Starting phenix.real_space_refine on Thu Jul 2 09:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsq_30841/07_2026/7dsq_30841_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsq_30841/07_2026/7dsq_30841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dsq_30841/07_2026/7dsq_30841_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsq_30841/07_2026/7dsq_30841_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsq_30841/07_2026/7dsq_30841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsq_30841/07_2026/7dsq_30841.map" } resolution = 3.4 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians I 2 10.91 5 P 1 5.49 5 S 27 5.16 5 C 4917 2.51 5 N 1189 2.21 5 O 1371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7507 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3661 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 447} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 133 Unusual residues: {'3PH': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 15} Link IDs: {None: 17} Time building chain proxies: 1.49, per 1000 atoms: 0.20 Number of scatterers: 7507 At special positions: 0 Unit cell: (81.525, 85.873, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 2 52.95 S 27 16.00 P 1 15.00 O 1371 8.00 N 1189 7.00 C 4917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=1.68 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 267.9 milliseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 57.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.610A pdb=" N LEU A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 3.845A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.671A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.191A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.814A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 247' Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.915A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.564A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.597A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 3.549A pdb=" N SER A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.706A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.909A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.802A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.652A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 81 through 110 removed outlier: 4.404A pdb=" N ALA B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 93 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.863A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 removed outlier: 4.042A pdb=" N LYS B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 138 " --> pdb=" O TRP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.505A pdb=" N SER B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 145 through 157 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.691A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 182 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 219 removed outlier: 3.540A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 253 removed outlier: 3.952A pdb=" N ALA B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 297 removed outlier: 3.706A pdb=" N LEU B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Proline residue: B 275 - end of helix removed outlier: 3.693A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.548A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.735A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 339 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.685A pdb=" N PHE B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.793A pdb=" N HIS B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 421 " --> pdb=" O TRP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.505A pdb=" N PHE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.520A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.529A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227 Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 removed outlier: 5.944A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG A 349 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.771A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.546A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA6, first strand: chain 'A' and resid 593 through 594 336 hydrogen bonds defined for protein. 