Starting phenix.real_space_refine on Wed Mar 12 05:30:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnt_37672/03_2025/8wnt_37672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnt_37672/03_2025/8wnt_37672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wnt_37672/03_2025/8wnt_37672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnt_37672/03_2025/8wnt_37672.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnt_37672/03_2025/8wnt_37672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnt_37672/03_2025/8wnt_37672.cif" } resolution = 3.42 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= -0.004 sd= 0.081 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 32 5.16 5 C 4764 2.51 5 N 1201 2.21 5 O 1312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 7309 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3656 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3577 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 23, '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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.66 Number of scatterers: 7309 At special positions: 0 Unit cell: (105.439, 110.874, 105.439, 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 32 16.00 O 1312 8.00 N 1201 7.00 C 4764 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 154 " 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 A 701 " - " ASN A 366 " " NAG A 702 " - " ASN A 425 " " NAG A 703 " - " ASN A 507 " " NAG C 1 " - " ASN A 382 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 3 sheets defined 59.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 179 through 207 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.913A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 4.028A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.524A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.534A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.978A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 4.015A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.634A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.621A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.721A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.981A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.250A pdb=" N GLY B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 100 removed outlier: 3.828A pdb=" N GLY B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.566A pdb=" N THR B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.680A pdb=" N SER B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 207 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 234 through 242 removed outlier: 5.077A pdb=" N GLN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 260 through 290 Proline residue: B 266 - end of helix removed outlier: 3.771A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 3.530A pdb=" N ALA B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.611A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.609A pdb=" N PHE B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 347 removed outlier: 3.862A pdb=" N VAL B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 379 removed outlier: 3.621A pdb=" N ILE B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 386 Processing helix chain 'B' and resid 387 through 413 removed outlier: 3.583A pdb=" N TYR B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 399 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR B 402 " --> pdb=" O CYS B 398 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 removed outlier: 3.739A pdb=" N ILE B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 458 removed outlier: 4.190A pdb=" N CYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.700A pdb=" N HIS B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 479 " --> pdb=" O CYS B 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.803A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N CYS A 432 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 466 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.535A pdb=" N PHE A 545 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 622 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER A 599 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576 384 hydrogen bonds defined for protein. 1110 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: 1.84 Time building geometry restraints manager: 2.26 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: 1770 1.33 - 1.45: 1565 1.45 - 1.57: 4111 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 7496 Sorted by residual: bond pdb=" N ASP B 106 " pdb=" CA ASP B 106 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.55e+00 bond pdb=" N THR B 289 " pdb=" CA THR B 289 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.80e+00 bond pdb=" N SER B 299 " pdb=" CA SER B 299 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.22e-02 6.72e+03 6.68e+00 bond pdb=" N SER B 69 " pdb=" CA SER B 69 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.91e+00 bond pdb=" N SER A 391 " pdb=" CA SER A 391 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.39e+00 ... (remaining 7491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 10073 2.63 - 5.25: 115 5.25 - 7.88: 10 7.88 - 10.51: 2 10.51 - 13.13: 