Starting phenix.real_space_refine on Tue Mar 11 17:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqt_15589/03_2025/8aqt_15589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqt_15589/03_2025/8aqt_15589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aqt_15589/03_2025/8aqt_15589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqt_15589/03_2025/8aqt_15589.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqt_15589/03_2025/8aqt_15589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqt_15589/03_2025/8aqt_15589.cif" } resolution = 4.4 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= -0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4033 2.51 5 N 1055 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4744 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1535 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 10, 'TRANS': 182} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.12, per 1000 atoms: 0.65 Number of scatterers: 6321 At special positions: 0 Unit cell: (86.086, 91.3836, 116.547, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1196 8.00 N 1055 7.00 C 4033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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-ASN " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 847.7 milliseconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 48.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 56 through 80 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.623A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.350A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 4.222A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.509A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.847A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.827A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.592A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.030A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 239' Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.756A pdb=" N TYR A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.503A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.330A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.733A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.368A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.070A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.076A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.995A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.682A pdb=" N LYS A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.645A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.258A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.777A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.968A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.721A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.934A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.210A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.875A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.885A pdb=" N THR A 347 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.597A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 564 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: 1.45 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1476 1.33 - 1.45: 1554 1.45 - 1.58: 3405 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6494 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CA SER B 477 " pdb=" CB SER B 477 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.69e-02 3.50e+03 6.75e+00 bond pdb=" C PRO B 479 " pdb=" O PRO B 479 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.30e-02 5.92e+03 4.40e+00 bond pdb=" CB PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.41e-02 5.03e+03 2.44e+00 ... (remaining 6489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 8664 2.27 - 4.53: 133 4.53 - 6.80: 17 6.80 - 9.06: 4 9.06 - 11.33: 1 Bond angle restraints: 8819 Sorted by residual: angle pdb=" C PRO B 479 " pdb=" CA PRO B 479 " pdb=" CB PRO B 479 " ideal model delta sigma weight residual 111.56 100.23 11.33 1.65e+00 3.67e-01 4.71e+01 angle pdb=" N PRO B 479 " pdb=" CA PRO B 479 " pdb=" C PRO B 479 " ideal model delta sigma weight residual 112.47 121.36 -8.89 2.06e+00 2.36e-01 1.86e+01 angle pdb=" N GLN A 287 " pdb=" CA GLN A 287 " pdb=" C GLN A 287 " ideal model delta sigma weight residual 114.31 109.56 4.75 1.29e+00 6.01e-01 1.35e+01 angle pdb=" N PRO A 389 " pdb=" CA PRO A 389 " pdb=" C PRO A 389 " ideal model delta sigma weight residual 112.47 119.46 -6.99 2.06e+00 2.36e-01 1.15e+01 angle pdb=" C ILE A 468 " pdb=" CA ILE A 468 " pdb=" CB ILE A 468 " ideal model delta sigma weight residual 109.33 112.46 -3.13 9.80e-01 1.04e+00 1.02e+01 ... (remaining 8814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 3664 24.45 - 48.90: 187 48.90 - 73.36: 28 73.36 - 97.81: 3 97.81 - 122.26: 3 Dihedral angle restraints: 3885 sinusoidal: 1600 harmonic: 2285 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 156.68 -63.68 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -139.48 53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.79 53.21 1 1.00e+01 1.00e-02 3.85e+01 ... (remaining 3882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 730 0.050 - 0.101: 170 0.101 - 0.151: 26 0.151 - 0.201: 2 0.201 - 0.252: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA PRO A 389 " pdb=" N PRO A 389 " pdb=" C PRO A 389 " pdb=" CB PRO A 389 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA CYS B 480 " pdb=" N CYS B 