Starting phenix.real_space_refine on Wed Mar 12 16:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsq_30841/03_2025/7dsq_30841_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsq_30841/03_2025/7dsq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2025/7dsq_30841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2025/7dsq_30841.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2025/7dsq_30841_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsq_30841/03_2025/7dsq_30841_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.08, per 1000 atoms: 0.68 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: 2.18 Conformation dependent library (CDL) restraints added in 822.7 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: 0.70 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: 1.99 Time building geometry restraints manager: 2.41 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: 4526 35.67 - 71.34: 127 71.34 - 107.01: 20 107.01 - 142.68: 31 142.68 - 178.35: 7 Dihedral angle restraints: 4711 sinusoidal: 2032 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 4708 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.010 0.219 7678 Z= 0.656 Angle : 1.194 11.552 10456 Z= 0.634 Chirality : 0.489 5.917 1232 Planarity : 0.008 0.080 1279 Dihedral : 22.623 178.347 2986 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP A 220 HIS 0.006 0.001 HIS A 539 PHE 0.021 0.003 PHE B 351 TYR 0.028 0.003 TYR B 259 ARG 0.005 0.001 ARG A 556 *********************** 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 : 0.802 Fit side-chains revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7941 (mm) cc_final: 0.7548 (pp) REVERT: A 191 TRP cc_start: 0.8300 (m100) cc_final: 0.8075 (m100) REVERT: A 332 LYS cc_start: 0.8851 (tttp) cc_final: 0.8455 (tmmt) REVERT: A 365 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8698 (tp-100) REVERT: B 77 LYS cc_start: 0.7743 (tttm) cc_final: 0.7516 (ttmt) REVERT: B 120 MET cc_start: 0.8112 (ttm) cc_final: 0.7854 (mtp) REVERT: B 137 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9013 (pt) REVERT: B 386 LEU cc_start: 0.9069 (mm) cc_final: 0.8843 (mm) REVERT: B 412 ILE cc_start: 0.8879 (mm) cc_final: 0.8632 (mm) REVERT: B 417 TRP cc_start: 0.7347 (t-100) cc_final: 0.7073 (t-100) REVERT: B 477 TRP cc_start: 0.8750 (t60) cc_final: 0.8414 (t60) REVERT: B 478 TRP cc_start: 0.8613 (t60) cc_final: 0.8358 (t60) outliers start: 7 outliers final: 3 residues processed: 161 average time/residue: 0.2020 time to fit residues: 43.5091 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 : 0.814 ------------------------------------------------------------------------------- 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 78 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 275 GLN A 353 ASN A 396 ASN A 539 HIS A 561 ASN B 273 ASN B 497 GLN B 501 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114446 restraints weight = 7664.855| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.20 r_work: 0.3170 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7678 Z= 0.207 Angle : 1.254 33.605 10456 Z= 0.492 Chirality : 0.111 1.864 1232 Planarity : 0.006 0.052 1279 Dihedral : 23.174 178.531 1352 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.31 % Favored : 92.15 % Rotamer: Outliers : 2.16 % Allowed : 12.69 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.25), residues: 930 helix: -0.94 (0.22), residues: 492 sheet: -0.85 (0.60), residues: 67 loop : -2.99 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 89 HIS 0.004 0.001 HIS A 539 PHE 0.014 0.002 PHE B 252 TYR 0.020 0.001 TYR B 259 ARG 0.005 0.000 ARG A 440 *********************** 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 146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.750 Fit side-chains REVERT: A 191 TRP cc_start: 0.8408 (m100) cc_final: 0.8172 (m100) REVERT: A 332 LYS cc_start: 0.8943 (tttp) cc_final: 0.8529 (tmmt) REVERT: A 365 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8589 (tp-100) REVERT: A 529 ASP cc_start: 0.8400 (t0) cc_final: 0.8142 (t0) REVERT: B 369 GLN cc_start: 0.8344 (mt0) cc_final: 0.8126 (pt0) REVERT: B 386 LEU cc_start: 0.9017 (mm) cc_final: 0.8688 (mm) REVERT: B 412 ILE cc_start: 0.8747 (mm) cc_final: 0.8530 (mm) REVERT: B 477 TRP cc_start: 0.8791 (t60) cc_final: 0.8538 (t60) REVERT: B 478 TRP cc_start: 0.8660 (t60) cc_final: 0.8314 (t60) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.1861 time to fit residues: 34.6720 Evaluate side-chains 125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 326 THR 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 74 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 24 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3730 r_free = 0.3730 target = 0.145691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114311 restraints weight = 8134.872| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.26 r_work: 0.3191 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7678 Z= 0.176 Angle : 1.216 32.066 10456 Z= 0.466 Chirality : 0.109 1.823 1232 Planarity : 0.005 0.045 1279 Dihedral : 23.003 178.946 1349 