1 Bond angle restraints: 10201 Sorted by residual: angle pdb=" N LEU B 296 " pdb=" CA LEU B 296 " pdb=" C LEU B 296 " ideal model delta sigma weight residual 112.23 105.16 7.07 1.26e+00 6.30e-01 3.15e+01 angle pdb=" CB MET B 356 " pdb=" CG MET B 356 " pdb=" SD MET B 356 " ideal model delta sigma weight residual 112.70 125.83 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C ARG B 360 " pdb=" N HIS B 361 " pdb=" CA HIS B 361 " ideal model delta sigma weight residual 121.54 128.67 -7.13 1.91e+00 2.74e-01 1.40e+01 angle pdb=" N PRO A 311 " pdb=" CA PRO A 311 " pdb=" C PRO A 311 " ideal model delta sigma weight residual 113.81 119.08 -5.27 1.45e+00 4.76e-01 1.32e+01 angle pdb=" N SER B 242 " pdb=" CA SER B 242 " pdb=" C SER B 242 " ideal model delta sigma weight residual 111.81 107.52 4.29 1.44e+00 4.82e-01 8.86e+00 ... (remaining 10196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3831 18.00 - 36.00: 462 36.00 - 54.00: 112 54.00 - 72.00: 15 72.00 - 90.00: 13 Dihedral angle restraints: 4433 sinusoidal: 1773 harmonic: 2660 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual 93.00 173.67 -80.67 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA LEU B 236 " pdb=" C LEU B 236 " pdb=" N ALA B 237 " pdb=" CA ALA B 237 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASN B 395 " pdb=" C ASN B 395 " pdb=" N TYR B 396 " pdb=" CA TYR B 396 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 4430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 998 0.055 - 0.110: 158 0.110 - 0.165: 19 0.165 - 0.220: 3 0.220 - 0.275: 2 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CA LEU B 296 " pdb=" N LEU B 296 " pdb=" C LEU B 296 " pdb=" CB LEU B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL B 439 " pdb=" CA VAL B 439 " pdb=" CG1 VAL B 439 " pdb=" CG2 VAL B 439 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 1177 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 295 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU B 295 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU B 295 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 296 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 472 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO B 473 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 316 " 0.012 2.00e-02 2.50e+03 1.65e-02 6.81e+00 pdb=" CG TRP B 316 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 316 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 316 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 316 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 316 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 316 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 316 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 316 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 316 " -0.001 2.00e-02 2.50e+03 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1366 2.77 - 3.30: 7142 3.30 - 3.83: 12016 3.83 - 4.37: 13384 4.37 - 4.90: 23536 Nonbonded interactions: 57444 Sorted by model distance: nonbonded pdb=" O VAL B 391 " pdb=" ND2 ASN B 395 " model vdw 2.232 3.120 nonbonded pdb=" O ILE B 53 " pdb=" N ALA B1001 " model vdw 2.234 3.120 nonbonded pdb=" OE2 GLU A 605 " pdb=" OG SER A 608 " model vdw 2.253 3.040 nonbonded pdb=" O LYS B 472 " pdb=" NE2 HIS B 477 " model vdw 2.258 3.120 nonbonded pdb=" O SER B 230 " pdb=" OG SER B 230 " model vdw 2.265 3.040 ... (remaining 57439 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 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: 1.330 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.240 Find NCS groups from input model: 0.100 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.004 0.061 7496 Z= 0.231 Angle : 0.668 13.133 10201 Z= 0.354 Chirality : 0.043 0.275 1180 Planarity : 0.005 0.070 1269 Dihedral : 16.761 89.998 2726 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.60 % Favored : 94.18 % Rotamer: Outliers : 0.77 % Allowed : 24.71 % Favored : 74.52 % 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: 0.29 (0.28), residues: 928 helix: 0.89 (0.24), residues: 494 sheet: 1.48 (0.79), residues: 46 loop : -0.83 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 316 HIS 0.004 0.001 HIS B 477 PHE 0.016 0.001 PHE B 463 TYR 0.026 0.001 TYR B 399 ARG 0.002 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 PHE cc_start: 0.7995 (m-80) cc_final: 0.7698 (m-10) outliers start: 6 outliers final: 2 residues processed: 100 average time/residue: 0.1916 time to fit residues: 27.3232 Evaluate side-chains 95 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.0670 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 543 HIS B 211 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131896 restraints weight = 10521.327| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.27 r_work: 0.3452 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7496 Z= 0.181 Angle : 0.601 8.067 10201 Z= 0.302 Chirality : 0.041 0.243 1180 Planarity : 0.004 0.057 1269 Dihedral : 4.904 33.076 1104 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.28 % Favored : 94.50 % Rotamer: Outliers : 2.43 % Allowed : 22.02 % Favored : 75.54 % 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: 0.86 (0.29), residues: 928 helix: 1.46 (0.24), residues: 504 sheet: 1.57 (0.79), residues: 