480 " pdb=" C CYS B 480 " pdb=" CB CYS B 480 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 926 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PRO A 389 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 475 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ALA B 475 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA B 475 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 476 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 469 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.030 5.00e-02 4.00e+02 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 6506 3.26 - 3.81: 9278 3.81 - 4.35: 11190 4.35 - 4.90: 17785 Nonbonded interactions: 44966 Sorted by model distance: nonbonded pdb=" O LEU A 370 " pdb=" ND1 HIS A 374 " model vdw 2.165 3.120 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.225 3.040 nonbonded pdb=" OE2 GLU A 227 " pdb=" OH TYR A 454 " model vdw 2.226 3.040 nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.239 3.040 nonbonded pdb=" NZ LYS A 247 " pdb=" O LEU A 281 " model vdw 2.240 3.120 ... (remaining 44961 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6494 Z= 0.215 Angle : 0.695 11.326 8819 Z= 0.394 Chirality : 0.044 0.252 929 Planarity : 0.006 0.122 1142 Dihedral : 14.457 122.259 2401 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.43 % Favored : 93.79 % Rotamer: Outliers : 0.45 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.14 % 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: -1.80 (0.29), residues: 773 helix: -0.56 (0.30), residues: 297 sheet: 2.44 (1.08), residues: 22 loop : -1.91 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 48 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE A 390 TYR 0.009 0.001 TYR A 215 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8580 (mt0) cc_final: 0.8254 (mt0) REVERT: A 74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 461 TRP cc_start: 0.7929 (m-10) cc_final: 0.7554 (m-10) REVERT: A 539 LEU cc_start: 0.7599 (mt) cc_final: 0.7331 (tp) REVERT: B 386 LYS cc_start: 0.9115 (pttm) cc_final: 0.8733 (tttm) REVERT: B 421 TYR cc_start: 0.8677 (m-80) cc_final: 0.8354 (m-80) REVERT: B 466 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7391 (mmm160) outliers start: 3 outliers final: 3 residues processed: 173 average time/residue: 0.2066 time to fit residues: 46.0382 Evaluate side-chains 96 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.0770 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 69 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: A 76 GLN A 188 ASN A 508 ASN B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.142437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.126942 restraints weight = 31122.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.129136 restraints weight = 22379.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.130752 restraints weight = 17105.793| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6494 Z= 0.228 Angle : 0.668 10.046 8819 Z= 0.336 Chirality : 0.047 0.339 929 Planarity : 0.006 0.121 1142 Dihedral : 8.966 109.917 913 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.43 % Favored : 94.31 % Rotamer: Outliers : 0.30 % Allowed : 4.45 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.56 (0.29), residues: 773 helix: -0.21 (0.31), residues: 284 sheet: 1.44 (1.06), residues: 25 loop : -1.79 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 374 PHE 0.030 0.002 PHE A 592 TYR 0.012 0.001 TYR A 215 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8114 (m-30) cc_final: 0.7696 (m-30) REVERT: A 74 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 539 LEU cc_start: 0.8061 (mt) cc_final: 0.7393 (tp) REVERT: A 579 MET cc_start: 0.1366 (ttp) cc_final: 0.1135 (ttt) REVERT: B 386 LYS cc_start: 0.9007 (pttm) cc_final: 0.8584 (tttm) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1996 time to fit residues: 32.1781 Evaluate side-chains 92 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 41 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.143087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.128185 restraints weight = 31851.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.130326 restraints weight = 23208.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.131867 restraints weight = 17744.099| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6494 Z= 0.189 Angle : 0.625 9.362 8819 Z= 0.311 Chirality : 0.047 0.338 929 Planarity : 0.005 0.119 1142 Dihedral : 8.509 106.594 913 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.53 % Favored : 95.08 % Rotamer: Outliers : 0.15 % Allowed : 3.26 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.55 (0.29), residues: 773 helix: -0.21 (0.31), residues: 291 sheet: 1.29 (1.02), residues: 25 loop : -1.79 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.004 0.001 HIS A 374 PHE 0.021 0.001 PHE A 452 TYR 0.016 0.001 TYR B 421 ARG 0.004 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8195 (m-30) cc_final: 0.7906 (m-30) REVERT: A 74 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7999 (tm-30) REVERT: A 539 LEU cc_start: 0.7980 (mt) cc_final: 0.7449 (tp) REVERT: B 390 LEU cc_start: 0.9131 (mp) cc_final: 0.8518 (tp) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.2129 time to fit residues: 34.4024 Evaluate side-chains 94 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 58 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.140942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.125641 restraints weight = 31731.