Starting phenix.real_space_refine on Sun May 11 02:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnt_37672/05_2025/8wnt_37672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnt_37672/05_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_37672/05_2025/8wnt_37672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnt_37672/05_2025/8wnt_37672.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnt_37672/05_2025/8wnt_37672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnt_37672/05_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-5687/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: 4.77, per 1000 atoms: 0.65 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: 1.68 Conformation dependent library (CDL) restraints added in 988.5 milliseconds 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: 0.68 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: 2.03 Time building geometry restraints manager: 2.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- 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 7502 Z= 0.181 Angle : 0.673 13.133 10218 Z= 0.355 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 2.39388 ( 12) link_BETA1-4 : bond 0.00201 ( 1) link_BETA1-4 : angle 1.23603 ( 3) hydrogen bonds : bond 0.19351 ( 384) hydrogen bonds : angle 7.57181 ( 1110) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.40104 ( 2) covalent geometry : bond 0.00359 ( 7496) covalent geometry : angle 0.66788 (10201) *********************** 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 : 0.737 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: 0.1664 time to fit residues: 23.4114 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 : 0.800 ------------------------------------------------------------------------------- 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 = 0.180651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131927 restraints weight = 10521.350| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.27 r_work: 0.3455 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 7502 Z= 0.127 Angle : 0.609 8.067 10218 Z= 0.303 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 2.84087 ( 12) link_BETA1-4 : bond 0.00489 ( 1) link_BETA1-4 : angle 1.06528 ( 3) hydrogen bonds : bond 0.04489 ( 384) hydrogen bonds : angle 4.94065 ( 1110) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.13813 ( 2) covalent geometry : bond 0.00279 ( 7496) covalent geometry : angle 0.60098 (10201) *********************** 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 : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 PHE cc_start: 0.8384 (m-80) cc_final: 0.8123 (m-10) REVERT: B 164 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7719 (tt) REVERT: B 194 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8056 (mtmm) REVERT: B 308 GLU cc_start: 0.8416 (pp20) cc_final: 0.8203 (pp20) REVERT: B 347 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7187 (mt-10) REVERT: B 464 PHE cc_start: 0.7302 (m-10) cc_final: 0.6802 (m-10) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 0.1591 time to fit residues: 27.9533 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 : 0.929 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.179883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129230 restraints weight = 10591.753| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.39 r_work: 0.3426 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7502 Z= 0.139 Angle : 0.607 8.290 10218 Z= 0.301 Chirality : 0.041 0.230 1180 Planarity : 0.004 0.054 1269 Dihedral : 4.594 31.174 1100 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.39 % Favored : 94.40 % Rotamer: Outliers : 3.33 % Allowed : 21.51 % 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: 0.94 (0.29), residues: 928 helix: 1.54 (0.24), residues: 500 sheet: 1.68 (0.79), residues: 46 loop : -0.75 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.004 0.001 HIS A 557 PHE 0.012 0.001 PHE A 524 TYR 0.024 0.002 TYR B 399 ARG 0.001 0.000 ARG B 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 2.69173 ( 12) link_BETA1-4 : bond 0.00371 ( 1) link_BETA1-4 : angle 1.27220 ( 3) hydrogen bonds : bond 0.04309 ( 384) hydrogen bonds : angle 4.62515 ( 1110) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.21994 ( 2) covalent geometry : bond 0.00324 ( 7496) covalent geometry : angle 0.59966 (10201) *********************** 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: 26 poor density : 95 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8215 (mmtp) REVERT: B 122 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8005 (tt) REVERT: B 194 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8226 (mtmm) REVERT: B 308 GLU cc_start: 0.8481 (pp20) cc_final: 0.8235 (pp20) REVERT: B 404 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (tt) REVERT: B 477 HIS cc_start: 0.7870 (m-70) cc_final: 0.7607 (m-70) outliers start: 26 outliers final: 16 residues processed: 117 average time/residue: 0.1810 time to fit residues: 29.0084 Evaluate side-chains 113 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 246 LYS 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: 0.7980 chunk 34 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 84 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.3102 ------------------------------------------------------------------------------- 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 176 ASN B 211 GLN B 389 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.170140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120731 restraints weight = 10703.641| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.21 r_work: 0.3310 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7502 Z= 0.266 Angle : 0.743 8.347 10218 Z= 0.372 Chirality : 0.047 0.259 1180 Planarity : 0.005 0.055 1269 Dihedral : 5.190 39.796 1100 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.89 % Rotamer: Outliers : 5.12 % Allowed : 21.90 % Favored : 72.98 % 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: 0.46 (0.28), residues: 928 helix: 1.16 (0.24), residues: 493 sheet: 1.33 (0.72), residues: 46 loop : -0.92 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 469 HIS 0.010 0.001 HIS A 557 PHE 0.024 0.002 PHE A 524 TYR 0.043 0.003 TYR B 399 ARG 0.003 0.001 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 2.92768 ( 12) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 1.59875 ( 3) hydrogen bonds : bond 0.05668 ( 384) hydrogen