46 loop : -0.75 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 316 HIS 0.004 0.001 HIS B 477 PHE 0.015 0.001 PHE A 627 TYR 0.021 0.001 TYR B 399 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 PHE cc_start: 0.8386 (m-80) cc_final: 0.8124 (m-10) REVERT: B 164 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7719 (tt) REVERT: B 194 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8062 (mtmm) REVERT: B 308 GLU cc_start: 0.8419 (pp20) cc_final: 0.8203 (pp20) REVERT: B 347 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 464 PHE cc_start: 0.7299 (m-10) cc_final: 0.6804 (m-10) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 0.2186 time to fit residues: 38.4516 Evaluate side-chains 103 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 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 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS B 211 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.180243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129700 restraints weight = 10588.534| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.38 r_work: 0.3432 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7496 Z= 0.203 Angle : 0.595 8.312 10201 Z= 0.297 Chirality : 0.041 0.229 1180 Planarity : 0.004 0.055 1269 Dihedral : 4.579 30.988 1100 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.28 % Favored : 94.50 % Rotamer: Outliers : 3.46 % Allowed : 21.38 % Favored : 75.16 % 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: 0.95 (0.29), residues: 928 helix: 1.58 (0.24), residues: 499 sheet: 1.68 (0.79), residues: 46 loop : -0.77 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.003 0.001 HIS B 361 PHE 0.012 0.001 PHE A 524 TYR 0.023 0.002 TYR B 399 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: B 122 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 194 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8222 (mtmm) REVERT: B 308 GLU cc_start: 0.8470 (pp20) cc_final: 0.8225 (pp20) REVERT: B 404 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7949 (tt) REVERT: B 477 HIS cc_start: 0.7882 (m-70) cc_final: 0.7619 (m-70) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 0.2083 time to fit residues: 33.7423 Evaluate side-chains 111 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS A 557 HIS B 176 ASN B 211 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.173307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124049 restraints weight = 10644.206| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.24 r_work: 0.3355 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7496 Z= 0.317 Angle : 0.661 8.319 10201 Z= 0.331 Chirality : 0.044 0.241 1180 Planarity : 0.004 0.055 1269 Dihedral : 4.812 32.659 1100 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.71 % Favored : 94.18 % Rotamer: Outliers : 4.23 % Allowed : 22.02 % Favored : 73.75 % 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: 0.72 (0.28), residues: 928 helix: 1.34 (0.24), residues: 501 sheet: 1.62 (0.76), residues: 46 loop : -0.82 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 469 HIS 0.007 0.001 HIS A 557 PHE 0.020 0.001 PHE A 524 TYR 0.038 0.002 TYR B 399 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5760 (mm) REVERT: B 56 SER cc_start: 0.8909 (p) cc_final: 0.8675 (t) REVERT: B 122 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8058 (tt) REVERT: B 194 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8211 (mtmm) REVERT: B 233 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.5347 (t-90) REVERT: B 308 GLU cc_start: 0.8547 (pp20) cc_final: 0.8245 (pp20) REVERT: B 316 TRP cc_start: 0.7591 (p-90) cc_final: 0.7223 (p-90) REVERT: B 404 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 477 HIS cc_start: 0.7896 (m-70) cc_final: 0.7551 (m-70) outliers start: 33 outliers final: 21 residues processed: 127 average time/residue: 0.2088 time to fit residues: 37.4242 Evaluate side-chains 118 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 32 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 543 HIS B 211 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128583 restraints weight = 10480.052| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.35 r_work: 0.3418 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.177 Angle : 0.591 7.868 10201 Z= 0.294 Chirality : 0.041 0.223 1180 Planarity : 0.004 0.050 1269 Dihedral : 4.580 28.794 1100 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.99 % Allowed : 21.77 % Favored : 73.24 % 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: 0.97 (0.29), residues: 928 helix: 1.56 (0.24), residues: 501 sheet: 1.65 (0.78), residues: 46 loop : -0.72 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 124 HIS 0.004 0.001 HIS B 361 PHE 0.012 0.001 PHE A 542 TYR 0.030 0.001 TYR B 399 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7069 (pt0) REVERT: B 56 SER cc_start: 0.8844 (p) cc_final: 0.8618 (t) REVERT: B 194 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8241 (mtmm) REVERT: B 233 HIS cc_start: 0.6815 (OUTLIER) cc_final: 0.5331 (t-90) REVERT: B 260 ASP cc_start: 0.8159 (t70) cc_final: 0.7839 (t70) REVERT: B 308 GLU cc_start: 0.8517 (pp20) cc_final: 0.8272 (pp20) REVERT: B 316 TRP cc_start: 0.7583 (p-90) cc_final: 0.7250 (p-90) REVERT: B 404 