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.127886 restraints weight = 22425.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.129501 restraints weight = 16971.556| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6494 Z= 0.197 Angle : 0.640 9.614 8819 Z= 0.314 Chirality : 0.046 0.345 929 Planarity : 0.005 0.117 1142 Dihedral : 8.361 106.280 913 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.05 % Favored : 94.70 % Rotamer: Outliers : 0.15 % Allowed : 3.26 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.46 (0.29), residues: 773 helix: -0.18 (0.31), residues: 288 sheet: 0.67 (1.05), residues: 23 loop : -1.64 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.005 0.001 HIS A 374 PHE 0.024 0.002 PHE A 452 TYR 0.015 0.001 TYR A 497 ARG 0.006 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8071 (m-30) cc_final: 0.7754 (m-30) REVERT: A 74 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8076 (tm-30) REVERT: A 383 MET cc_start: 0.8184 (ptp) cc_final: 0.7561 (tpt) REVERT: A 534 LYS cc_start: 0.5865 (mtmm) cc_final: 0.5664 (ttpp) REVERT: A 539 LEU cc_start: 0.7842 (mt) cc_final: 0.7250 (tp) REVERT: B 356 LYS cc_start: 0.7414 (mmtt) cc_final: 0.7101 (mmtt) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2128 time to fit residues: 31.0841 Evaluate side-chains 91 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.0370 chunk 55 optimal weight: 0.6980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.125048 restraints weight = 31619.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.127349 restraints weight = 22139.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.129046 restraints weight = 16638.259| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6494 Z= 0.187 Angle : 0.621 9.368 8819 Z= 0.301 Chirality : 0.046 0.336 929 Planarity : 0.005 0.115 1142 Dihedral : 8.181 105.838 913 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Rotamer: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.44 (0.30), residues: 773 helix: -0.24 (0.31), residues: 298 sheet: 0.71 (1.05), residues: 23 loop : -1.59 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.001 PHE A 452 TYR 0.010 0.001 TYR A 510 ARG 0.005 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8283 (m-30) cc_final: 0.7967 (m-30) REVERT: A 74 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 202 TYR cc_start: 0.7323 (t80) cc_final: 0.7090 (t80) REVERT: A 383 MET cc_start: 0.8087 (ptp) cc_final: 0.7415 (tpt) REVERT: A 539 LEU cc_start: 0.7810 (mt) cc_final: 0.7292 (tp) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.2121 time to fit residues: 30.7932 Evaluate side-chains 84 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 51 optimal weight: 0.0170 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.140295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.125268 restraints weight = 31980.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.127585 restraints weight = 22415.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.129233 restraints weight = 16860.208| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6494 Z= 0.186 Angle : 0.632 9.348 8819 Z= 0.309 Chirality : 0.046 0.314 929 Planarity : 0.005 0.113 1142 Dihedral : 8.014 104.628 913 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.05 % Favored : 94.70 % Rotamer: Outliers : 0.15 % Allowed : 2.37 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.33 (0.30), residues: 773 helix: -0.09 (0.31), residues: 291 sheet: 0.68 (1.06), residues: 23 loop : -1.55 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.003 0.001 HIS A 374 PHE 0.037 0.001 PHE A 592 TYR 0.010 0.001 TYR A 510 ARG 0.009 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8159 (m-30) cc_final: 0.7818 (m-30) REVERT: A 74 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 539 LEU cc_start: 0.7902 (mt) cc_final: 0.7203 (tp) REVERT: A 579 MET cc_start: 0.1713 (ttp) cc_final: 0.1438 (tpp) REVERT: B 390 LEU cc_start: 0.9119 (mt) cc_final: 0.8483 (tp) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.2119 time to fit residues: 30.4066 Evaluate side-chains 81 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 442 GLN A 508 ASN B 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.132131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.116609 restraints weight = 31219.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.119011 restraints weight = 21605.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.120718 restraints weight = 15979.609| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6494 Z= 0.272 Angle : 0.730 9.614 8819 Z= 0.369 Chirality : 0.048 0.255 929 Planarity : 0.006 0.114 1142 Dihedral : 8.804 109.943 913 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.66 % Rotamer: Outliers : 0.15 % Allowed : 1.63 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 773 helix: -0.41 (0.30), residues: 302 sheet: 0.79 (1.06), residues: 23 loop : -1.74 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 459 HIS 0.008 0.002 HIS A 373 PHE 0.021 0.002 PHE A 452 TYR 0.015 0.002 TYR A 207 ARG 0.008 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 MET cc_start: 0.5899 (mmt) cc_final: 0.5664 (mmt) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.2145 time to fit residues: 28.8897 Evaluate side-chains 72 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.0010 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.135637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.120140 restraints weight = 30637.