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.42 % Favored : 92.37 % Rotamer: Outliers : 2.16 % Allowed : 14.34 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 930 helix: 0.02 (0.23), residues: 493 sheet: -0.84 (0.59), residues: 69 loop : -2.66 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 417 HIS 0.003 0.000 HIS B 367 PHE 0.020 0.001 PHE B 474 TYR 0.021 0.001 TYR A 469 ARG 0.004 0.000 ARG A 440 *********************** 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 139 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8570 (m100) cc_final: 0.8341 (m100) REVERT: A 332 LYS cc_start: 0.8983 (tttp) cc_final: 0.8632 (ttpt) REVERT: A 365 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8617 (tt0) REVERT: A 440 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8264 (mmm-85) REVERT: A 529 ASP cc_start: 0.8725 (t0) cc_final: 0.8518 (t0) REVERT: B 365 MET cc_start: 0.9022 (mtt) cc_final: 0.8696 (mtt) REVERT: B 369 GLN cc_start: 0.8443 (mt0) cc_final: 0.8212 (pt0) REVERT: B 386 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8712 (mm) REVERT: B 478 TRP cc_start: 0.8695 (t60) cc_final: 0.8275 (t60) outliers start: 17 outliers final: 11 residues processed: 129 average time/residue: 0.1670 time to fit residues: 30.4220 Evaluate side-chains 122 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111429 restraints weight = 7694.796| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.16 r_work: 0.3148 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7678 Z= 0.289 Angle : 1.244 33.442 10456 Z= 0.483 Chirality : 0.108 1.803 1232 Planarity : 0.004 0.042 1279 Dihedral : 23.003 177.203 1349 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.17 % Favored : 91.61 % Rotamer: Outliers : 2.66 % Allowed : 16.75 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 930 helix: 0.37 (0.24), residues: 485 sheet: -0.48 (0.61), residues: 67 loop : -2.43 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.003 0.001 HIS A 557 PHE 0.012 0.002 PHE B 344 TYR 0.025 0.002 TYR A 469 ARG 0.003 0.000 ARG B 421 *********************** 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 135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8356 (mm) cc_final: 0.7818 (pp) REVERT: A 191 TRP cc_start: 0.8607 (m100) cc_final: 0.8367 (m100) REVERT: A 332 LYS cc_start: 0.9016 (tttp) cc_final: 0.8650 (ttpt) REVERT: A 365 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8640 (tt0) REVERT: A 529 ASP cc_start: 0.8786 (t0) cc_final: 0.8572 (t0) REVERT: B 218 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 304 GLN cc_start: 0.5928 (tp40) cc_final: 0.5707 (tp-100) REVERT: B 309 GLU cc_start: 0.8232 (mp0) cc_final: 0.7663 (mp0) REVERT: B 365 MET cc_start: 0.9097 (mtt) cc_final: 0.8828 (mtt) REVERT: B 369 GLN cc_start: 0.8456 (mt0) cc_final: 0.8217 (pt0) REVERT: B 386 LEU cc_start: 0.9102 (mm) cc_final: 0.8761 (mm) REVERT: B 451 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: B 478 TRP cc_start: 0.8685 (t60) cc_final: 0.8319 (t60) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.1738 time to fit residues: 30.4235 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 : 0.788 ------------------------------------------------------------------------------- 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 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 440 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109594 restraints weight = 7903.300| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.18 r_work: 0.3085 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7678 Z= 0.340 Angle : 1.263 34.091 10456 Z= 0.493 Chirality : 0.108 1.790 1232 Planarity : 0.004 0.040 1279 Dihedral : 23.121 176.753 1349 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.25 % Favored : 90.54 % Rotamer: Outliers : 3.55 % Allowed : 18.02 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.27), residues: 930 helix: 0.40 (0.23), residues: 485 sheet: -0.43 (0.62), residues: 67 loop : -2.29 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.004 0.001 HIS A 557 PHE 0.026 0.002 PHE B 474 TYR 0.028 0.002 TYR A 469 ARG 0.003 0.000 ARG A 212 *********************** 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 138 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.869 Fit side-chains REVERT: A 191 TRP cc_start: 0.8594 (m100) cc_final: 0.8354 (m100) REVERT: A 332 LYS cc_start: 0.9062 (tttp) cc_final: 0.8685 (ttpt) REVERT: A 365 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8683 (tt0) REVERT: A 529 ASP cc_start: 0.8785 (t0) cc_final: 0.8576 (t0) REVERT: B 103 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7526 (t80) REVERT: B 218 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 304 GLN cc_start: 0.6133 (tp40) cc_final: 0.5807 (tp-100) REVERT: B 309 GLU cc_start: 0.8134 (mp0) cc_final: 0.7776 (mp0) REVERT: B 369 GLN cc_start: 0.8441 (mt0) cc_final: 0.8223 (pt0) REVERT: B 386 LEU cc_start: 0.9157 (mm) cc_final: 0.8857 (mm) REVERT: B 451 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6259 (m-80) REVERT: B 478 TRP cc_start: 0.8698 (t60) cc_final: 0.8447 (t60) outliers start: 28 outliers final: 20 residues processed: 127 