt) REVERT: E 248 MET cc_start: 0.7688 (mtm) cc_final: 0.7325 (mtm) REVERT: E 251 VAL cc_start: 0.8654 (p) cc_final: 0.7897 (p) REVERT: E 254 MET cc_start: 0.7467 (ppp) cc_final: 0.6923 (ppp) REVERT: E 274 ILE cc_start: 0.7984 (mt) cc_final: 0.7769 (mt) REVERT: E 291 ARG cc_start: 0.7579 (ttm110) cc_final: 0.6921 (ttm110) REVERT: E 305 THR cc_start: 0.8654 (p) cc_final: 0.8263 (t) REVERT: F 47 TYR cc_start: 0.8155 (t80) cc_final: 0.7757 (t80) REVERT: F 128 LEU cc_start: 0.8162 (mt) cc_final: 0.7926 (mt) REVERT: F 155 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 254 MET cc_start: 0.7352 (tpt) cc_final: 0.6782 (tpt) REVERT: G 469 ARG cc_start: 0.9108 (tpt90) cc_final: 0.8876 (tpt90) REVERT: G 488 ARG cc_start: 0.6788 (tpt90) cc_final: 0.6551 (tpt170) REVERT: G 543 MET cc_start: 0.6578 (mmp) cc_final: 0.6088 (mmp) REVERT: G 568 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7759 (mmm160) REVERT: G 611 MET cc_start: 0.7427 (ptp) cc_final: 0.7065 (ptp) REVERT: I 370 MET cc_start: 0.8032 (mmp) cc_final: 0.7714 (mmp) REVERT: I 488 ARG cc_start: 0.2417 (ptt-90) cc_final: 0.0781 (mmt-90) outliers start: 5 outliers final: 0 residues processed: 538 average time/residue: 0.1302 time to fit residues: 104.7843 Evaluate side-chains 518 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN B 246 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS D 261 ASN E 80 HIS ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 HIS I 315 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.211389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155051 restraints weight = 35796.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.160655 restraints weight = 21430.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.164447 restraints weight = 14797.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166977 restraints weight = 11267.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168782 restraints weight = 9293.300| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20229 Z= 0.230 Angle : 0.612 8.944 27449 Z= 0.332 Chirality : 0.044 0.240 3108 Planarity : 0.005 0.071 3597 Dihedral : 4.726 19.469 2769 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2470 helix: -0.05 (0.16), residues: 1064 sheet: -0.63 (0.29), residues: 338 loop : -1.37 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 210 TYR 0.025 0.002 TYR B 143 PHE 0.041 0.002 PHE A 61 TRP 0.024 0.002 TRP A 211 HIS 0.005 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (20229) covalent geometry : angle 0.61196 / 0.33 (27449) hydrogen bonds : bond 0.04841 / 3.24 ( 848) hydrogen bonds : angle 5.89995 / 4.22 ( 2439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8521 (t60) cc_final: 0.7981 (t60) REVERT: A 143 TYR cc_start: 0.8190 (t80) cc_final: 0.7565 (t80) REVERT: A 182 PHE cc_start: 0.6358 (m-10) cc_final: 0.5909 (m-10) REVERT: A 208 MET cc_start: 0.7959 (mpp) cc_final: 0.7503 (mpp) REVERT: B 25 ASP cc_start: 0.8081 (t0) cc_final: 0.7696 (t0) REVERT: B 68 MET cc_start: 0.6970 (tmm) cc_final: 0.6768 (tmm) REVERT: B 135 ASN cc_start: 0.8213 (p0) cc_final: 0.7984 (p0) REVERT: B 217 LEU cc_start: 0.7646 (tp) cc_final: 0.7029 (tp) REVERT: B 248 MET cc_start: 0.7033 (mmp) cc_final: 0.6654 (mmp) REVERT: B 290 PHE cc_start: 0.7976 (t80) cc_final: 0.7664 (t80) REVERT: C 30 VAL cc_start: 0.8204 (t) cc_final: 0.7628 (m) REVERT: C 51 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7295 (ttp80) REVERT: C 57 ILE cc_start: 0.8520 (mm) cc_final: 0.8304 (mt) REVERT: C 158 LEU cc_start: 0.8211 (tt) cc_final: 0.7490 (tt) REVERT: C 163 ARG cc_start: 0.7388 (mpp-170) cc_final: 0.6983 (mpp-170) REVERT: C 235 HIS cc_start: 0.6055 (p-80) cc_final: 0.5852 (p-80) REVERT: C 254 MET cc_start: 0.7268 (ttp) cc_final: 0.6999 (ttp) REVERT: C 257 GLN cc_start: 0.8533 (tp-100) cc_final: 0.7942 (tp-100) REVERT: C 305 THR cc_start: 0.8771 (t) cc_final: 0.8491 (t) REVERT: C 308 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 22 PHE cc_start: 0.8569 (m-80) cc_final: 0.8299 (m-10) REVERT: D 29 MET cc_start: 0.7130 (mmm) cc_final: 0.6859 (mmm) REVERT: D 40 VAL cc_start: 0.8709 (t) cc_final: 0.8398 (m) REVERT: D 72 TYR cc_start: 0.7698 (m-80) cc_final: 0.7374 (m-80) REVERT: D 87 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7323 (ttm110) REVERT: D 96 ASN cc_start: 0.7835 (m-40) cc_final: 0.7574 (m-40) REVERT: D 119 GLN cc_start: 0.7970 (pm20) cc_final: 0.7710 (pm20) REVERT: D 180 ARG cc_start: 0.8266 (mpt180) cc_final: 0.7682 (mpt180) REVERT: D 181 LEU cc_start: 0.8248 (tp) cc_final: 0.7983 (tp) REVERT: D 224 ASN cc_start: 0.8764 (m110) cc_final: 0.8435 (m110) REVERT: D 225 GLU cc_start: 0.7495 (mp0) cc_final: 0.6809 (mp0) REVERT: D 238 ASN cc_start: 0.9156 (p0) cc_final: 0.8776 (p0) REVERT: D 243 GLU cc_start: 0.8251 (mp0) cc_final: 0.7891 (mp0) REVERT: D 268 MET cc_start: 0.7600 (tpp) cc_final: 0.7017 (tpt) REVERT: D 278 GLU cc_start: 0.7626 (tp30) cc_final: 0.7363 (tp30) REVERT: D 282 ILE cc_start: 0.8212 (tt) cc_final: 0.7881 (tt) REVERT: D 294 PHE cc_start: 0.8197 (t80) cc_final: 0.7691 (t80) REVERT: D 302 GLU cc_start: 0.8203 (pm20) cc_final: 0.8001 (pm20) REVERT: D 303 ARG cc_start: 0.8389 (ttm110) cc_final: 0.8186 (ttm110) REVERT: E 28 MET cc_start: 0.7172 (ptp) cc_final: 0.6604 (ptp) REVERT: E 29 MET cc_start: 0.6189 (tpt) cc_final: 0.5773 (tpt) REVERT: E 48 LEU cc_start: 0.8148 (tt) cc_final: 0.7913 (tt) REVERT: E 69 VAL cc_start: 0.8403 (t) cc_final: 0.7695 (p) REVERT: E 90 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.4221 (t60) REVERT: E 227 ASN cc_start: 0.8653 (m110) cc_final: 0.8398 (m110) REVERT: E 247 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7282 (ptmt) REVERT: E 248 MET cc_start: 0.7705 (mtm) cc_final: 0.7390 (mtm) REVERT: E 251 VAL cc_start: 0.8760 (p) cc_final: 0.8110 (p) REVERT: E 254 MET cc_start: 0.7494 (ppp) cc_final: 0.6944 (ppp) REVERT: E 274 ILE cc_start: 0.7931 (mt) cc_final: 0.7652 (mt) REVERT: E 291 ARG cc_start: 0.7598 (ttm110) cc_final: 0.6998 (ttm110) REVERT: F 44 ASP cc_start: 0.7482 (t0) cc_final: 0.7199 (t0) REVERT: F 47 TYR cc_start: 0.8271 (t80) cc_final: 0.7782 (t80) REVERT: F 128 LEU cc_start: 0.8232 (mt) cc_final: 0.7978 (mt) REVERT: F 155 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7861 (tm-30) REVERT: H 254 MET cc_start: 0.7453 (tpt) cc_final: 0.6888 (tpt) REVERT: G 421 LEU cc_start: 0.8603 (mt) cc_final: 0.8386 (mt) REVERT: G 469 ARG cc_start: 0.9189 (tpt90) cc_final: 0.8825 (tpp-160) REVERT: G 543 MET cc_start: 0.6653 (mmp) cc_final: 0.6150 (mmp) REVERT: G 568 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7709 (mmm160) REVERT: G 611 MET cc_start: 0.7398 (ptp) cc_final: 0.7007 (ptp) REVERT: d 42 MET cc_start: 0.1608 (tpt) cc_final: 0.1375 (tpt) REVERT: d 134 MET cc_start: 0.7204 (tmm) cc_final: 0.6970 (tmm) REVERT: I 370 MET cc_start: 0.7999 (mmp) cc_final: 0.7677 (mmp) REVERT: I 488 ARG cc_start: 0.2771 (ptt-90) cc_final: 0.0786 (mmt-90) REVERT: I 503 ARG cc_start: 0.3740 (ttm110) cc_final: 0.3323 (ttm110) outliers start: 2 outliers final: 0 residues processed: 550 average time/residue: 0.1337 time to fit residues: 110.2427 Evaluate side-chains 533 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 29 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 111 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN C 135 ASN C 176 HIS D 261 ASN E 83 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.221634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162465 restraints weight = 37424.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168794 restraints weight = 22168.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173070 restraints weight = 15121.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175879 restraints weight = 11454.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.177923 restraints weight = 9423.256| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20229 Z= 0.116 Angle : 0.555 12.095 27449 Z= 0.290 Chirality : 0.042 0.203 3108 Planarity : 0.005 0.064 3597 Dihedral : 4.440 17.910 2769 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2470 helix: 0.07 (0.16), residues: 1090 sheet: -0.55 (0.30), residues: 327 loop : -1.25 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 210 TYR 0.024 0.001 TYR C 219 PHE 0.021 0.001 PHE D 314 TRP 0.026 0.002 TRP F 130 HIS 0.005 0.001 HIS I 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (20229) covalent geometry : angle 0.55451 / 0.29 (27449) hydrogen bonds : bond 0.03691 / 2.48 ( 848) hydrogen bonds : angle 5.45969 / 3.87 ( 2439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 533 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9181 (mt) cc_final: 0.8799 (mt) REVERT: A 68 MET cc_start: 0.4891 (tpt) cc_final: 0.4203 (tpt) REVERT: A 143 TYR cc_start: 0.8195 (t80) cc_final: 0.7618 (t80) REVERT: A 182 PHE cc_start: 0.6332 (m-10) cc_final: 0.5876 (m-10) REVERT: A 208 MET cc_start: 0.7878 (mpp) cc_final: 0.7426 (mpp) REVERT: B 25 ASP cc_start: 0.7787 (t0) cc_final: 0.7478 (t0) REVERT: B 135 ASN cc_start: 0.8199 (p0) cc_final: 0.7923 (p0) REVERT: B 217 LEU cc_start: 0.7528 (tp) cc_final: 0.6870 (tp) REVERT: B 246 ASN cc_start: 0.7990 (m110) cc_final: 0.7057 (t0) REVERT: B 248 MET cc_start: 0.6877 (mmp) cc_final: 0.6290 (mmp) REVERT: B 290 PHE cc_start: 0.7999 (t80) cc_final: 0.7579 (t80) REVERT: C 30 VAL cc_start: 0.8043 (t) cc_final: 0.7497 (m) REVERT: C 47 TYR cc_start: 0.8040 (t80) cc_final: 0.7735 (t80) REVERT: C 51 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7166 (ttp80) REVERT: C 95 VAL cc_start: 0.9050 (p) cc_final: 0.8815 (m) REVERT: C 104 ILE cc_start: 0.8495 (mt) cc_final: 0.8284 (mt) REVERT: C 109 LYS cc_start: 0.6899 (mppt) cc_final: 0.6683 (mppt) REVERT: C 163 ARG cc_start: 0.7288 (mpp-170) cc_final: 0.6861 (mpp-170) REVERT: C 254 MET cc_start: 0.7337 (ttp) cc_final: 0.6974 (ttp) REVERT: C 257 GLN cc_start: 0.8505 (tp-100) cc_final: 0.7879 (tp-100) REVERT: C 305 THR cc_start: 0.8651 (t) cc_final: 0.8352 (t) REVERT: C 308 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 22 PHE cc_start: 0.8547 (m-80) cc_final: 0.8305 (m-10) REVERT: D 40 VAL cc_start: 0.8654 (t) cc_final: 0.8336 (m) REVERT: D 72 TYR cc_start: 0.7673 (m-80) cc_final: 0.7455 (m-80) REVERT: D 96 ASN cc_start: 0.7695 (m-40) cc_final: 0.7453 (m-40) REVERT: D 180 ARG cc_start: 0.8167 (mpt180) cc_final: 0.7892 (mmt-90) REVERT: D 224 ASN cc_start: 0.8609 (m110) cc_final: 0.8248 (m110) REVERT: D 225 GLU cc_start: 0.7211 (mp0) cc_final: 0.6438 (mp0) REVERT: D 238 ASN cc_start: 0.9140 (p0) cc_final: 0.8734 (p0) REVERT: D 243 GLU cc_start: 0.8184 (mp0) cc_final: 0.7819 (mp0) REVERT: D 248 MET cc_start: 0.8622 (mmm) cc_final: 0.8287 (tpp) REVERT: D 254 MET cc_start: 0.8375 (ptp) cc_final: 0.8093 (ptp) REVERT: D 268 MET cc_start: 0.7592 (tpp) cc_final: 0.7029 (tpp) REVERT: D 272 THR cc_start: 0.8274 (p) cc_final: 0.7562 (p) REVERT: D 278 GLU cc_start: 0.7585 (tp30) cc_final: 0.7306 (tp30) REVERT: D 294 PHE cc_start: 0.8213 (t80) cc_final: 0.7687 (t80) REVERT: D 302 GLU cc_start: 0.8215 (pm20) cc_final: 0.7974 (pm20) REVERT: D 303 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8093 (ttm110) REVERT: E 28 MET cc_start: 0.7134 (ptp) cc_final: 0.6567 (ptp) REVERT: E 29 MET cc_start: 0.6128 (tpt) cc_final: 0.5746 (tpt) REVERT: E 44 ASP cc_start: 0.8741 (t0) cc_final: 0.8298 (t0) REVERT: E 144 ASP cc_start: 0.7597 (p0) cc_final: 0.7373 (p0) REVERT: E 159 GLU cc_start: 0.6705 (tt0) cc_final: 0.6488 (tt0) REVERT: E 247 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7756 (ptmt) REVERT: E 248 MET cc_start: 0.7731 (mtm) cc_final: 0.7286 (mtm) REVERT: E 251 VAL cc_start: 0.8729 (p) cc_final: 0.7984 (p) REVERT: E 254 MET cc_start: 0.7544 (ppp) cc_final: 0.6994 (ppp) REVERT: E 274 ILE cc_start: 0.7928 (mt) cc_final: 0.7721 (mt) REVERT: E 291 ARG cc_start: 0.7502 (ttm110) cc_final: 0.6946 (ttm110) REVERT: E 299 ASP cc_start: 0.7682 (t0) cc_final: 0.7432 (p0) REVERT: E 305 THR cc_start: 0.8726 (p) cc_final: 0.8302 (t) REVERT: E 309 PHE cc_start: 0.8288 (m-80) cc_final: 0.8084 (m-80) REVERT: F 44 ASP cc_start: 0.7478 (t0) cc_final: 0.7185 (t0) REVERT: F 47 TYR cc_start: 0.8100 (t80) cc_final: 0.7697 (t80) REVERT: F 128 LEU cc_start: 0.8182 (mt) cc_final: 0.7903 (mt) REVERT: F 155 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7884 (tm-30) REVERT: F 290 PHE cc_start: 0.6742 (t80) cc_final: 0.6498 (t80) REVERT: H 248 MET cc_start: 0.8543 (ttm) cc_final: 0.6836 (ttm) REVERT: H 254 MET cc_start: 0.7368 (tpt) cc_final: 0.6751 (tpt) REVERT: H 276 TRP cc_start: 0.7033 (t60) cc_final: 0.6671 (t-100) REVERT: G 421 LEU cc_start: 0.8558 (mt) cc_final: 0.8352 (mt) REVERT: G 428 ARG cc_start: 0.7548 (mpp80) cc_final: 0.6529 (mpp80) REVERT: G 440 ASP cc_start: 0.8978 (t0) cc_final: 