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.122521 restraints weight = 20871.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.124218 restraints weight = 15303.790| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6494 Z= 0.196 Angle : 0.685 10.158 8819 Z= 0.336 Chirality : 0.046 0.300 929 Planarity : 0.005 0.113 1142 Dihedral : 8.335 106.647 913 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 0.15 % Allowed : 1.19 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.50 (0.30), residues: 773 helix: -0.30 (0.31), residues: 302 sheet: 1.26 (1.04), residues: 25 loop : -1.68 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.004 0.001 HIS A 540 PHE 0.017 0.002 PHE A 592 TYR 0.009 0.001 TYR B 421 ARG 0.007 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8213 (m-30) cc_final: 0.7946 (m-30) REVERT: A 60 GLN cc_start: 0.8769 (mt0) cc_final: 0.8542 (mt0) REVERT: A 74 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 108 LEU cc_start: 0.7465 (tt) cc_final: 0.6675 (mp) REVERT: A 360 MET cc_start: 0.5440 (mmp) cc_final: 0.5126 (mmp) REVERT: A 557 MET cc_start: 0.5773 (mmt) cc_final: 0.5489 (mmt) REVERT: B 390 LEU cc_start: 0.9155 (mt) cc_final: 0.8622 (tp) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.1910 time to fit residues: 27.3951 Evaluate side-chains 78 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 68 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.133956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.118152 restraints weight = 30864.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.120489 restraints weight = 21148.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.122211 restraints weight = 15598.099| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6494 Z= 0.215 Angle : 0.693 9.443 8819 Z= 0.341 Chirality : 0.047 0.287 929 Planarity : 0.005 0.112 1142 Dihedral : 8.316 105.913 913 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.52 (0.30), residues: 773 helix: -0.34 (0.30), residues: 302 sheet: 1.25 (1.03), residues: 25 loop : -1.68 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.002 TRP A 461 HIS 0.004 0.001 HIS A 353 PHE 0.017 0.002 PHE A 592 TYR 0.010 0.001 TYR A 510 ARG 0.017 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8172 (m-30) cc_final: 0.7877 (m-30) REVERT: A 45 LEU cc_start: 0.8697 (mm) cc_final: 0.8496 (mm) REVERT: A 60 GLN cc_start: 0.8750 (mt0) cc_final: 0.8508 (mt0) REVERT: A 74 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 108 LEU cc_start: 0.7722 (tt) cc_final: 0.7146 (mp) REVERT: A 360 MET cc_start: 0.5193 (mmp) cc_final: 0.4937 (mmp) REVERT: A 379 ILE cc_start: 0.8589 (tp) cc_final: 0.8347 (tp) REVERT: A 591 LEU cc_start: 0.8211 (tt) cc_final: 0.7926 (mm) REVERT: B 466 ARG cc_start: 0.8423 (mmm160) cc_final: 0.7971 (mmm160) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.1936 time to fit residues: 26.9409 Evaluate side-chains 74 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.119561 restraints weight = 31317.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.121786 restraints weight = 21460.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.123392 restraints weight = 15728.127| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6494 Z= 0.195 Angle : 0.682 9.374 8819 Z= 0.334 Chirality : 0.047 0.287 929 Planarity : 0.005 0.112 1142 Dihedral : 8.189 104.474 913 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.08 % Favored : 93.79 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.55 (0.30), residues: 773 helix: -0.40 (0.30), residues: 310 sheet: 1.28 (1.03), residues: 25 loop : -1.69 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP A 461 HIS 0.002 0.001 HIS A 505 PHE 0.017 0.001 PHE A 512 TYR 0.012 0.001 TYR A 237 ARG 0.014 0.001 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8193 (m-30) cc_final: 0.7886 (m-30) REVERT: A 60 GLN cc_start: 0.8783 (mt0) cc_final: 0.8576 (mt0) REVERT: A 74 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 108 LEU cc_start: 0.7827 (tt) cc_final: 0.7396 (mp) REVERT: A 190 MET cc_start: 0.8358 (tpp) cc_final: 0.8041 (tpt) REVERT: A 379 ILE cc_start: 0.8679 (tp) cc_final: 0.8423 (tp) REVERT: B 465 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7157 (tm-30) REVERT: B 466 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7713 (mmm160) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2039 time to fit residues: 26.2185 Evaluate side-chains 79 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.0370 chunk 69 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 57 optimal weight: 0.0030 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.120648 restraints weight = 32262.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.122951 restraints weight = 22217.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.124484 restraints weight = 16387.754| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6494 Z= 0.191 Angle : 0.670 9.408 8819 Z= 0.324 Chirality : 0.046 0.277 929 Planarity : 0.005 0.109 1142 Dihedral : 7.886 101.193 913 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 0.15 % Allowed : 0.59 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.30), residues: 773 helix: -0.32 (0.30), residues: 310 sheet: 1.32 (1.02), residues: 25 loop : -1.70 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 461 HIS 0.002 0.001 HIS A 239 PHE 0.013 0.001 PHE A 592 TYR 0.010 0.001 TYR A 510 ARG 0.010 0.001 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.24 seconds wall clock time: 40 minutes 27.74 seconds (2427.74 seconds total)