975 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: 0.89 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 2569 1.37 - 1.57: 5047 1.57 - 1.76: 20 1.76 - 1.95: 40 1.95 - 2.14: 2 Bond restraints: 7678 Sorted by residual: bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.550 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CBG Y01 B 602 " pdb=" CBI Y01 B 602 " ideal model delta sigma weight residual 1.537 1.386 0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CAI Y01 B 603 " pdb=" CAK Y01 B 603 " ideal model delta sigma weight residual 1.492 1.637 -0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" CBG Y01 B 603 " pdb=" CBI Y01 B 603 " ideal model delta sigma weight residual 1.537 1.397 0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 7673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 9912 2.31 - 4.62: 434 4.62 - 6.93: 72 6.93 - 9.24: 29 9.24 - 11.55: 9 Bond angle restraints: 10456 Sorted by residual: angle pdb=" N LYS B 453 " pdb=" CA LYS B 453 " pdb=" C LYS B 453 " ideal model delta sigma weight residual 114.62 108.18 6.44 1.14e+00 7.69e-01 3.20e+01 angle pdb=" N ASN B 230 " pdb=" CA ASN B 230 " pdb=" C ASN B 230 " ideal model delta sigma weight residual 109.31 117.18 -7.87 1.42e+00 4.96e-01 3.07e+01 angle pdb=" C PHE B 233 " pdb=" N GLU B 234 " pdb=" CA GLU B 234 " ideal model delta sigma weight residual 121.54 131.90 -10.36 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C ASN B 226 " pdb=" N LEU B 227 " pdb=" CA LEU B 227 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.51e+01 angle pdb=" C PRO B 373 " pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta sigma weight residual 120.33 123.94 -3.61 8.00e-01 1.56e+00 2.03e+01 ... (remaining 10451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 4523 35.67 - 71.34: 121 71.34 - 107.01: 20 107.01 - 142.68: 31 142.68 - 178.35: 7 Dihedral angle restraints: 4702 sinusoidal: 2023 harmonic: 2679 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -156.33 70.33 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA GLY B 235 " pdb=" C GLY B 235 " pdb=" N THR B 236 " pdb=" CA THR B 236 " ideal model delta harmonic sigma weight residual -180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA SER A 409 " pdb=" C SER A 409 " pdb=" N GLY A 410 " pdb=" CA GLY A 410 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 4699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.183: 1222 1.183 - 2.367: 0 2.367 - 3.550: 0 3.550 - 4.733: 0 4.733 - 5.917: 10 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -2.98 5.92 2.00e-01 2.50e+01 8.75e+02 chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -2.96 5.89 2.00e-01 2.50e+01 8.69e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.65 -5.50 2.00e-01 2.50e+01 7.57e+02 ... (remaining 1229 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 164 " 0.052 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO B 165 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 166 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO B 167 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 619 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.041 5.00e-02 4.00e+02 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.83: 2374 2.83 - 3.36: 6826 3.36 - 3.89: 12288 3.89 - 4.43: 14509 4.43 - 4.96: 25146 Nonbonded interactions: 61143 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG1 THR B 62 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.297 3.040 nonbonded pdb=" O HOH B 706 " pdb=" O HOH B 707 " model vdw 2.304 3.040 nonbonded pdb=" O LEU B 371 " pdb=" O HOH B 701 " model vdw 2.310 3.040 nonbonded pdb=" OG SER B 308 " pdb=" OD2 ASP B 314 " model vdw 2.321 3.040 ... (remaining 61138 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.011 0.354 7687 Z= 0.542 Angle : 1.244 17.773 10482 Z= 0.645 Chirality : 0.489 5.917 1232 Planarity : 0.008 0.080 1279 Dihedral : 22.550 178.347 2977 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.86 % Allowed : 8.82 % Favored : 90.32 % Rotamer: Outliers : 0.89 % Allowed : 7.99 % Favored : 91.12 % 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: -4.52 (0.20), residues: 930 helix: -2.77 (0.16), residues: 476 sheet: -0.76 (0.63), residues: 62 loop : -3.61 (0.23), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 556 TYR 0.028 0.003 TYR B 259 PHE 0.021 0.003 PHE B 351 TRP 0.010 0.002 TRP A 220 HIS 0.006 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.01046 / 0.50 ( 7678) covalent geometry : angle 1.19430 / 0.63 (10456) SS BOND : bond 0.35359 / 18.61 ( 1) SS BOND : angle 6.74025 / 3.82 ( 2) hydrogen bonds : bond 0.19511 / 13.86 ( 336) hydrogen bonds : angle 6.73477 / 4.64 ( 975) link_BETA1-4 : bond 0.02346 / 1.13 ( 4) link_BETA1-4 : angle 7.04705 / 4.00 ( 12) link_NAG-ASN : bond 0.00203 / 0.10 ( 4) link_NAG-ASN : angle 7.14172 / 3.