0.8741 (t0) REVERT: G 469 ARG cc_start: 0.9174 (tpt90) cc_final: 0.8793 (tpp-160) REVERT: G 543 MET cc_start: 0.6536 (mmp) cc_final: 0.6029 (mmp) REVERT: G 568 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7720 (mmm160) REVERT: G 611 MET cc_start: 0.7437 (ptp) cc_final: 0.7055 (ptp) REVERT: d 42 MET cc_start: 0.1632 (tpt) cc_final: 0.1402 (tpt) REVERT: d 134 MET cc_start: 0.7132 (tmm) cc_final: 0.6904 (tmm) REVERT: I 370 MET cc_start: 0.8083 (mmp) cc_final: 0.7744 (mmp) REVERT: I 488 ARG cc_start: 0.2665 (ptt-90) cc_final: 0.0919 (mmt-90) REVERT: I 503 ARG cc_start: 0.3708 (ttm110) cc_final: 0.3435 (ttm110) outliers start: 1 outliers final: 0 residues processed: 534 average time/residue: 0.1347 time to fit residues: 107.3558 Evaluate side-chains 515 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 0.2980 chunk 231 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 169 optimal weight: 0.0070 chunk 184 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN B 218 ASN C 135 ASN C 176 HIS D 261 ASN E 83 GLN E 224 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN G 528 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.221487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.161878 restraints weight = 37890.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168167 restraints weight = 22608.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.172395 restraints weight = 15525.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.175232 restraints weight = 11823.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.176843 restraints weight = 9747.992| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20229 Z= 0.108 Angle : 0.541 12.660 27449 Z= 0.281 Chirality : 0.042 0.171 3108 Planarity : 0.004 0.048 3597 Dihedral : 4.336 17.804 2769 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.17), residues: 2470 helix: 0.20 (0.16), residues: 1088 sheet: -0.37 (0.30), residues: 316 loop : -1.19 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.020 0.001 TYR D 219 PHE 0.026 0.001 PHE C 314 TRP 0.020 0.002 TRP B 276 HIS 0.003 0.001 HIS I 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (20229) covalent geometry : angle 0.54098 / 0.28 (27449) hydrogen bonds : bond 0.03482 / 2.35 ( 848) hydrogen bonds : angle 5.27446 / 3.73 ( 2439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 536 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9172 (mt) cc_final: 0.8802 (mt) REVERT: A 68 MET cc_start: 0.4820 (tpt) cc_final: 0.4266 (tpt) REVERT: A 143 TYR cc_start: 0.8236 (t80) cc_final: 0.7666 (t80) REVERT: A 182 PHE cc_start: 0.6293 (m-10) cc_final: 0.5837 (m-10) REVERT: A 208 MET cc_start: 0.7901 (mpp) cc_final: 0.7455 (mpp) REVERT: B 68 MET cc_start: 0.6986 (tmm) cc_final: 0.6715 (tmm) REVERT: B 135 ASN cc_start: 0.8196 (p0) cc_final: 0.7662 (p0) REVERT: B 217 LEU cc_start: 0.7515 (tp) cc_final: 0.6948 (tp) REVERT: B 246 ASN cc_start: 0.7928 (m110) cc_final: 0.6985 (t0) REVERT: B 248 MET cc_start: 0.6863 (mmp) cc_final: 0.6359 (mmp) REVERT: B 290 PHE cc_start: 0.7957 (t80) cc_final: 0.7548 (t80) REVERT: C 30 VAL cc_start: 0.8138 (t) cc_final: 0.7544 (m) REVERT: C 47 TYR cc_start: 0.8056 (t80) cc_final: 0.7739 (t80) REVERT: C 51 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7116 (ttp80) REVERT: C 104 ILE cc_start: 0.8411 (mt) cc_final: 0.8184 (mt) REVERT: C 186 ASN cc_start: 0.7992 (m-40) cc_final: 0.7522 (m-40) REVERT: C 254 MET cc_start: 0.7238 (ttp) cc_final: 0.6894 (ttp) REVERT: C 257 GLN cc_start: 0.8503 (tp-100) cc_final: 0.7856 (tp-100) REVERT: C 260 ILE cc_start: 0.8713 (mp) cc_final: 0.8489 (mp) REVERT: C 305 THR cc_start: 0.8611 (t) cc_final: 0.8359 (t) REVERT: C 308 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7751 (mm-30) REVERT: D 22 PHE cc_start: 0.8537 (m-80) cc_final: 0.8282 (m-10) REVERT: D 28 MET cc_start: 0.7099 (pmm) cc_final: 0.6893 (pmm) REVERT: D 29 MET cc_start: 0.7070 (mmm) cc_final: 0.6852 (mmm) REVERT: D 40 VAL cc_start: 0.8698 (t) cc_final: 0.8321 (m) REVERT: D 72 TYR cc_start: 0.7685 (m-80) cc_final: 0.7400 (m-80) REVERT: D 96 ASN cc_start: 0.7708 (m-40) cc_final: 0.7453 (m-40) REVERT: D 180 ARG cc_start: 0.8109 (mpt180) cc_final: 0.7843 (mmt-90) REVERT: D 224 ASN cc_start: 0.8633 (m110) cc_final: 0.8231 (m110) REVERT: D 225 GLU cc_start: 0.7181 (mp0) cc_final: 0.6318 (mp0) REVERT: D 238 ASN cc_start: 0.9124 (p0) cc_final: 0.8755 (p0) REVERT: D 243 GLU cc_start: 0.8197 (mp0) cc_final: 0.7819 (mp0) REVERT: D 268 MET cc_start: 0.7537 (tpp) cc_final: 0.6945 (tpp) REVERT: D 278 GLU cc_start: 0.7571 (tp30) cc_final: 0.7295 (tp30) REVERT: D 282 ILE cc_start: 0.7681 (tt) cc_final: 0.7334 (tt) REVERT: D 294 PHE cc_start: 0.8168 (t80) cc_final: 0.7631 (t80) REVERT: D 302 GLU cc_start: 0.8242 (pm20) cc_final: 0.7990 (pm20) REVERT: D 303 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7987 (ttm110) REVERT: D 309 PHE cc_start: 0.8458 (m-80) cc_final: 0.8193 (m-80) REVERT: E 28 MET cc_start: 0.7152 (ptp) cc_final: 0.6690 (ptp) REVERT: E 29 MET cc_start: 0.6189 (tpt) cc_final: 0.5803 (tpt) REVERT: E 44 ASP cc_start: 0.8580 (t0) cc_final: 0.8194 (t0) REVERT: E 144 ASP cc_start: 0.7628 (p0) cc_final: 0.7412 (p0) REVERT: E 247 LYS cc_start: 0.8272 (ptmt) cc_final: 0.7731 (ptmt) REVERT: E 248 MET cc_start: 0.7723 (mtm) cc_final: 0.7268 (mtm) REVERT: E 274 ILE cc_start: 0.7941 (mt) cc_final: 0.7737 (mt) REVERT: E 291 ARG cc_start: 0.7507 (ttm110) cc_final: 0.6977 (ttm110) REVERT: E 299 ASP cc_start: 0.7637 (t0) cc_final: 0.7416 (p0) REVERT: F 44 ASP cc_start: 0.7440 (t0) cc_final: 0.7190 (t0) REVERT: F 47 TYR cc_start: 0.8139 (t80) cc_final: 0.7633 (t80) REVERT: F 128 LEU cc_start: 0.8180 (mt) cc_final: 0.7906 (mt) REVERT: F 155 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 290 PHE cc_start: 0.6727 (t80) cc_final: 0.6472 (t80) REVERT: H 248 MET cc_start: 0.8552 (ttm) cc_final: 0.6764 (ttm) REVERT: H 254 MET cc_start: 0.7383 (tpt) cc_final: 0.6753 (tpt) REVERT: H 276 TRP cc_start: 0.7063 (t60) cc_final: 0.6620 (t-100) REVERT: G 427 MET cc_start: 0.7069 (mmm) cc_final: 0.6578 (mmm) REVERT: G 428 ARG cc_start: 0.7511 (mpp80) cc_final: 0.6602 (mpp80) REVERT: G 440 ASP cc_start: 0.8991 (t0) cc_final: 0.8760 (t0) REVERT: G 469 ARG cc_start: 0.9203 (tpt90) cc_final: 0.8733 (tpm170) REVERT: G 543 MET cc_start: 0.6515 (mmp) cc_final: 0.6078 (mmp) REVERT: G 568 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7692 (mmm160) REVERT: G 611 MET cc_start: 0.7449 (ptp) cc_final: 0.7066 (ptp) REVERT: d 42 MET cc_start: 0.1611 (tpt) cc_final: 0.1389 (tpt) REVERT: d 134 MET cc_start: 0.7086 (tmm) cc_final: 0.6884 (tmm) REVERT: I 370 MET cc_start: 0.8116 (mmp) cc_final: 0.7800 (mmp) REVERT: I 488 ARG cc_start: 0.2624 (ptt-90) cc_final: 0.0903 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 538 average time/residue: 0.1459 time to fit residues: 117.1389 Evaluate side-chains 514 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 187 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 186 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 233 optimal weight: 30.