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7959 (tt) REVERT: B 464 PHE cc_start: 0.7447 (m-10) cc_final: 0.7189 (m-10) REVERT: B 469 TRP cc_start: 0.7715 (t-100) cc_final: 0.7510 (t-100) REVERT: B 477 HIS cc_start: 0.7981 (m-70) cc_final: 0.7517 (m-70) outliers start: 39 outliers final: 23 residues processed: 132 average time/residue: 0.1677 time to fit residues: 31.0021 Evaluate side-chains 122 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS B 211 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.180054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129338 restraints weight = 10495.504| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.37 r_work: 0.3415 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.184 Angle : 0.595 8.198 10201 Z= 0.297 Chirality : 0.041 0.222 1180 Planarity : 0.004 0.049 1269 Dihedral : 4.475 31.489 1100 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.35 % Allowed : 23.43 % Favored : 72.22 % 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: 1.05 (0.29), residues: 928 helix: 1.64 (0.24), residues: 501 sheet: 1.62 (0.77), residues: 46 loop : -0.70 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.003 0.000 HIS B 361 PHE 0.013 0.001 PHE B 314 TYR 0.031 0.002 TYR B 399 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7605 (Cg_exo) cc_final: 0.7316 (Cg_endo) REVERT: A 529 ASP cc_start: 0.8098 (t0) cc_final: 0.7868 (t0) REVERT: A 621 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: B 122 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 194 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8202 (mtmm) REVERT: B 233 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.5398 (t-90) REVERT: B 260 ASP cc_start: 0.8206 (t70) cc_final: 0.7895 (t70) REVERT: B 308 GLU cc_start: 0.8549 (pp20) cc_final: 0.8275 (pp20) REVERT: B 316 TRP cc_start: 0.7652 (p-90) cc_final: 0.7328 (p-90) REVERT: B 404 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7977 (tt) REVERT: B 469 TRP cc_start: 0.7676 (t-100) cc_final: 0.7445 (t-100) REVERT: B 477 HIS cc_start: 0.7900 (m-70) cc_final: 0.7429 (m-70) outliers start: 34 outliers final: 22 residues processed: 127 average time/residue: 0.1660 time to fit residues: 29.6081 Evaluate side-chains 122 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 15 optimal weight: 0.0980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.179324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128310 restraints weight = 10451.026| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.35 r_work: 0.3406 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.206 Angle : 0.610 10.643 10201 Z= 0.302 Chirality : 0.041 0.223 1180 Planarity : 0.004 0.048 1269 Dihedral : 4.497 35.430 1100 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.23 % Allowed : 23.94 % Favored : 71.83 % 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: 1.12 (0.29), residues: 928 helix: 1.70 (0.24), residues: 501 sheet: 1.57 (0.77), residues: 46 loop : -0.66 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 364 HIS 0.003 0.001 HIS B 361 PHE 0.020 0.001 PHE B 314 TYR 0.031 0.002 TYR B 399 ARG 0.001 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7639 (Cg_exo) cc_final: 0.7357 (Cg_endo) REVERT: A 529 ASP cc_start: 0.8102 (t0) cc_final: 0.7875 (t0) REVERT: A 618 GLU cc_start: 0.7438 (mp0) cc_final: 0.6897 (mt-10) REVERT: A 621 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6996 (pt0) REVERT: B 122 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8060 (tt) REVERT: B 164 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7676 (tt) REVERT: B 194 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8093 (mtmm) REVERT: B 233 HIS cc_start: 0.6801 (OUTLIER) cc_final: 0.5512 (t-90) REVERT: B 260 ASP cc_start: 0.8224 (t70) cc_final: 0.7904 (t70) REVERT: B 308 GLU cc_start: 0.8553 (pp20) cc_final: 0.8287 (pp20) REVERT: B 404 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 464 PHE cc_start: 0.7454 (m-10) cc_final: 0.7240 (m-10) REVERT: B 469 TRP cc_start: 0.7718 (t-100) cc_final: 0.7450 (t-100) REVERT: B 477 HIS cc_start: 0.7924 (m-70) cc_final: 0.7441 (m-70) outliers start: 33 outliers final: 22 residues processed: 123 average time/residue: 0.1652 time to fit residues: 28.9184 Evaluate side-chains 118 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.175744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124485 restraints weight = 10502.672| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.33 r_work: 0.3356 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7496 Z= 0.299 Angle : 0.675 9.226 10201 Z= 0.336 Chirality : 0.043 0.235 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.719 38.300 1100 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.61 % Allowed : 23.94 % Favored : 71.45 % 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: 0.90 (0.29), residues: 928 helix: 1.53 (0.24), residues: 495 sheet: 1.29 (0.72), residues: 46 loop : -0.70 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 364 HIS 0.003 0.001 HIS B 361 PHE 0.022 0.002 PHE B 314 TYR 0.045 0.002 TYR B 399 ARG 0.002 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7778 (Cg_exo) cc_final: 0.7500 (Cg_endo) REVERT: A 339 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6179 (mm) REVERT: A 621 