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7942 (mm) cc_final: 0.7550 (pp) REVERT: A 191 TRP cc_start: 0.8301 (m100) cc_final: 0.8075 (m100) REVERT: A 332 LYS cc_start: 0.8851 (tttp) cc_final: 0.8456 (tmmt) REVERT: A 365 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8697 (tp-100) REVERT: B 77 LYS cc_start: 0.7742 (tttm) cc_final: 0.7516 (ttmt) REVERT: B 120 MET cc_start: 0.8117 (ttm) cc_final: 0.7858 (mtp) REVERT: B 137 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9015 (pt) REVERT: B 386 LEU cc_start: 0.9068 (mm) cc_final: 0.8843 (mm) REVERT: B 412 ILE cc_start: 0.8882 (mm) cc_final: 0.8636 (mm) REVERT: B 417 TRP cc_start: 0.7350 (t-100) cc_final: 0.7075 (t-100) REVERT: B 477 TRP cc_start: 0.8751 (t60) cc_final: 0.8414 (t60) REVERT: B 478 TRP cc_start: 0.8613 (t60) cc_final: 0.8357 (t60) outliers start: 7 outliers final: 3 residues processed: 161 average time/residue: 0.0781 time to fit residues: 17.1113 Evaluate side-chains 124 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 275 GLN A 353 ASN A 396 ASN A 539 HIS A 561 ASN B 273 ASN B 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114185 restraints weight = 7545.391| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.16 r_work: 0.3173 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7687 Z= 0.154 Angle : 1.285 33.731 10482 Z= 0.502 Chirality : 0.109 1.798 1232 Planarity : 0.006 0.051 1279 Dihedral : 23.088 178.097 1343 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.31 % Favored : 92.15 % Rotamer: Outliers : 2.28 % Allowed : 12.82 % Favored : 84.90 % 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: -2.59 (0.25), residues: 930 helix: -0.91 (0.22), residues: 492 sheet: -0.84 (0.60), residues: 67 loop : -2.98 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.021 0.001 TYR B 259 PHE 0.014 0.002 PHE B 252 TRP 0.009 0.001 TRP B 89 HIS 0.004 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 7678) covalent geometry : angle 1.26197 / 0.49 (10456) SS BOND : bond 0.00849 / 0.45 ( 1) SS BOND : angle 4.48739 / 2.55 ( 2) hydrogen bonds : bond 0.05012 / 3.29 ( 336) hydrogen bonds : angle 4.47991 / 3.11 ( 975) link_BETA1-4 : bond 0.01294 / 0.62 ( 4) link_BETA1-4 : angle 3.99193 / 2.34 ( 12) link_NAG-ASN : bond 0.00372 / 0.19 ( 4) link_NAG-ASN : angle 5.95334 / 3.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.268 Fit side-chains REVERT: A 191 TRP cc_start: 0.8520 (m100) cc_final: 0.8286 (m100) REVERT: A 332 LYS cc_start: 0.8974 (tttp) cc_final: 0.8538 (tmmt) REVERT: A 365 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8707 (tp-100) REVERT: A 529 ASP cc_start: 0.8649 (t0) cc_final: 0.8425 (t0) REVERT: B 386 LEU cc_start: 0.9065 (mm) cc_final: 0.8750 (mm) REVERT: B 412 ILE cc_start: 0.8814 (mm) cc_final: 0.8600 (mm) REVERT: B 477 TRP cc_start: 0.8811 (t60) cc_final: 0.8574 (t60) REVERT: B 478 TRP cc_start: 0.8696 (t60) cc_final: 0.8321 (t60) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 0.0736 time to fit residues: 13.8924 Evaluate side-chains 126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 ASN B 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114348 restraints weight = 7825.249| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.20 r_work: 0.3151 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7687 Z= 0.141 Angle : 1.248 32.289 10482 Z= 0.479 Chirality : 0.109 1.824 1232 Planarity : 0.005 0.044 1279 Dihedral : 22.978 179.180 1340 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.63 % Favored : 92.04 % Rotamer: Outliers : 2.28 % Allowed : 14.85 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.65 (0.27), residues: 930 helix: -0.03 (0.23), residues: 492 sheet: -0.81 (0.59), residues: 69 loop : -2.65 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 195 TYR 0.022 0.001 TYR A 469 PHE 0.021 0.001 PHE B 474 TRP 0.020 0.001 TRP B 417 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7678) covalent geometry : angle 1.22735 / 0.47 (10456) SS BOND : bond 0.00931 / 0.49 ( 1) SS BOND : angle 4.47580 / 2.52 ( 2) hydrogen bonds : bond 0.04377 / 2.89 ( 336) hydrogen bonds : angle 4.11433 / 2.88 ( 975) link_BETA1-4 : bond 0.01305 / 0.63 ( 4) link_BETA1-4 : angle 3.81092 / 2.21 ( 12) link_NAG-ASN : bond 0.00317 / 0.16 ( 4) link_NAG-ASN : angle 5.51131 / 3.