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN C 135 ASN C 176 HIS D 261 ASN E 83 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.220594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160572 restraints weight = 37021.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166605 restraints weight = 22471.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170770 restraints weight = 15573.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173653 restraints weight = 11930.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175627 restraints weight = 9859.398| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20229 Z= 0.133 Angle : 0.554 9.351 27449 Z= 0.293 Chirality : 0.043 0.187 3108 Planarity : 0.004 0.051 3597 Dihedral : 4.402 19.187 2769 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2470 helix: 0.19 (0.16), residues: 1089 sheet: -0.39 (0.30), residues: 318 loop : -1.15 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 503 TYR 0.016 0.001 TYR F 63 PHE 0.021 0.002 PHE E 309 TRP 0.035 0.002 TRP C 276 HIS 0.004 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (20229) covalent geometry : angle 0.55440 / 0.29 (27449) hydrogen bonds : bond 0.03566 / 2.41 ( 848) hydrogen bonds : angle 5.27352 / 3.74 ( 2439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9192 (mt) cc_final: 0.8825 (mt) REVERT: A 61 PHE cc_start: 0.8076 (m-80) cc_final: 0.7870 (m-80) REVERT: A 66 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.6940 (mmt-90) REVERT: A 68 MET cc_start: 0.4883 (tpt) cc_final: 0.4317 (tpt) REVERT: A 143 TYR cc_start: 0.8218 (t80) cc_final: 0.7655 (t80) REVERT: A 182 PHE cc_start: 0.6266 (m-10) cc_final: 0.5908 (m-10) REVERT: A 208 MET cc_start: 0.7974 (mpp) cc_final: 0.7519 (mpp) REVERT: B 68 MET cc_start: 0.6997 (tmm) cc_final: 0.6605 (tmm) REVERT: B 135 ASN cc_start: 0.8223 (p0) cc_final: 0.7797 (p0) REVERT: B 217 LEU cc_start: 0.7580 (tp) cc_final: 0.6995 (tp) REVERT: B 248 MET cc_start: 0.6868 (mmp) cc_final: 0.6281 (mmp) REVERT: B 254 MET cc_start: 0.6831 (ptp) cc_final: 0.6585 (ptp) REVERT: B 290 PHE cc_start: 0.7986 (t80) cc_final: 0.7588 (t80) REVERT: C 30 VAL cc_start: 0.8044 (t) cc_final: 0.7537 (m) REVERT: C 47 TYR cc_start: 0.8093 (t80) cc_final: 0.7827 (t80) REVERT: C 51 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7166 (ttp80) REVERT: C 57 ILE cc_start: 0.8506 (mm) cc_final: 0.8288 (mt) REVERT: C 109 LYS cc_start: 0.6927 (mppt) cc_final: 0.6515 (mppt) REVERT: C 186 ASN cc_start: 0.8010 (m-40) cc_final: 0.7547 (m-40) REVERT: C 254 MET cc_start: 0.7368 (ttp) cc_final: 0.6989 (ttp) REVERT: C 257 GLN cc_start: 0.8562 (tp-100) cc_final: 0.7870 (tp-100) REVERT: C 260 ILE cc_start: 0.8691 (mp) cc_final: 0.8489 (mp) REVERT: C 305 THR cc_start: 0.8651 (t) cc_final: 0.8355 (t) REVERT: C 308 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7783 (mm-30) REVERT: D 29 MET cc_start: 0.7041 (mmm) cc_final: 0.6782 (mmm) REVERT: D 40 VAL cc_start: 0.8690 (t) cc_final: 0.8314 (m) REVERT: D 72 TYR cc_start: 0.7713 (m-80) cc_final: 0.7472 (m-80) REVERT: D 96 ASN cc_start: 0.7732 (m-40) cc_final: 0.7430 (m-40) REVERT: D 180 ARG cc_start: 0.8133 (mpt180) cc_final: 0.7688 (mpt180) REVERT: D 224 ASN cc_start: 0.8609 (m110) cc_final: 0.8224 (m110) REVERT: D 225 GLU cc_start: 0.7291 (mp0) cc_final: 0.6635 (mp0) REVERT: D 238 ASN cc_start: 0.9141 (p0) cc_final: 0.8746 (p0) REVERT: D 243 GLU cc_start: 0.8161 (mp0) cc_final: 0.7929 (mp0) REVERT: D 246 ASN cc_start: 0.8691 (m110) cc_final: 0.8295 (m110) REVERT: D 248 MET cc_start: 0.8660 (mmm) cc_final: 0.8325 (tpp) REVERT: D 278 GLU cc_start: 0.7577 (tp30) cc_final: 0.7364 (tp30) REVERT: D 294 PHE cc_start: 0.8152 (t80) cc_final: 0.7657 (t80) REVERT: D 302 GLU cc_start: 0.8244 (pm20) cc_final: 0.7949 (pm20) REVERT: D 303 ARG cc_start: 0.8376 (ttm110) cc_final: 0.8060 (ttm110) REVERT: E 15 THR cc_start: 0.7720 (p) cc_final: 0.7489 (m) REVERT: E 28 MET cc_start: 0.7188 (ptp) cc_final: 0.6750 (ptp) REVERT: E 29 MET cc_start: 0.6218 (tpt) cc_final: 0.5578 (tpt) REVERT: E 44 ASP cc_start: 0.8611 (t0) cc_final: 0.8236 (t0) REVERT: E 144 ASP cc_start: 0.7669 (p0) cc_final: 0.7454 (p0) REVERT: E 247 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7701 (ptmt) REVERT: E 248 MET cc_start: 0.7709 (mtm) cc_final: 0.7198 (mtm) REVERT: E 254 MET cc_start: 0.7444 (ppp) cc_final: 0.6849 (ppp) REVERT: E 291 ARG cc_start: 0.7513 (ttm110) cc_final: 0.7014 (ttm110) REVERT: E 305 THR cc_start: 0.8746 (p) cc_final: 0.8376 (t) REVERT: E 309 PHE cc_start: 0.8320 (m-80) cc_final: 0.8035 (m-80) REVERT: F 44 ASP cc_start: 0.7440 (t0) cc_final: 0.7190 (t0) REVERT: F 47 TYR cc_start: 0.8241 (t80) cc_final: 0.7745 (t80) REVERT: F 128 LEU cc_start: 0.8205 (mt) cc_final: 0.7942 (mt) REVERT: F 155 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7951 (tm-30) REVERT: H 248 MET cc_start: 0.8518 (ttm) cc_final: 0.6540 (ttm) REVERT: H 254 MET cc_start: 0.7467 (tpt) cc_final: 0.6801 (tpt) REVERT: H 276 TRP cc_start: 0.7136 (t60) cc_final: 0.6419 (t-100) REVERT: G 421 LEU cc_start: 0.8580 (mt) cc_final: 0.8369 (mt) REVERT: G 427 MET cc_start: 0.7184 (mmm) cc_final: 0.6931 (mmm) REVERT: G 440 ASP cc_start: 0.9004 (t0) cc_final: 0.8756 (t0) REVERT: G 469 ARG cc_start: 0.9201 (tpt90) cc_final: 0.8785 (tpm170) REVERT: G 543 MET cc_start: 0.6609 (mmp) cc_final: 0.6139 (mmp) REVERT: G 611 MET cc_start: 0.7421 (ptp) cc_final: 0.7011 (ptp) REVERT: d 134 MET cc_start: 0.7103 (tmm) cc_final: 0.6899 (tmm) REVERT: I 370 MET cc_start: 0.8096 (mmp) cc_final: 0.7772 (mmp) REVERT: I 488 ARG cc_start: 0.2679 (ptt-90) cc_final: 0.0896 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.1474 time to fit residues: 116.6740 Evaluate side-chains 517 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 108 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 203 optimal weight: 50.0000 chunk 217 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 198 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS D 261 ASN E 83 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 HIS ** I 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.213207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153092 restraints weight = 37860.