average time/residue: 0.1730 time to fit residues: 30.9672 Evaluate side-chains 128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 198 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 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 416 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111224 restraints weight = 7790.471| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.12 r_work: 0.3116 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7678 Z= 0.243 Angle : 1.229 33.691 10456 Z= 0.474 Chirality : 0.108 1.792 1232 Planarity : 0.004 0.038 1279 Dihedral : 23.154 176.890 1349 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.28 % Favored : 91.40 % Rotamer: Outliers : 2.79 % Allowed : 19.42 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 930 helix: 0.67 (0.24), residues: 487 sheet: -0.35 (0.61), residues: 67 loop : -2.22 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.002 0.001 HIS A 557 PHE 0.013 0.001 PHE B 403 TYR 0.029 0.002 TYR A 469 ARG 0.007 0.000 ARG A 440 *********************** 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 135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8605 (m100) cc_final: 0.8369 (m100) REVERT: A 332 LYS cc_start: 0.9006 (tttp) cc_final: 0.8671 (ttpt) REVERT: A 365 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8658 (tt0) REVERT: A 529 ASP cc_start: 0.8766 (t0) cc_final: 0.8562 (t0) REVERT: B 103 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7102 (t80) REVERT: B 218 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 309 GLU cc_start: 0.8111 (mp0) cc_final: 0.7806 (mp0) REVERT: B 333 LEU cc_start: 0.8833 (mt) cc_final: 0.8474 (mt) REVERT: B 369 GLN cc_start: 0.8394 (mt0) cc_final: 0.8147 (pt0) REVERT: B 386 LEU cc_start: 0.9109 (mm) cc_final: 0.8789 (mm) REVERT: B 451 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: B 478 TRP cc_start: 0.8682 (t60) cc_final: 0.8450 (t60) outliers start: 22 outliers final: 18 residues processed: 126 average time/residue: 0.1822 time to fit residues: 31.6937 Evaluate side-chains 127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 371 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 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114992 restraints weight = 7699.667| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.11 r_work: 0.3186 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7678 Z= 0.177 Angle : 1.201 32.861 10456 Z= 0.459 Chirality : 0.109 1.800 1232 Planarity : 0.004 0.037 1279 Dihedral : 23.115 179.651 1349 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.06 % Favored : 91.72 % Rotamer: Outliers : 2.66 % Allowed : 20.30 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.28), residues: 930 helix: 1.04 (0.24), residues: 486 sheet: -0.49 (0.59), residues: 69 loop : -2.19 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 492 HIS 0.003 0.001 HIS B 420 PHE 0.020 0.001 PHE B 439 TYR 0.031 0.001 TYR A 469 ARG 0.007 0.000 ARG A 440 *********************** 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 143 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.887 Fit side-chains REVERT: A 191 TRP cc_start: 0.8570 (m100) cc_final: 0.8344 (m100) REVERT: A 332 LYS cc_start: 0.8983 (tttp) cc_final: 0.8637 (ttpt) REVERT: A 336 GLU cc_start: 0.8708 (pt0) cc_final: 0.8381 (pp20) REVERT: A 365 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8597 (tt0) REVERT: B 103 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6915 (t80) REVERT: B 218 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 309 GLU cc_start: 0.8076 (mp0) cc_final: 0.7861 (mp0) REVERT: B 369 GLN cc_start: 0.8337 (mt0) cc_final: 0.8073 (pt0) REVERT: B 386 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 478 TRP cc_start: 0.8650 (t60) cc_final: 0.8294 (t60) REVERT: B 497 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8075 (mm-40) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.1807 time to fit residues: 33.8502 Evaluate side-chains 133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 371 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.0000 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115516 restraints weight = 8325.541| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.24 r_work: 0.3209 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7678 Z= 0.166 Angle : 1.197 31.932 10456 Z= 0.457 Chirality : 0.109 1.807 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.949 178.216 1349 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.41 % Allowed : 20.18 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 930 helix: 1.27 (0.25), residues: 487 sheet: -0.38 (0.61), residues: 69 loop : -2.15 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 89 HIS 0.003 0.001 HIS A 266 PHE 0.034 0.001 PHE B 95 TYR 0.030 0.001 TYR A 469 ARG 0.006 0.000 ARG A 440 *********************** 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 144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.778 Fit side-chains REVERT: A 191 TRP cc_start: 0.8381 (m100) cc_final: 0.8066 (m100) REVERT: A 280 GLN cc_start: 0.8210 (mt0) cc_final: 0.7561 (mm-40) REVERT: A 332 LYS cc_start: 0.8944 (tttp) cc_final: 0.8622 (ttpt) REVERT: A 365 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8469 (tt0) REVERT: B 103 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6749 (t80) REVERT: B 218 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 386 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 478 TRP cc_start: 0.8567 (t60) cc_final: 0.8359 (t60) outliers start: 19 outliers final: 12 residues processed: 135 average time/residue: 0.1804 time to fit residues: 33.7291 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 386 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 0.0020 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115842 restraints weight = 7868.834| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.16 r_work: 0.3206 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7678 Z= 0.182 Angle : 1.209 31.882 10456 Z= 0.463 Chirality : 0.110 1.810 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.921 177.485 1349 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.28 % Allowed : 20.43 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 930 helix: 1.40 (0.24), residues: 485 sheet: -0.35 (0.61), residues: 69 loop : -2.11 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 405 HIS 0.002 0.001 HIS B 367 PHE 0.033 0.001 PHE B 95 TYR 0.031 0.001 TYR A 469 ARG 0.006 0.000 ARG A 440 *********************** 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 130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.832 Fit side-chains REVERT: A 191 TRP cc_start: 0.8479 (m100) cc_final: 0.8171 (m100) REVERT: A 280 GLN cc_start: 0.8248 (mt0) cc_final: 0.7595 (mm-40) REVERT: A 336 GLU cc_start: 0.8379 (pp20) cc_final: 0.8020 (pm20) REVERT: A 365 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8569 (tt0) REVERT: B 103 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6914 (t80) REVERT: B 218 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 333 LEU cc_start: 0.8810 (mt) cc_final: 0.8456 (mt) REVERT: B 386 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8719 (mm) REVERT: B 415 MET cc_start: 0.7604 (tmm) cc_final: 0.7369 (ttt) REVERT: B 451 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: B 478 TRP cc_start: 0.8621 (t60) cc_final: 0.8387 (t60) outliers start: 18 outliers final: 15 residues processed: 123 average time/residue: 0.1831 time to fit residues: 31.2955 Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 420 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112557 restraints weight = 7604.229| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.11 r_work: 0.3146 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7678 Z= 0.259 Angle : 1.231 32.251 10456 Z= 0.477 Chirality : 0.110 1.799 1232 Planarity : 0.004 0.039 1279 Dihedral : 23.068 178.173 1349 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.16 % Allowed : 20.43 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 930 helix: 1.30 (0.24), residues: 487 sheet: -0.25 (0.61), residues: 67 loop : -2.05 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 431 HIS 0.002 0.001 HIS A 557 PHE 0.034 0.002 PHE B 95 TYR 0.030 0.002 TYR A 469 ARG 0.006 0.000 ARG A 440 ********************** 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 129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.770 Fit side-chains REVERT: A 191 TRP cc_start: 0.8496 (m100) cc_final: 0.8189 (m100) REVERT: A 280 GLN cc_start: 0.8285 (mt0) cc_final: 0.7624 (mm-40) REVERT: A 336 GLU cc_start: 0.8367 (pp20) cc_final: 0.8027 (pm20) REVERT: A 365 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8614 (tt0) REVERT: B 103 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7098 (t80) REVERT: B 218 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 386 LEU cc_start: 0.9092 (mm) cc_final: 0.8762 (mm) REVERT: B 415 MET cc_start: 0.7590 (tmm) cc_final: 0.7261 (ttt) REVERT: B 451 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: B 478 TRP cc_start: 0.8635 (t60) cc_final: 0.8386 (t60) outliers start: 17 outliers final: 15 residues processed: 122 average time/residue: 0.1938 time to fit residues: 32.6619 Evaluate side-chains 126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 420 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 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 = 0.3710 r_free = 0.3710 target = 0.144053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113757 restraints weight = 7640.858| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.15 r_work: 0.3182 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7678 Z= 0.200 Angle : 1.215 31.872 10456 Z= 0.468 Chirality : 0.110 1.799 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.957 177.052 1349 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.28 % Allowed : 20.81 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.29), residues: 930 helix: 1.39 (0.24), residues: 487 sheet: -0.26 (0.61), residues: 67 loop : -2.06 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.032 0.002 PHE B 95 TYR 0.030 0.001 TYR A 469 ARG 0.006 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.95 seconds wall clock time: 66 minutes 28.10 seconds (3988.10 seconds total)