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8559 (m100) cc_final: 0.8326 (m100) REVERT: A 332 LYS cc_start: 0.9025 (tttp) cc_final: 0.8658 (ttpt) REVERT: A 365 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8679 (tt0) REVERT: A 529 ASP cc_start: 0.8781 (t0) cc_final: 0.8559 (t0) REVERT: B 103 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 304 GLN cc_start: 0.5848 (tp40) cc_final: 0.5638 (tp-100) REVERT: B 386 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8702 (mm) REVERT: B 478 TRP cc_start: 0.8651 (t60) cc_final: 0.8228 (t60) outliers start: 18 outliers final: 11 residues processed: 123 average time/residue: 0.0655 time to fit residues: 11.4972 Evaluate side-chains 119 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112362 restraints weight = 7801.505| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.17 r_work: 0.3155 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7687 Z= 0.168 Angle : 1.254 33.336 10482 Z= 0.483 Chirality : 0.108 1.803 1232 Planarity : 0.004 0.041 1279 Dihedral : 22.921 177.242 1340 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.17 % Favored : 91.61 % Rotamer: Outliers : 2.79 % Allowed : 16.88 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.18 (0.27), residues: 930 helix: 0.40 (0.24), residues: 485 sheet: -0.60 (0.60), residues: 69 loop : -2.46 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.025 0.001 TYR A 469 PHE 0.015 0.002 PHE B 399 TRP 0.009 0.001 TRP B 405 HIS 0.002 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7678) covalent geometry : angle 1.23410 / 0.48 (10456) SS BOND : bond 0.00919 / 0.48 ( 1) SS BOND : angle 4.67066 / 2.60 ( 2) hydrogen bonds : bond 0.04395 / 2.89 ( 336) hydrogen bonds : angle 4.09835 / 2.88 ( 975) link_BETA1-4 : bond 0.01323 / 0.63 ( 4) link_BETA1-4 : angle 3.70958 / 2.16 ( 12) link_NAG-ASN : bond 0.00305 / 0.15 ( 4) link_NAG-ASN : angle 5.30191 / 2.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8609 (m100) cc_final: 0.8364 (m100) REVERT: A 332 LYS cc_start: 0.8992 (tttp) cc_final: 0.8642 (ttpt) REVERT: A 365 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8636 (tt0) REVERT: A 529 ASP cc_start: 0.8760 (t0) cc_final: 0.8544 (t0) REVERT: B 218 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 386 LEU cc_start: 0.9103 (mm) cc_final: 0.8768 (mm) REVERT: B 478 TRP cc_start: 0.8703 (t60) cc_final: 0.8334 (t60) outliers start: 22 outliers final: 18 residues processed: 126 average time/residue: 0.0609 time to fit residues: 11.0823 Evaluate side-chains 128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 404 ASN B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114971 restraints weight = 7495.805| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.11 r_work: 0.3192 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7687 Z= 0.128 Angle : 1.231 33.342 10482 Z= 0.469 Chirality : 0.108 1.811 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.875 176.983 1340 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.85 % Favored : 91.94 % Rotamer: Outliers : 2.66 % Allowed : 19.04 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.77 (0.28), residues: 930 helix: 0.77 (0.24), residues: 486 sheet: -0.50 (0.61), residues: 69 loop : -2.31 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.030 0.001 TYR A 469 PHE 0.027 0.001 PHE B 474 TRP 0.008 0.001 TRP B 405 HIS 0.002 0.000 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7678) covalent geometry : angle 1.21235 / 0.46 (10456) SS BOND : bond 0.00891 / 0.47 ( 1) SS BOND : angle 4.60240 / 2.53 ( 2) hydrogen bonds : bond 0.03848 / 2.52 ( 336) hydrogen bonds : angle 3.90137 / 2.74 ( 975) link_BETA1-4 : bond 0.01263 / 0.61 ( 4) link_BETA1-4 : angle 3.57736 / 2.07 ( 12) link_NAG-ASN : bond 0.00267 / 0.13 ( 4) link_NAG-ASN : angle 5.10092 / 2.