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159152 restraints weight = 22288.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.163256 restraints weight = 15251.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.165956 restraints weight = 11604.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.167942 restraints weight = 9581.892| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20229 Z= 0.168 Angle : 0.583 14.700 27449 Z= 0.307 Chirality : 0.043 0.201 3108 Planarity : 0.005 0.055 3597 Dihedral : 4.519 18.674 2769 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2470 helix: 0.17 (0.16), residues: 1076 sheet: -0.35 (0.30), residues: 324 loop : -1.23 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 503 TYR 0.022 0.002 TYR I 562 PHE 0.026 0.002 PHE F 179 TRP 0.028 0.002 TRP C 276 HIS 0.007 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (20229) covalent geometry : angle 0.58339 / 0.31 (27449) hydrogen bonds : bond 0.03792 / 2.57 ( 848) hydrogen bonds : angle 5.36361 / 3.81 ( 2439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9167 (mt) cc_final: 0.8775 (mt) REVERT: A 61 PHE cc_start: 0.8085 (m-80) cc_final: 0.7874 (m-80) REVERT: A 68 MET cc_start: 0.4905 (tpt) cc_final: 0.4426 (tpt) REVERT: A 143 TYR cc_start: 0.8349 (t80) cc_final: 0.7793 (t80) REVERT: A 182 PHE cc_start: 0.6306 (m-10) cc_final: 0.5842 (m-10) REVERT: A 208 MET cc_start: 0.8082 (mpp) cc_final: 0.7630 (mpp) REVERT: B 68 MET cc_start: 0.6991 (tmm) cc_final: 0.6527 (tmm) REVERT: B 135 ASN cc_start: 0.8214 (p0) cc_final: 0.7782 (p0) REVERT: B 149 ASP cc_start: 0.7433 (t0) cc_final: 0.7161 (t0) REVERT: B 217 LEU cc_start: 0.7576 (tp) cc_final: 0.7025 (tp) REVERT: B 248 MET cc_start: 0.7140 (mmp) cc_final: 0.6412 (mmp) REVERT: B 290 PHE cc_start: 0.8085 (t80) cc_final: 0.7685 (t80) REVERT: C 30 VAL cc_start: 0.8058 (t) cc_final: 0.7504 (m) REVERT: C 47 TYR cc_start: 0.8250 (t80) cc_final: 0.7937 (t80) REVERT: C 51 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7205 (ttp80) REVERT: C 254 MET cc_start: 0.7479 (ttp) cc_final: 0.7021 (ttp) REVERT: C 257 GLN cc_start: 0.8623 (tp-100) cc_final: 0.7968 (tp-100) REVERT: C 260 ILE cc_start: 0.8652 (mp) cc_final: 0.8409 (mp) REVERT: C 305 THR cc_start: 0.8762 (t) cc_final: 0.8455 (t) REVERT: C 308 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7899 (mm-30) REVERT: D 22 PHE cc_start: 0.8542 (m-10) cc_final: 0.8286 (m-10) REVERT: D 40 VAL cc_start: 0.8686 (t) cc_final: 0.8317 (m) REVERT: D 72 TYR cc_start: 0.7783 (m-80) cc_final: 0.7442 (m-80) REVERT: D 73 HIS cc_start: 0.8313 (t-90) cc_final: 0.8091 (t-90) REVERT: D 96 ASN cc_start: 0.7765 (m-40) cc_final: 0.7453 (m-40) REVERT: D 119 GLN cc_start: 0.8035 (pm20) cc_final: 0.7714 (pm20) REVERT: D 180 ARG cc_start: 0.8148 (mpt180) cc_final: 0.7684 (mpt180) REVERT: D 224 ASN cc_start: 0.8539 (m110) cc_final: 0.8119 (m110) REVERT: D 225 GLU cc_start: 0.7186 (mp0) cc_final: 0.6443 (mp0) REVERT: D 235 HIS cc_start: 0.7497 (t-90) cc_final: 0.7296 (t-90) REVERT: D 238 ASN cc_start: 0.9143 (p0) cc_final: 0.8858 (p0) REVERT: D 243 GLU cc_start: 0.8273 (mp0) cc_final: 0.7883 (mp0) REVERT: D 278 GLU cc_start: 0.7656 (tp30) cc_final: 0.7416 (tp30) REVERT: D 282 ILE cc_start: 0.7866 (tt) cc_final: 0.7565 (tt) REVERT: D 285 ASP cc_start: 0.7657 (t0) cc_final: 0.7432 (t0) REVERT: D 294 PHE cc_start: 0.8170 (t80) cc_final: 0.7658 (t80) REVERT: D 302 GLU cc_start: 0.8269 (pm20) cc_final: 0.8010 (pm20) REVERT: D 303 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8056 (ttm110) REVERT: D 309 PHE cc_start: 0.8482 (m-80) cc_final: 0.8217 (m-80) REVERT: E 15 THR cc_start: 0.7784 (p) cc_final: 0.7512 (m) REVERT: E 28 MET cc_start: 0.7222 (ptp) cc_final: 0.6821 (ptp) REVERT: E 29 MET cc_start: 0.6222 (tpt) cc_final: 0.5527 (tpt) REVERT: E 44 ASP cc_start: 0.8614 (t0) cc_final: 0.8249 (t0) REVERT: E 69 VAL cc_start: 0.8369 (t) cc_final: 0.7648 (p) REVERT: E 247 LYS cc_start: 0.8263 (ptmt) cc_final: 0.7714 (ptmt) REVERT: E 248 MET cc_start: 0.7754 (mtm) cc_final: 0.7297 (mtm) REVERT: E 254 MET cc_start: 0.7583 (ppp) cc_final: 0.6989 (ppp) REVERT: E 271 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6815 (tpp80) REVERT: E 291 ARG cc_start: 0.7573 (ttm110) cc_final: 0.7068 (ttm110) REVERT: E 305 THR cc_start: 0.8784 (p) cc_final: 0.8429 (t) REVERT: E 309 PHE cc_start: 0.8405 (m-80) cc_final: 0.8114 (m-80) REVERT: F 44 ASP cc_start: 0.7420 (t0) cc_final: 0.7201 (t0) REVERT: F 47 TYR cc_start: 0.8278 (t80) cc_final: 0.7582 (t80) REVERT: F 128 LEU cc_start: 0.8206 (mt) cc_final: 0.7882 (mt) REVERT: F 155 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7970 (tm-30) REVERT: F 290 PHE cc_start: 0.6781 (t80) cc_final: 0.6510 (t80) REVERT: H 248 MET cc_start: 0.8529 (ttm) cc_final: 0.7269 (ttm) REVERT: H 254 MET cc_start: 0.7542 (tpt) cc_final: 0.6885 (tpt) REVERT: H 276 TRP cc_start: 0.7207 (t60) cc_final: 0.6901 (t-100) REVERT: G 421 LEU cc_start: 0.8626 (mt) cc_final: 0.8421 (mt) REVERT: G 427 MET cc_start: 0.7262 (mmm) cc_final: 0.6979 (mmm) REVERT: G 440 ASP cc_start: 0.8992 (t0) cc_final: 0.8756 (t0) REVERT: G 468 SER cc_start: 0.6993 (p) cc_final: 0.6777 (p) REVERT: G 469 ARG cc_start: 0.9270 (tpt90) cc_final: 0.8862 (tpm170) REVERT: G 543 MET cc_start: 0.6648 (mmp) cc_final: 0.6172 (mmp) REVERT: G 611 MET cc_start: 0.7488 (ptp) cc_final: 0.7054 (ptp) REVERT: d 134 MET cc_start: 0.7140 (tmm) cc_final: 0.6921 (tmm) REVERT: I 370 MET cc_start: 0.8030 (mmp) cc_final: 0.7729 (mmp) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.1459 time to fit residues: 115.9105 Evaluate side-chains 512 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 78 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 83 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 HIS ** I 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.218804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159089 restraints weight = 36662.