Starting phenix.real_space_refine on Tue Sep 24 12:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsq_30841/09_2024/7dsq_30841_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsq_30841/09_2024/7dsq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsq_30841/09_2024/7dsq_30841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsq_30841/09_2024/7dsq_30841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsq_30841/09_2024/7dsq_30841_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsq_30841/09_2024/7dsq_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-5461/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: 5.04, per 1000 atoms: 0.67 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: 2.23 Conformation dependent library (CDL) restraints added in 884.2 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: 0.87 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: 1.89 Time building geometry restraints manager: 2.49 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.630 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 0.827 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: 0.2002 time to fit residues: 43.0051 Evaluate side-chains 124 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.880 Fit side-chains REVERT: A 191 TRP cc_start: 0.8325 (m100) cc_final: 0.8099 (m100) REVERT: A 332 LYS cc_start: 0.8879 (tttp) cc_final: 0.8504 (tmmt) REVERT: A 365 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8529 (tp-100) REVERT: A 529 ASP cc_start: 0.7745 (t0) cc_final: 0.7482 (t0) REVERT: B 120 MET cc_start: 0.8303 (ttm) cc_final: 0.8069 (mtp) REVERT: B 386 LEU cc_start: 0.8997 (mm) cc_final: 0.8677 (mm) REVERT: B 412 ILE cc_start: 0.8744 (mm) cc_final: 0.8501 (mm) REVERT: B 477 TRP cc_start: 0.8721 (t60) cc_final: 0.8450 (t60) REVERT: B 478 TRP cc_start: 0.8566 (t60) cc_final: 0.8249 (t60) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.1929 time to fit residues: 35.7101 Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 46 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2025 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= 0.187 Angle : 1.223 32.215 10456 Z= 0.470 Chirality : 0.109 1.825 1232 Planarity : 0.005 0.045 1279 Dihedral : 23.027 179.027 1349 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.42 % Favored : 92.37 % 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 (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: -1.65 (0.27), residues: 930 helix: -0.03 (0.23), residues: 493 sheet: -0.86 (0.59), residues: 69 loop : -2.66 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 417 HIS 0.005 0.001 HIS B 367 PHE 0.021 0.001 PHE B 474 TYR 0.022 0.001 TYR A 469 ARG 0.003 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 138 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8334 (m100) cc_final: 0.8121 (m100) REVERT: A 332 LYS cc_start: 0.8921 (tttp) cc_final: 0.8612 (ttpt) REVERT: A 365 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8524 (tt0) REVERT: A 529 ASP cc_start: 0.7758 (t0) cc_final: 0.7514 (t0) REVERT: B 120 MET cc_start: 0.8341 (ttm) cc_final: 0.7902 (mtp) REVERT: B 365 MET cc_start: 0.8685 (mtt) cc_final: 0.8298 (mtt) REVERT: B 386 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8644 (mm) REVERT: B 478 TRP cc_start: 0.8512 (t60) cc_final: 0.8157 (t60) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.1715 time to fit residues: 30.4269 Evaluate side-chains 120 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU 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 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 83 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2286 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= 0.173 Angle : 1.207 32.989 10456 Z= 0.461 Chirality : 0.108 1.812 1232 Planarity : 0.004 0.040 1279 Dihedral : 22.888 177.000 1349 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.85 % Favored : 91.94 % Rotamer: Outliers : 2.28 % Allowed : 16.12 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.06 (0.28), residues: 930 helix: 0.50 (0.24), residues: 493 sheet: -0.61 (0.60), residues: 69 loop : -2.45 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS B 420 PHE 0.017 0.001 PHE B 399 TYR 0.027 0.001 TYR A 469 ARG 0.007 0.000 ARG A 440 *********************** 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 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.8360 (m100) cc_final: 0.8125 (m100) REVERT: A 332 LYS cc_start: 0.8910 (tttp) cc_final: 0.8600 (ttpt) REVERT: A 365 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8497 (tt0) REVERT: B 309 GLU cc_start: 0.7849 (mp0) cc_final: 0.7555 (mp0) REVERT: B 333 LEU cc_start: 0.8620 (mt) cc_final: 0.8276 (mt) REVERT: B 365 MET cc_start: 0.8687 (mtt) cc_final: 0.8434 (mtt) REVERT: B 386 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 478 TRP cc_start: 0.8506 (t60) cc_final: 0.8113 (t60) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.1772 time to fit residues: 33.6354 Evaluate side-chains 122 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 386 LEU Chi-restraints excluded: chain B residue 420 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2443 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 : 1.228 33.574 10456 