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8570 (m100) cc_final: 0.8349 (m100) REVERT: A 332 LYS cc_start: 0.8977 (tttp) cc_final: 0.8666 (ttpt) REVERT: A 365 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8594 (tt0) REVERT: B 103 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 218 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7816 (tm-30) REVERT: B 304 GLN cc_start: 0.5653 (tp40) cc_final: 0.5367 (tp-100) REVERT: B 309 GLU cc_start: 0.8114 (mp0) cc_final: 0.7619 (mp0) REVERT: B 333 LEU cc_start: 0.8805 (mt) cc_final: 0.8454 (mt) REVERT: B 386 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8728 (mm) REVERT: B 478 TRP cc_start: 0.8635 (t60) cc_final: 0.8227 (t60) outliers start: 21 outliers final: 16 residues processed: 131 average time/residue: 0.0654 time to fit residues: 12.3117 Evaluate side-chains 130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 0.0020 chunk 80 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114236 restraints weight = 7065.475| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.04 r_work: 0.3187 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7687 Z= 0.136 Angle : 1.231 33.483 10482 Z= 0.470 Chirality : 0.108 1.812 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.889 177.666 1340 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.49 % Favored : 91.29 % Rotamer: Outliers : 2.54 % Allowed : 19.54 % Favored : 77.92 % 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: -0.55 (0.28), residues: 930 helix: 0.97 (0.24), residues: 486 sheet: -0.47 (0.61), residues: 69 loop : -2.21 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.030 0.001 TYR A 469 PHE 0.032 0.001 PHE B 95 TRP 0.008 0.001 TRP B 405 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7678) covalent geometry : angle 1.21433 / 0.46 (10456) SS BOND : bond 0.01071 / 0.56 ( 1) SS BOND : angle 4.22776 / 2.41 ( 2) hydrogen bonds : bond 0.03886 / 2.55 ( 336) hydrogen bonds : angle 3.87263 / 2.72 ( 975) link_BETA1-4 : bond 0.01154 / 0.55 ( 4) link_BETA1-4 : angle 3.51388 / 2.04 ( 12) link_NAG-ASN : bond 0.00273 / 0.14 ( 4) link_NAG-ASN : angle 4.88492 / 2.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.179 Fit side-chains REVERT: A 191 TRP cc_start: 0.8582 (m100) cc_final: 0.8359 (m100) REVERT: A 332 LYS cc_start: 0.8990 (tttp) cc_final: 0.8675 (ttpt) REVERT: A 365 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8594 (tt0) REVERT: A 440 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8336 (mmm-85) REVERT: B 103 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7257 (t80) REVERT: B 218 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7871 (tm-30) REVERT: B 309 GLU cc_start: 0.8082 (mp0) cc_final: 0.7877 (mp0) REVERT: B 333 LEU cc_start: 0.8796 (mt) cc_final: 0.8439 (mt) REVERT: B 386 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8720 (mm) REVERT: B 478 TRP cc_start: 0.8632 (t60) cc_final: 0.8240 (t60) REVERT: B 497 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8437 (mm-40) outliers start: 20 outliers final: 17 residues processed: 121 average time/residue: 0.0636 time to fit residues: 11.1548 Evaluate side-chains 126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113468 restraints weight = 7841.201| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.15 r_work: 0.3179 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7687 Z= 0.145 Angle : 1.233 33.261 10482 Z= 0.472 Chirality : 0.109 1.805 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.938 178.630 1340 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.79 % Allowed : 19.80 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.44 (0.28), residues: 930 helix: 1.08 (0.24), residues: 486 sheet: -0.48 (0.60), residues: 69 loop : -2.17 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 421 TYR 0.030 0.001 TYR A 469 PHE 0.030 0.002 PHE B 95 TRP 0.008 0.001 TRP B 405 HIS 0.005 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 7678) covalent geometry : angle 1.21685 / 0.47 (10456) SS BOND : bond 0.00943 / 0.50 ( 1) SS BOND : angle 4.43278 / 2.52 ( 2) hydrogen bonds : bond 0.03928 / 2.58 ( 336) hydrogen bonds : angle 3.89667 / 2.73 ( 975) link_BETA1-4 : bond 0.01221 / 0.59 ( 4) link_BETA1-4 : angle 3.46284 / 2.02 ( 12) link_NAG-ASN : bond 0.00266 / 0.13 ( 4) link_NAG-ASN : angle 4.71169 / 2.