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165008 restraints weight = 22237.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169098 restraints weight = 15463.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.171855 restraints weight = 11867.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.173608 restraints weight = 9847.757| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20229 Z= 0.197 Angle : 0.620 13.331 27449 Z= 0.326 Chirality : 0.044 0.206 3108 Planarity : 0.005 0.084 3597 Dihedral : 4.656 24.660 2769 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2470 helix: 0.06 (0.16), residues: 1071 sheet: -0.51 (0.29), residues: 338 loop : -1.33 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 503 TYR 0.024 0.002 TYR E 39 PHE 0.028 0.002 PHE F 179 TRP 0.036 0.003 TRP F 130 HIS 0.005 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (20229) covalent geometry : angle 0.62031 / 0.33 (27449) hydrogen bonds : bond 0.04012 / 2.70 ( 848) hydrogen bonds : angle 5.51038 / 3.93 ( 2439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9196 (mt) cc_final: 0.8801 (mt) REVERT: A 61 PHE cc_start: 0.8122 (m-80) cc_final: 0.7916 (m-80) REVERT: A 66 ARG cc_start: 0.7683 (mpt90) cc_final: 0.7130 (mpt90) REVERT: A 68 MET cc_start: 0.4865 (tpt) cc_final: 0.4409 (tpt) REVERT: A 143 TYR cc_start: 0.8185 (t80) cc_final: 0.7636 (t80) REVERT: A 182 PHE cc_start: 0.6262 (m-10) cc_final: 0.5801 (m-10) REVERT: A 208 MET cc_start: 0.8118 (mpp) cc_final: 0.7650 (mpp) REVERT: B 68 MET cc_start: 0.6946 (tmm) cc_final: 0.6541 (tmm) REVERT: B 69 VAL cc_start: 0.7496 (p) cc_final: 0.6630 (t) REVERT: B 135 ASN cc_start: 0.8138 (p0) cc_final: 0.7884 (p0) REVERT: B 217 LEU cc_start: 0.7628 (tp) cc_final: 0.7028 (tp) REVERT: B 248 MET cc_start: 0.7055 (mmp) cc_final: 0.6526 (mmt) REVERT: B 290 PHE cc_start: 0.8033 (t80) cc_final: 0.7649 (t80) REVERT: C 30 VAL cc_start: 0.8054 (t) cc_final: 0.7590 (m) REVERT: C 47 TYR cc_start: 0.8195 (t80) cc_final: 0.7961 (t80) REVERT: C 51 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7253 (ttp80) REVERT: C 254 MET cc_start: 0.7348 (ttp) cc_final: 0.6934 (ttp) REVERT: C 257 GLN cc_start: 0.8639 (tp-100) cc_final: 0.7992 (tp-100) REVERT: C 260 ILE cc_start: 0.8648 (mp) cc_final: 0.8421 (mp) REVERT: C 305 THR cc_start: 0.8736 (t) cc_final: 0.8423 (t) REVERT: D 40 VAL cc_start: 0.8694 (t) cc_final: 0.8346 (m) REVERT: D 72 TYR cc_start: 0.7750 (m-80) cc_final: 0.7467 (m-80) REVERT: D 96 ASN cc_start: 0.7792 (m-40) cc_final: 0.7490 (m-40) REVERT: D 119 GLN cc_start: 0.7862 (pm20) cc_final: 0.7583 (pm20) REVERT: D 135 ASN cc_start: 0.8112 (p0) cc_final: 0.7725 (p0) REVERT: D 180 ARG cc_start: 0.8129 (mpt180) cc_final: 0.7691 (mpt180) REVERT: D 219 TYR cc_start: 0.7897 (m-10) cc_final: 0.7647 (m-10) REVERT: D 224 ASN cc_start: 0.8543 (m110) cc_final: 0.8096 (m110) REVERT: D 225 GLU cc_start: 0.7145 (mp0) cc_final: 0.6385 (mp0) REVERT: D 238 ASN cc_start: 0.9184 (p0) cc_final: 0.8895 (p0) REVERT: D 243 GLU cc_start: 0.8202 (mp0) cc_final: 0.7844 (mp0) REVERT: D 248 MET cc_start: 0.8669 (mmm) cc_final: 0.8324 (tpp) REVERT: D 294 PHE cc_start: 0.8170 (t80) cc_final: 0.7669 (t80) REVERT: D 302 GLU cc_start: 0.8212 (pm20) cc_final: 0.7963 (pm20) REVERT: D 303 ARG cc_start: 0.8426 (ttm110) cc_final: 0.8028 (ttm110) REVERT: D 309 PHE cc_start: 0.8501 (m-80) cc_final: 0.8202 (m-80) REVERT: E 15 THR cc_start: 0.7894 (p) cc_final: 0.7651 (m) REVERT: E 28 MET cc_start: 0.7190 (ptp) cc_final: 0.6775 (ptp) REVERT: E 29 MET cc_start: 0.6267 (tpt) cc_final: 0.5641 (tpt) REVERT: E 44 ASP cc_start: 0.8643 (t0) cc_final: 0.8311 (t0) REVERT: E 69 VAL cc_start: 0.8425 (t) cc_final: 0.7718 (p) REVERT: E 144 ASP cc_start: 0.7682 (p0) cc_final: 0.7464 (p0) REVERT: E 246 ASN cc_start: 0.7920 (t0) cc_final: 0.7608 (t0) REVERT: E 247 LYS cc_start: 0.8263 (ptmt) cc_final: 0.7820 (ptmt) REVERT: E 248 MET cc_start: 0.7730 (mtm) cc_final: 0.7253 (mtm) REVERT: E 254 MET cc_start: 0.7503 (ppp) cc_final: 0.6947 (ppp) REVERT: E 291 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7013 (ttm110) REVERT: E 305 THR cc_start: 0.8788 (p) cc_final: 0.8390 (t) REVERT: E 309 PHE cc_start: 0.8388 (m-80) cc_final: 0.8119 (m-80) REVERT: F 44 ASP cc_start: 0.7404 (t0) cc_final: 0.7193 (t0) REVERT: F 47 TYR cc_start: 0.8285 (t80) cc_final: 0.7560 (t80) REVERT: F 83 GLN cc_start: 0.7865 (pt0) cc_final: 0.7637 (pt0) REVERT: F 128 LEU cc_start: 0.8234 (mt) cc_final: 0.7934 (mt) REVERT: F 155 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7987 (tm-30) REVERT: F 290 PHE cc_start: 0.6769 (t80) cc_final: 0.6502 (t80) REVERT: H 248 MET cc_start: 0.8443 (ttm) cc_final: 0.7074 (ttm) REVERT: H 254 MET cc_start: 0.7613 (tpt) cc_final: 0.6917 (tpt) REVERT: H 276 TRP cc_start: 0.7231 (t60) cc_final: 0.6845 (t-100) REVERT: G 421 LEU cc_start: 0.8625 (mt) cc_final: 0.8424 (mt) REVERT: G 427 MET cc_start: 0.7306 (mmm) cc_final: 0.6980 (mmm) REVERT: G 440 ASP cc_start: 0.8997 (t0) cc_final: 0.8753 (t0) REVERT: G 468 SER cc_start: 0.7016 (p) cc_final: 0.6644 (p) REVERT: G 543 MET cc_start: 0.6679 (mmp) cc_final: 0.6236 (mmp) REVERT: G 611 MET cc_start: 0.7474 (ptp) cc_final: 0.7034 (ptp) REVERT: d 134 MET cc_start: 0.7132 (tmm) cc_final: 0.6928 (tmm) REVERT: I 370 MET cc_start: 0.8092 (mmp) cc_final: 0.7789 (mmp) REVERT: I 542 MET cc_start: 0.5237 (tmm) cc_final: 0.4880 (tpp) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.1473 time to fit residues: 119.5260 Evaluate side-chains 524 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN C 135 ASN C 176 HIS D 261 ASN E 83 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.214799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159096 restraints weight = 35653.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164861 restraints weight = 21316.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168785 restraints weight = 14613.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171387 restraints weight = 11094.