Z= 0.473 Chirality : 0.108 1.811 1232 Planarity : 0.004 0.039 1279 Dihedral : 22.922 176.797 1349 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.66 % Allowed : 17.77 % Favored : 79.57 % 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: -0.76 (0.28), residues: 930 helix: 0.75 (0.24), residues: 486 sheet: -0.47 (0.61), residues: 69 loop : -2.25 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 557 PHE 0.039 0.002 PHE B 95 TYR 0.028 0.002 TYR A 469 ARG 0.006 0.000 ARG A 440 *********************** 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 133 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.885 Fit side-chains REVERT: A 191 TRP cc_start: 0.8335 (m100) cc_final: 0.8096 (m100) REVERT: A 332 LYS cc_start: 0.8920 (tttp) cc_final: 0.8627 (ttpt) REVERT: A 365 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8520 (tt0) REVERT: B 103 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7053 (t80) REVERT: B 218 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 304 GLN cc_start: 0.5844 (tp40) cc_final: 0.5542 (tp-100) REVERT: B 309 GLU cc_start: 0.7880 (mp0) cc_final: 0.7626 (mp0) REVERT: B 386 LEU cc_start: 0.9038 (mm) cc_final: 0.8677 (mm) REVERT: B 478 TRP cc_start: 0.8486 (t60) cc_final: 0.8130 (t60) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.1674 time to fit residues: 29.8694 Evaluate side-chains 122 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 103 TYR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2563 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= 0.197 Angle : 1.209 33.496 10456 Z= 0.463 Chirality : 0.108 1.812 1232 Planarity : 0.004 0.038 1279 Dihedral : 22.906 178.176 1349 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.66 % Allowed : 18.15 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.51 (0.28), residues: 930 helix: 0.99 (0.24), residues: 486 sheet: -0.38 (0.61), residues: 69 loop : -2.19 (0.32), residues: 375 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 0.035 0.002 PHE B 95 TYR 0.029 0.001 TYR A 469 ARG 0.006 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 130 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.823 Fit side-chains REVERT: A 191 TRP cc_start: 0.8342 (m100) cc_final: 0.8100 (m100) REVERT: A 332 LYS cc_start: 0.8898 (tttp) cc_final: 0.8621 (ttpt) REVERT: A 365 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8491 (tt0) REVERT: B 103 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6710 (t80) REVERT: B 218 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 309 GLU cc_start: 0.7810 (mp0) cc_final: 0.7569 (mp0) REVERT: B 333 LEU cc_start: 0.8615 (mt) cc_final: 0.8265 (mt) REVERT: B 386 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 478 TRP cc_start: 0.8480 (t60) cc_final: 0.8279 (t60) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.1803 time to fit residues: 29.9891 Evaluate side-chains 126 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 108 THR 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 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 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2786 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= 0.167 Angle : 1.192 32.856 10456 Z= 0.454 Chirality : 0.109 1.812 1232 Planarity : 0.004 0.039 1279 Dihedral : 22.869 179.914 1349 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.28 % Allowed : 19.42 % 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 (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: -0.23 (0.29), residues: 930 helix: 1.27 (0.25), residues: 485 sheet: -0.14 (0.63), residues: 65 loop : -2.14 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS A 266 PHE 0.033 0.001 PHE B 95 TYR 0.030 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 137 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.846 Fit side-chains REVERT: A 191 TRP cc_start: 0.8252 (m100) cc_final: 0.7956 (m100) REVERT: A 332 LYS cc_start: 0.8872 (tttp) cc_final: 0.8628 (ttpt) REVERT: A 365 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8464 (tt0) REVERT: A 452 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8194 (mtp85) REVERT: B 103 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6756 (t80) REVERT: B 218 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 309 GLU cc_start: 0.7832 (mp0) cc_final: 0.7624 (mp0) REVERT: B 333 LEU cc_start: 0.8622 (mt) cc_final: 0.8268 (mt) REVERT: B 386 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8638 (mm) REVERT: B 478 TRP cc_start: 0.8453 (t60) cc_final: 0.8111 (t60) REVERT: B 497 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7857 (mm-40) outliers start: 18 outliers final: 15 residues processed: 128 average time/residue: 0.1787 time to fit residues: 32.0049 Evaluate side-chains 126 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2845 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= 0.190 Angle : 1.202 32.371 10456 Z= 0.459 Chirality : 0.109 1.810 1232 Planarity : 0.004 0.039 1279 Dihedral : 22.881 178.906 1349 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.16 % Allowed : 18.91 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.11 (0.29), residues: 930 helix: 1.37 (0.25), residues: 485 sheet: -0.33 (0.62), residues: 69 loop : -2.04 (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 319 PHE 0.031 0.001 PHE B 95 TYR 0.028 0.001 TYR A 469 ARG 0.007 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 129 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.877 Fit side-chains REVERT: A 191 TRP cc_start: 0.8222 (m100) cc_final: 0.7922 (m100) REVERT: A 332 LYS cc_start: 0.8867 (tttp) cc_final: 0.8644 (ttpt) REVERT: A 365 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8468 (tt0) REVERT: B 103 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6692 (t80) REVERT: B 218 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 333 LEU cc_start: 0.8619 (mt) cc_final: 0.8274 (mt) REVERT: B 386 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8659 (mm) REVERT: B 478 TRP cc_start: 0.8459 (t60) cc_final: 0.8068 (t60) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 0.1643 time to fit residues: 28.6287 Evaluate side-chains 127 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 108 THR 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 451 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2960 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= 0.183 Angle : 1.197 31.877 10456 Z= 0.457 Chirality : 0.110 1.812 1232 Planarity : 0.004 0.039 1279 Dihedral : 22.845 177.349 1349 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.16 % Allowed : 18.78 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.00 (0.29), residues: 930 helix: 1.49 (0.25), residues: 486 sheet: -0.29 (0.63), residues: 69 loop : -2.05 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 405 HIS 0.003 0.001 HIS B 319 PHE 0.030 0.001 PHE B 95 TYR 0.029 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 131 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.876 Fit side-chains REVERT: A 191 TRP cc_start: 0.8182 (m100) cc_final: 0.7867 (m100) REVERT: A 280 GLN cc_start: 0.7887 (mt0) cc_final: 0.7334 (mm-40) REVERT: A 332 LYS cc_start: 0.8869 (tttp) cc_final: 0.8653 (ttpt) REVERT: A 365 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8466 (tt0) REVERT: A 452 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8217 (mtp85) REVERT: B 103 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6755 (t80) REVERT: B 218 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 333 LEU cc_start: 0.8612 (mt) cc_final: 0.8270 (mt) REVERT: B 386 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8644 (mm) REVERT: B 478 TRP cc_start: 0.8462 (t60) cc_final: 0.8068 (t60) outliers start: 17 outliers final: 15 residues processed: 124 average time/residue: 0.1712 time to fit residues: 29.9185 Evaluate side-chains 129 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7678 Z= 0.231 Angle : 1.213 32.056 10456 Z= 0.467 Chirality : 0.110 1.808 1232 Planarity : 0.004 0.039 1279 Dihedral : 22.924 178.315 1349 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.16 % Allowed : 19.04 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.01 (0.29), residues: 930 helix: 1.44 (0.24), residues: 486 sheet: -0.34 (0.62), residues: 69 loop : -1.97 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 431 HIS 0.002 0.001 HIS A 539 PHE 0.029 0.002 PHE B 95 TYR 0.028 0.001 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 126 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.886 Fit side-chains REVERT: A 191 TRP cc_start: 0.8212 (m100) cc_final: 0.7913 (m100) REVERT: A 280 GLN cc_start: 0.7908 (mt0) cc_final: 0.7348 (mm-40) REVERT: A 332 LYS cc_start: 0.8891 (tttp) cc_final: 0.8651 (ttpt) REVERT: A 365 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8499 (tt0) REVERT: B 103 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 218 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 333 LEU cc_start: 0.8645 (mt) cc_final: 0.8431 (mt) REVERT: B 386 LEU cc_start: 0.9029 (mm) cc_final: 0.8681 (mm) REVERT: B 478 TRP cc_start: 0.8494 (t60) cc_final: 0.8109 (t60) REVERT: B 497 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8066 (mm-40) outliers start: 17 outliers final: 16 residues processed: 119 average time/residue: 0.1645 time to fit residues: 28.1043 Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 108 THR 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 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3730 r_free = 0.3730 target = 0.146090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114677 restraints weight = 8068.998| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.24 r_work: 0.3175 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3034 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= 0.189 Angle : 1.201 31.705 10456 Z= 0.461 Chirality : 0.110 1.816 1232 Planarity : 0.004 0.039 1279 Dihedral : 22.822 178.056 1349 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.28 % Allowed : 19.42 % 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 (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: 0.07 (0.29), residues: 930 helix: 1.53 (0.24), residues: 487 sheet: -0.31 (0.62), residues: 69 loop : -1.98 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 89 HIS 0.002 0.000 HIS B 319 PHE 0.029 0.002 PHE B 95 TYR 0.029 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: 1744.43 seconds wall clock time: 31 minutes 40.27 seconds (1900.27 seconds total)