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.269 Fit side-chains REVERT: A 191 TRP cc_start: 0.8593 (m100) cc_final: 0.8368 (m100) REVERT: A 332 LYS cc_start: 0.9000 (tttp) cc_final: 0.8693 (ttpt) REVERT: A 365 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8601 (tt0) REVERT: A 440 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8360 (mmm-85) REVERT: B 103 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7148 (t80) REVERT: B 218 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 309 GLU cc_start: 0.8137 (mp0) cc_final: 0.7886 (mp0) REVERT: B 333 LEU cc_start: 0.8800 (mt) cc_final: 0.8447 (mt) REVERT: B 386 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8717 (mm) REVERT: B 418 LEU cc_start: 0.8635 (tt) cc_final: 0.8391 (tt) REVERT: B 478 TRP cc_start: 0.8607 (t60) cc_final: 0.8211 (t60) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.0660 time to fit residues: 11.6375 Evaluate side-chains 125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114304 restraints weight = 7774.166| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.13 r_work: 0.3180 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7687 Z= 0.133 Angle : 1.218 32.471 10482 Z= 0.464 Chirality : 0.109 1.802 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.955 179.519 1340 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.66 % Allowed : 20.18 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.24 (0.29), residues: 930 helix: 1.25 (0.25), residues: 487 sheet: -0.44 (0.60), residues: 69 loop : -2.09 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.030 0.001 TYR A 469 PHE 0.030 0.001 PHE B 95 TRP 0.012 0.001 TRP B 417 HIS 0.001 0.000 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7678) covalent geometry : angle 1.20338 / 0.46 (10456) SS BOND : bond 0.00840 / 0.44 ( 1) SS BOND : angle 4.29196 / 2.43 ( 2) hydrogen bonds : bond 0.03782 / 2.47 ( 336) hydrogen bonds : angle 3.84783 / 2.68 ( 975) link_BETA1-4 : bond 0.01169 / 0.56 ( 4) link_BETA1-4 : angle 3.34221 / 1.95 ( 12) link_NAG-ASN : bond 0.00269 / 0.13 ( 4) link_NAG-ASN : angle 4.43250 / 2.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.280 Fit side-chains REVERT: A 186 LEU cc_start: 0.8666 (mm) cc_final: 0.8401 (mt) REVERT: A 191 TRP cc_start: 0.8506 (m100) cc_final: 0.8252 (m100) REVERT: A 332 LYS cc_start: 0.9004 (tttp) cc_final: 0.8659 (ttpt) REVERT: A 336 GLU cc_start: 0.8713 (pt0) cc_final: 0.8494 (pp20) REVERT: A 365 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8593 (tt0) REVERT: A 440 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8345 (mmm-85) REVERT: B 103 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 218 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 309 GLU cc_start: 0.8051 (mp0) cc_final: 0.7839 (mp0) REVERT: B 333 LEU cc_start: 0.8795 (mt) cc_final: 0.8443 (mt) REVERT: B 386 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8705 (mm) REVERT: B 417 TRP cc_start: 0.7905 (t60) cc_final: 0.7292 (t60) REVERT: B 478 TRP cc_start: 0.8608 (t60) cc_final: 0.8231 (t60) REVERT: B 497 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7983 (mm-40) outliers start: 21 outliers final: 19 residues processed: 125 average time/residue: 0.0662 time to fit residues: 11.9591 Evaluate side-chains 129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114966 restraints weight = 7762.798| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.17 r_work: 0.3190 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7687 Z= 0.123 Angle : 1.208 31.905 10482 Z= 0.459 Chirality : 0.110 1.808 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.898 177.505 1340 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.66 % Allowed : 19.42 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.08 (0.29), residues: 930 helix: 1.41 (0.25), residues: 486 sheet: -0.38 (0.61), residues: 69 loop : -2.04 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.029 0.001 TYR A 469 PHE 0.028 0.001 PHE B 95 TRP 0.011 0.001 TRP B 417 HIS 0.001 0.000 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7678) covalent geometry : angle 1.19517 / 0.46 (10456) SS BOND : bond 0.00837 / 0.44 ( 1) SS BOND : angle 4.11369 / 2.32 ( 2) hydrogen bonds : bond 0.03600 / 2.35 ( 336) hydrogen bonds : angle 3.78214 / 2.63 ( 975) link_BETA1-4 : bond 0.01107 / 0.53 ( 4) link_BETA1-4 : angle 3.20154 / 1.87 ( 12) link_NAG-ASN : bond 0.00277 / 0.14 ( 4) link_NAG-ASN : angle 4.09695 / 2.