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173056 restraints weight = 9110.370| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20229 Z= 0.122 Angle : 0.583 14.093 27449 Z= 0.304 Chirality : 0.043 0.209 3108 Planarity : 0.004 0.077 3597 Dihedral : 4.498 21.898 2769 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2470 helix: 0.16 (0.16), residues: 1076 sheet: -0.36 (0.31), residues: 305 loop : -1.20 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 568 TYR 0.021 0.001 TYR I 562 PHE 0.030 0.001 PHE D 283 TRP 0.043 0.002 TRP F 130 HIS 0.004 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (20229) covalent geometry : angle 0.58323 / 0.30 (27449) hydrogen bonds : bond 0.03467 / 2.37 ( 848) hydrogen bonds : angle 5.35941 / 3.80 ( 2439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9172 (mt) cc_final: 0.8772 (mt) REVERT: A 66 ARG cc_start: 0.7568 (mpt90) cc_final: 0.7062 (mpt90) REVERT: A 68 MET cc_start: 0.4786 (tpt) cc_final: 0.4334 (tpt) REVERT: A 143 TYR cc_start: 0.8126 (t80) cc_final: 0.7605 (t80) REVERT: A 182 PHE cc_start: 0.6229 (m-10) cc_final: 0.5850 (m-10) REVERT: A 208 MET cc_start: 0.7964 (mpp) cc_final: 0.7523 (mpp) REVERT: B 68 MET cc_start: 0.6842 (tmm) cc_final: 0.6502 (tmm) REVERT: B 135 ASN cc_start: 0.8137 (p0) cc_final: 0.7880 (p0) REVERT: B 217 LEU cc_start: 0.7474 (tp) cc_final: 0.6960 (tp) REVERT: B 248 MET cc_start: 0.6834 (mmp) cc_final: 0.6359 (mmt) REVERT: B 254 MET cc_start: 0.6652 (ptp) cc_final: 0.6378 (ptp) REVERT: B 290 PHE cc_start: 0.7909 (t80) cc_final: 0.7549 (t80) REVERT: C 30 VAL cc_start: 0.8034 (t) cc_final: 0.7583 (m) REVERT: C 47 TYR cc_start: 0.8068 (t80) cc_final: 0.7822 (t80) REVERT: C 51 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7214 (ttp80) REVERT: C 141 ASP cc_start: 0.5500 (t0) cc_final: 0.5214 (t0) REVERT: C 186 ASN cc_start: 0.8030 (m-40) cc_final: 0.7533 (m-40) REVERT: C 257 GLN cc_start: 0.8566 (tp-100) cc_final: 0.7891 (tp-100) REVERT: C 260 ILE cc_start: 0.8598 (mp) cc_final: 0.8387 (mp) REVERT: D 40 VAL cc_start: 0.8721 (t) cc_final: 0.8364 (m) REVERT: D 72 TYR cc_start: 0.7710 (m-80) cc_final: 0.7435 (m-80) REVERT: D 96 ASN cc_start: 0.7701 (m-40) cc_final: 0.7369 (m-40) REVERT: D 119 GLN cc_start: 0.7829 (pm20) cc_final: 0.7409 (pm20) REVERT: D 135 ASN cc_start: 0.8107 (p0) cc_final: 0.7819 (p0) REVERT: D 151 MET cc_start: 0.7060 (tpp) cc_final: 0.6844 (mmm) REVERT: D 180 ARG cc_start: 0.8079 (mpt180) cc_final: 0.7669 (mpt180) REVERT: D 224 ASN cc_start: 0.8519 (m110) cc_final: 0.7960 (m110) REVERT: D 238 ASN cc_start: 0.9164 (p0) cc_final: 0.8852 (p0) REVERT: D 243 GLU cc_start: 0.8150 (mp0) cc_final: 0.7927 (mp0) REVERT: D 246 ASN cc_start: 0.8688 (m110) cc_final: 0.8303 (m110) REVERT: D 248 MET cc_start: 0.8640 (mmm) cc_final: 0.8346 (tpp) REVERT: D 268 MET cc_start: 0.7656 (tpp) cc_final: 0.7373 (tpp) REVERT: D 278 GLU cc_start: 0.7610 (tp30) cc_final: 0.7312 (tp30) REVERT: D 282 ILE cc_start: 0.7901 (tt) cc_final: 0.7570 (tt) REVERT: D 285 ASP cc_start: 0.7429 (t70) cc_final: 0.7062 (t70) REVERT: D 294 PHE cc_start: 0.8166 (t80) cc_final: 0.7649 (t80) REVERT: D 302 GLU cc_start: 0.8179 (pm20) cc_final: 0.7903 (pm20) REVERT: D 303 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7959 (ttm110) REVERT: D 309 PHE cc_start: 0.8419 (m-80) cc_final: 0.8146 (m-80) REVERT: E 15 THR cc_start: 0.7778 (p) cc_final: 0.7559 (m) REVERT: E 28 MET cc_start: 0.7143 (ptp) cc_final: 0.6720 (ptp) REVERT: E 29 MET cc_start: 0.6218 (tpt) cc_final: 0.5623 (tpt) REVERT: E 44 ASP cc_start: 0.8602 (t0) cc_final: 0.8259 (t0) REVERT: E 144 ASP cc_start: 0.7650 (p0) cc_final: 0.7410 (p0) REVERT: E 246 ASN cc_start: 0.7858 (t0) cc_final: 0.7551 (t0) REVERT: E 247 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7994 (ptpt) REVERT: E 248 MET cc_start: 0.7659 (mtm) cc_final: 0.7148 (mtm) REVERT: E 254 MET cc_start: 0.7463 (ppp) cc_final: 0.6920 (ppp) REVERT: E 291 ARG cc_start: 0.7456 (ttm110) cc_final: 0.6957 (ttm110) REVERT: E 305 THR cc_start: 0.8742 (p) cc_final: 0.8364 (t) REVERT: E 309 PHE cc_start: 0.8320 (m-80) cc_final: 0.8065 (m-80) REVERT: F 44 ASP cc_start: 0.7415 (t0) cc_final: 0.7200 (t0) REVERT: F 47 TYR cc_start: 0.8286 (t80) cc_final: 0.7564 (t80) REVERT: F 128 LEU cc_start: 0.8175 (mt) cc_final: 0.7886 (mt) REVERT: F 155 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7902 (tm-30) REVERT: F 290 PHE cc_start: 0.6622 (t80) cc_final: 0.6406 (t80) REVERT: H 248 MET cc_start: 0.8369 (ttm) cc_final: 0.6201 (ttm) REVERT: H 254 MET cc_start: 0.7374 (tpt) cc_final: 0.6734 (tpt) REVERT: H 276 TRP cc_start: 0.7202 (t60) cc_final: 0.6458 (t-100) REVERT: G 421 LEU cc_start: 0.8604 (mt) cc_final: 0.8365 (mt) REVERT: G 427 MET cc_start: 0.7210 (mmm) cc_final: 0.6894 (mmm) REVERT: G 440 ASP cc_start: 0.8964 (t0) cc_final: 0.8715 (t0) REVERT: G 468 SER cc_start: 0.6800 (p) cc_final: 0.6430 (p) REVERT: G 543 MET cc_start: 0.6513 (mmp) cc_final: 0.6072 (mmp) REVERT: G 611 MET cc_start: 0.7390 (ptp) cc_final: 0.6936 (ptp) REVERT: d 134 MET cc_start: 0.7150 (tmm) cc_final: 0.6937 (tmm) REVERT: I 370 MET cc_start: 0.8077 (mmp) cc_final: 0.7781 (mmp) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1459 time to fit residues: 114.8388 Evaluate side-chains 508 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 230 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 83 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 HIS ** I 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.215423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156322 restraints weight = 36121.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161988 restraints weight = 21645.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.165912 restraints weight = 14998.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168587 restraints weight = 11470.