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7153 (pt0) REVERT: B 122 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8031 (tt) REVERT: B 194 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8129 (mtmm) REVERT: B 233 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.5639 (t-90) REVERT: B 260 ASP cc_start: 0.8240 (t70) cc_final: 0.7931 (t0) REVERT: B 308 GLU cc_start: 0.8597 (pp20) cc_final: 0.8303 (pp20) REVERT: B 379 MET cc_start: 0.7517 (mmm) cc_final: 0.7128 (mtt) REVERT: B 404 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7969 (tt) REVERT: B 477 HIS cc_start: 0.7923 (m-70) cc_final: 0.7425 (m-70) outliers start: 36 outliers final: 25 residues processed: 123 average time/residue: 0.1523 time to fit residues: 27.0485 Evaluate side-chains 124 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.179136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128394 restraints weight = 10599.455| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.36 r_work: 0.3402 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7496 Z= 0.189 Angle : 0.620 9.569 10201 Z= 0.308 Chirality : 0.041 0.221 1180 Planarity : 0.004 0.046 1269 Dihedral : 4.530 38.018 1100 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.71 % Allowed : 25.10 % Favored : 71.19 % 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: 1.02 (0.29), residues: 928 helix: 1.64 (0.24), residues: 501 sheet: 1.25 (0.72), residues: 46 loop : -0.69 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 364 HIS 0.003 0.001 HIS B 361 PHE 0.018 0.001 PHE B 314 TYR 0.023 0.002 TYR A 469 ARG 0.001 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7810 (Cg_exo) cc_final: 0.7560 (Cg_endo) REVERT: A 339 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6056 (mm) REVERT: A 529 ASP cc_start: 0.8105 (t0) cc_final: 0.7879 (t0) REVERT: B 122 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8015 (tt) REVERT: B 194 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8063 (mtmm) REVERT: B 233 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.5608 (t-90) REVERT: B 260 ASP cc_start: 0.8231 (t70) cc_final: 0.7902 (t70) REVERT: B 262 ARG cc_start: 0.8579 (mtt90) cc_final: 0.8096 (ttm110) REVERT: B 308 GLU cc_start: 0.8540 (pp20) cc_final: 0.8272 (pp20) REVERT: B 404 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7977 (tt) REVERT: B 477 HIS cc_start: 0.7973 (m-70) cc_final: 0.7477 (m-70) outliers start: 29 outliers final: 21 residues processed: 115 average time/residue: 0.1583 time to fit residues: 26.2171 Evaluate side-chains 113 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 55 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133077 restraints weight = 10636.268| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.45 r_work: 0.3426 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7496 Z= 0.165 Angle : 0.611 9.500 10201 Z= 0.304 Chirality : 0.041 0.216 1180 Planarity : 0.004 0.046 1269 Dihedral : 4.351 36.706 1100 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.20 % Allowed : 25.86 % Favored : 70.93 % 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: 1.17 (0.29), residues: 928 helix: 1.81 (0.24), residues: 499 sheet: 1.25 (0.72), residues: 46 loop : -0.67 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 364 HIS 0.004 0.000 HIS B 361 PHE 0.025 0.001 PHE B 314 TYR 0.025 0.001 TYR B 399 ARG 0.001 0.000 ARG A 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7776 (Cg_exo) cc_final: 0.7522 (Cg_endo) REVERT: A 606 GLU cc_start: 0.6802 (pm20) cc_final: 0.6420 (mp0) REVERT: B 122 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8055 (tt) REVERT: B 194 LYS cc_start: 0.8540 (mtmm) cc_final: 0.7996 (mtmm) REVERT: B 233 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.5672 (t-90) REVERT: B 260 ASP cc_start: 0.8175 (t70) cc_final: 0.7852 (t70) REVERT: B 262 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8126 (ttm110) REVERT: B 308 GLU cc_start: 0.8517 (pp20) cc_final: 0.8272 (pp20) REVERT: B 375 THR cc_start: 0.8124 (m) cc_final: 0.7810 (m) REVERT: B 477 HIS cc_start: 0.8011 (m-70) cc_final: 0.7509 (m-70) outliers start: 25 outliers final: 19 residues processed: 115 average time/residue: 0.1518 time to fit residues: 25.3770 Evaluate side-chains 112 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 233 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 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 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129393 restraints weight = 10448.064| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.32 r_work: 0.3415 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7496 Z= 0.204 Angle : 0.652 10.127 10201 Z= 0.316 Chirality : 0.043 0.314 1180 Planarity : 0.004 0.048 1269 Dihedral : 4.373 39.372 1100 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.20 % Allowed : 25.99 % Favored : 70.81 % 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: 1.10 (0.29), residues: 928 helix: 1.74 (0.24), residues: 499 sheet: 1.18 (0.71), residues: 46 loop : -0.67 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 469 HIS 0.003 0.001 HIS B 361 PHE 0.023 0.001 PHE B 314 TYR 0.025 0.002 TYR B 399 ARG 0.001 0.000 ARG B 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.14 seconds wall clock time: 70 minutes 26.79 seconds (4226.79 seconds total)