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.283 Fit side-chains REVERT: A 186 LEU cc_start: 0.8639 (mm) cc_final: 0.8406 (mt) REVERT: A 191 TRP cc_start: 0.8484 (m100) cc_final: 0.8177 (m100) REVERT: A 280 GLN cc_start: 0.8288 (mt0) cc_final: 0.7618 (mm-40) REVERT: A 332 LYS cc_start: 0.8957 (tttp) cc_final: 0.8591 (ttpt) REVERT: A 365 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8573 (tt0) REVERT: A 440 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: B 103 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7036 (t80) REVERT: B 218 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 309 GLU cc_start: 0.8064 (mp0) cc_final: 0.7861 (mp0) REVERT: B 333 LEU cc_start: 0.8794 (mt) cc_final: 0.8441 (mt) REVERT: B 386 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8728 (mm) REVERT: B 417 TRP cc_start: 0.7741 (t60) cc_final: 0.7108 (t60) REVERT: B 478 TRP cc_start: 0.8594 (t60) cc_final: 0.8189 (t60) outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 0.0652 time to fit residues: 12.3406 Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114911 restraints weight = 7864.987| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.19 r_work: 0.3193 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7687 Z= 0.122 Angle : 1.205 31.704 10482 Z= 0.460 Chirality : 0.110 1.818 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.857 177.570 1340 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.54 % Allowed : 19.42 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.04 (0.29), residues: 930 helix: 1.54 (0.25), residues: 485 sheet: -0.34 (0.61), residues: 69 loop : -2.03 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.029 0.001 TYR A 469 PHE 0.026 0.001 PHE B 95 TRP 0.009 0.001 TRP B 417 HIS 0.001 0.000 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7678) covalent geometry : angle 1.19413 / 0.46 (10456) SS BOND : bond 0.00784 / 0.41 ( 1) SS BOND : angle 4.08695 / 2.30 ( 2) hydrogen bonds : bond 0.03484 / 2.27 ( 336) hydrogen bonds : angle 3.73712 / 2.60 ( 975) link_BETA1-4 : bond 0.01010 / 0.49 ( 4) link_BETA1-4 : angle 3.04634 / 1.78 ( 12) link_NAG-ASN : bond 0.00287 / 0.14 ( 4) link_NAG-ASN : angle 3.82363 / 2.20 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.228 Fit side-chains REVERT: A 186 LEU cc_start: 0.8577 (mm) cc_final: 0.8362 (mt) REVERT: A 191 TRP cc_start: 0.8451 (m100) cc_final: 0.8127 (m100) REVERT: A 280 GLN cc_start: 0.8303 (mt0) cc_final: 0.7646 (mm-40) REVERT: A 365 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8568 (tt0) REVERT: A 440 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8352 (mmm-85) REVERT: B 103 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6993 (t80) REVERT: B 218 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 333 LEU cc_start: 0.8794 (mt) cc_final: 0.8574 (mt) REVERT: B 386 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 417 TRP cc_start: 0.7781 (t60) cc_final: 0.7224 (t60) REVERT: B 478 TRP cc_start: 0.8578 (t60) cc_final: 0.8180 (t60) outliers start: 20 outliers final: 17 residues processed: 126 average time/residue: 0.0661 time to fit residues: 11.9832 Evaluate side-chains 127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113165 restraints weight = 8133.357| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.24 r_work: 0.3138 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7687 Z= 0.141 Angle : 1.214 31.862 10482 Z= 0.465 Chirality : 0.110 1.815 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.848 178.262 1340 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.54 % Allowed : 19.80 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.06 (0.29), residues: 930 helix: 1.54 (0.25), residues: 485 sheet: -0.36 (0.61), residues: 69 loop : -1.99 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 48 TYR 0.029 0.001 TYR A 469 PHE 0.026 0.002 PHE B 95 TRP 0.010 0.001 TRP B 417 HIS 0.002 0.000 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7678) covalent geometry : angle 1.20388 / 0.46 (10456) SS BOND : bond 0.00880 / 0.46 ( 1) SS BOND : angle 4.14928 / 2.33 ( 2) hydrogen bonds : bond 0.03761 / 2.46 ( 336) hydrogen bonds : angle 3.79849 / 2.64 ( 975) link_BETA1-4 : bond 0.00992 / 0.48 ( 4) link_BETA1-4 : angle 2.97560 / 1.75 ( 12) link_NAG-ASN : bond 0.00295 / 0.15 ( 4) link_NAG-ASN : angle 3.63539 / 2.12 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.75 seconds wall clock time: 32 minutes 18.81 seconds (1938.81 seconds total)