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170410 restraints weight = 9471.599| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20229 Z= 0.195 Angle : 0.623 13.059 27449 Z= 0.330 Chirality : 0.044 0.220 3108 Planarity : 0.005 0.083 3597 Dihedral : 4.672 21.439 2769 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.17), residues: 2470 helix: 0.04 (0.16), residues: 1072 sheet: -0.50 (0.30), residues: 332 loop : -1.33 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 180 TYR 0.024 0.002 TYR E 219 PHE 0.038 0.002 PHE A 61 TRP 0.039 0.003 TRP F 130 HIS 0.008 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (20229) covalent geometry : angle 0.62339 / 0.33 (27449) hydrogen bonds : bond 0.04004 / 2.72 ( 848) hydrogen bonds : angle 5.54777 / 3.97 ( 2439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 535 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7627 (mpt90) cc_final: 0.7114 (mpt90) REVERT: A 68 MET cc_start: 0.4857 (tpt) cc_final: 0.4453 (tpt) REVERT: A 143 TYR cc_start: 0.8193 (t80) cc_final: 0.7628 (t80) REVERT: A 182 PHE cc_start: 0.6267 (m-10) cc_final: 0.5824 (m-10) REVERT: A 208 MET cc_start: 0.8100 (mpp) cc_final: 0.7631 (mpp) REVERT: B 68 MET cc_start: 0.6919 (tmm) cc_final: 0.6479 (tmm) REVERT: B 217 LEU cc_start: 0.7508 (tp) cc_final: 0.6951 (tp) REVERT: B 248 MET cc_start: 0.7040 (mmp) cc_final: 0.6389 (mmt) REVERT: B 254 MET cc_start: 0.6757 (ptp) cc_final: 0.6515 (ptp) REVERT: B 290 PHE cc_start: 0.7988 (t80) cc_final: 0.7623 (t80) REVERT: C 30 VAL cc_start: 0.8147 (t) cc_final: 0.7944 (t) REVERT: C 47 TYR cc_start: 0.8248 (t80) cc_final: 0.7918 (t80) REVERT: C 51 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7498 (ttp80) REVERT: C 222 HIS cc_start: 0.8058 (t-90) cc_final: 0.7470 (t-90) REVERT: C 250 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7905 (mmp80) REVERT: C 257 GLN cc_start: 0.8584 (tp-100) cc_final: 0.7924 (tp-100) REVERT: C 260 ILE cc_start: 0.8593 (mp) cc_final: 0.8369 (mp) REVERT: D 22 PHE cc_start: 0.8599 (m-80) cc_final: 0.8361 (m-10) REVERT: D 40 VAL cc_start: 0.8705 (t) cc_final: 0.8353 (m) REVERT: D 68 MET cc_start: 0.7796 (mtp) cc_final: 0.7541 (mtp) REVERT: D 72 TYR cc_start: 0.7776 (m-80) cc_final: 0.7440 (m-80) REVERT: D 96 ASN cc_start: 0.7805 (m-40) cc_final: 0.7449 (m-40) REVERT: D 119 GLN cc_start: 0.7998 (pm20) cc_final: 0.7715 (pm20) REVERT: D 151 MET cc_start: 0.7312 (tpp) cc_final: 0.6992 (mmm) REVERT: D 180 ARG cc_start: 0.8123 (mpt180) cc_final: 0.7915 (mmt-90) REVERT: D 224 ASN cc_start: 0.8530 (m110) cc_final: 0.8120 (m110) REVERT: D 238 ASN cc_start: 0.9156 (p0) cc_final: 0.8853 (p0) REVERT: D 243 GLU cc_start: 0.8210 (mp0) cc_final: 0.7990 (mp0) REVERT: D 246 ASN cc_start: 0.8734 (m110) cc_final: 0.8349 (m110) REVERT: D 248 MET cc_start: 0.8638 (mmm) cc_final: 0.8267 (tpp) REVERT: D 278 GLU cc_start: 0.7658 (tp30) cc_final: 0.7372 (tp30) REVERT: D 282 ILE cc_start: 0.7987 (tt) cc_final: 0.7596 (tt) REVERT: D 285 ASP cc_start: 0.7491 (t70) cc_final: 0.7047 (t70) REVERT: D 294 PHE cc_start: 0.8166 (t80) cc_final: 0.7684 (t80) REVERT: D 302 GLU cc_start: 0.8242 (pm20) cc_final: 0.7996 (pm20) REVERT: D 303 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8073 (ttm110) REVERT: D 309 PHE cc_start: 0.8477 (m-80) cc_final: 0.8185 (m-80) REVERT: E 15 THR cc_start: 0.7925 (p) cc_final: 0.7671 (m) REVERT: E 28 MET cc_start: 0.7222 (ptp) cc_final: 0.6784 (ptp) REVERT: E 29 MET cc_start: 0.6279 (tpt) cc_final: 0.5648 (tpt) REVERT: E 44 ASP cc_start: 0.8640 (t0) cc_final: 0.8348 (t0) REVERT: E 69 VAL cc_start: 0.8412 (t) cc_final: 0.7730 (p) REVERT: E 144 ASP cc_start: 0.7774 (p0) cc_final: 0.7571 (p0) REVERT: E 180 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7283 (mmt-90) REVERT: E 207 GLN cc_start: 0.5493 (pm20) cc_final: 0.4931 (pm20) REVERT: E 246 ASN cc_start: 0.7916 (t0) cc_final: 0.7629 (t0) REVERT: E 247 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7825 (ptmt) REVERT: E 248 MET cc_start: 0.7704 (mtm) cc_final: 0.7203 (mtm) REVERT: E 254 MET cc_start: 0.7450 (ppp) cc_final: 0.6901 (ppp) REVERT: E 291 ARG cc_start: 0.7527 (ttm110) cc_final: 0.7045 (ttm110) REVERT: E 305 THR cc_start: 0.8763 (p) cc_final: 0.8367 (t) REVERT: E 309 PHE cc_start: 0.8367 (m-80) cc_final: 0.8118 (m-80) REVERT: F 44 ASP cc_start: 0.7428 (t0) cc_final: 0.7188 (t0) REVERT: F 47 TYR cc_start: 0.8282 (t80) cc_final: 0.7636 (t80) REVERT: F 83 GLN cc_start: 0.7811 (pt0) cc_final: 0.7592 (pt0) REVERT: F 128 LEU cc_start: 0.8229 (mt) cc_final: 0.7958 (mt) REVERT: F 155 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7953 (tm-30) REVERT: F 232 LYS cc_start: 0.9263 (tppt) cc_final: 0.9034 (tppp) REVERT: H 248 MET cc_start: 0.8384 (ttm) cc_final: 0.6987 (ttm) REVERT: H 254 MET cc_start: 0.7341 (tpt) cc_final: 0.7114 (tpt) REVERT: H 276 TRP cc_start: 0.7289 (t60) cc_final: 0.6815 (t-100) REVERT: G 421 LEU cc_start: 0.8653 (mt) cc_final: 0.8416 (mt) REVERT: G 427 MET cc_start: 0.7317 (mmm) cc_final: 0.6983 (mmm) REVERT: G 440 ASP cc_start: 0.8977 (t0) cc_final: 0.8736 (t0) REVERT: G 468 SER cc_start: 0.7002 (p) cc_final: 0.6659 (p) REVERT: G 543 MET cc_start: 0.6670 (mmp) cc_final: 0.6248 (mmp) REVERT: G 611 MET cc_start: 0.7414 (ptp) cc_final: 0.6932 (ptp) REVERT: d 134 MET cc_start: 0.7192 (tmm) cc_final: 0.6975 (tmm) REVERT: I 370 MET cc_start: 0.8125 (mmp) cc_final: 0.7835 (mmp) REVERT: I 542 MET cc_start: 0.5371 (tmm) cc_final: 0.4974 (tpt) outliers start: 1 outliers final: 1 residues processed: 535 average time/residue: 0.1475 time to fit residues: 118.0437 Evaluate side-chains 515 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 245 optimal weight: 30.0000 chunk 109 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 238 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN C 135 ASN C 176 HIS D 261 ASN E 83 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** G 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 HIS ** I 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.219930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161342 restraints weight = 36553.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167284 restraints weight = 21911.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171275 restraints weight = 15091.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173890 restraints weight = 11512.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175864 restraints weight = 9552.881| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20229 Z= 0.122 Angle : 0.580 13.592 27449 Z= 0.302 Chirality : 0.043 0.207 3108 Planarity : 0.004 0.076 3597 Dihedral : 4.490 23.077 2769 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2470 helix: 0.14 (0.16), residues: 1084 sheet: -0.44 (0.31), residues: 309 loop : -1.20 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 568 TYR 0.020 0.001 TYR I 562 PHE 0.023 0.001 PHE D 283 TRP 0.038 0.002 TRP F 130 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20229) covalent geometry : angle 0.58026 / 0.30 (27449) hydrogen bonds : bond 0.03407 / 2.33 ( 848) hydrogen bonds : angle 5.32502 / 3.78 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.68 seconds wall clock time: 67 minutes 13.85 seconds (4033.85 seconds total)