bonds : angle 4.94615 ( 1110) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.41585 ( 2) covalent geometry : bond 0.00637 ( 7496) covalent geometry : angle 0.73610 (10201) *********************** 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 141 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8149 (mmtt) REVERT: A 269 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: A 339 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5977 (mm) REVERT: B 56 SER cc_start: 0.8992 (p) cc_final: 0.8735 (t) REVERT: B 122 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7972 (tt) REVERT: B 194 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8179 (mtmm) REVERT: B 233 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.5467 (t-90) REVERT: B 308 GLU cc_start: 0.8610 (pp20) cc_final: 0.8268 (pp20) REVERT: B 404 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 477 HIS cc_start: 0.7957 (m-70) cc_final: 0.7585 (m-70) outliers start: 40 outliers final: 25 residues processed: 133 average time/residue: 0.1555 time to fit residues: 29.2045 Evaluate side-chains 119 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 246 LYS Chi-restraints excluded: chain A residue 269 GLN 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 A residue 625 LEU 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 276 VAL Chi-restraints excluded: chain B residue 279 VAL 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 462 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: 0.8980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.4135 r_free = 0.4135 target = 0.177784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126984 restraints weight = 10452.259| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.33 r_work: 0.3391 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7502 Z= 0.131 Angle : 0.613 8.438 10218 Z= 0.306 Chirality : 0.041 0.228 1180 Planarity : 0.004 0.051 1269 Dihedral : 4.814 37.009 1100 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.99 % Allowed : 22.28 % Favored : 72.73 % 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: 0.74 (0.28), residues: 928 helix: 1.37 (0.24), residues: 500 sheet: 1.51 (0.75), residues: 46 loop : -0.80 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 124 HIS 0.003 0.001 HIS B 361 PHE 0.013 0.001 PHE A 542 TYR 0.037 0.001 TYR B 399 ARG 0.001 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 4) link_NAG-ASN : angle 2.69484 ( 12) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 1.37763 ( 3) hydrogen bonds : bond 0.04341 ( 384) hydrogen bonds : angle 4.49064 ( 1110) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.51957 ( 2) covalent geometry : bond 0.00295 ( 7496) covalent geometry : angle 0.60552 (10201) *********************** 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 138 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7639 (Cg_exo) cc_final: 0.7368 (Cg_endo) REVERT: A 269 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: A 339 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5967 (mm) REVERT: B 56 SER cc_start: 0.8881 (p) cc_final: 0.8672 (t) REVERT: B 194 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8247 (mtmm) REVERT: B 233 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.5447 (t-90) REVERT: B 260 ASP cc_start: 0.8197 (t70) cc_final: 0.7887 (t70) REVERT: B 308 GLU cc_start: 0.8556 (pp20) cc_final: 0.8220 (pp20) REVERT: B 404 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8000 (tt) REVERT: B 469 TRP cc_start: 0.7641 (t-100) cc_final: 0.7377 (t-100) REVERT: B 477 HIS cc_start: 0.7923 (m-70) cc_final: 0.7491 (m-70) outliers start: 39 outliers final: 23 residues processed: 132 average time/residue: 0.1746 time to fit residues: 32.3316 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 : 0.909 ------------------------------------------------------------------------------- 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 269 GLN Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 296 GLN 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 B residue 86 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 233 HIS 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 320 VAL 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 486 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.177804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129323 restraints weight = 10538.364| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.39 r_work: 0.3397 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7502 Z= 0.126 Angle : 0.606 10.420 10218 Z= 0.298 Chirality : 0.041 0.223 1180 Planarity : 0.004 0.049 1269 Dihedral : 4.622 37.343 1100 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.97 % Allowed : 24.46 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 928 helix: 1.52 (0.24), residues: 501 sheet: 1.49 (0.76), residues: 46 loop : -0.74 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 364 HIS 0.003 0.001 HIS B 361 PHE 0.013 0.001 PHE B 314 TYR 0.033 0.002 TYR B 399 ARG 0.002 0.000 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 2.58445 ( 12) link_BETA1-4 : bond 0.00235 ( 1) link_BETA1-4 : angle 1.35392 ( 3) hydrogen bonds : bond 0.04023 ( 384) hydrogen bonds : angle 4.39042 ( 1110) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.51926 ( 2) covalent geometry : bond 0.00287 ( 7496) covalent geometry : angle 0.59920 (10201) *********************** 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 127 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7379 (Cg_endo) REVERT: A 269 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: A 339 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5769 (mm) REVERT: A 529 ASP cc_start: 0.8101 (t0) cc_final: 0.7876 (t0) REVERT: B 122 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8006 (tt) REVERT: B 194 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8204 (mtmm) REVERT: B 233 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.5543 (t-90) REVERT: B 260 ASP cc_start: 0.8209 (t70) cc_final: 0.7894 (t70) REVERT: B 308 GLU cc_start: 0.8577 (pp20) cc_final: 0.8285 (pp20) REVERT: B 375 THR cc_start: 0.8224 (m) cc_final: 0.7907 (m) REVERT: B 404 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 469 TRP cc_start: 0.7702 (t-100) cc_final: 0.7387 (t-100) REVERT: B 477 HIS cc_start: 0.8015 (m-70) cc_final: 0.7521 (m-70) outliers start: 31 outliers final: 21 residues processed: 123 average time/residue: 0.1644 time to fit residues: 28.2636 Evaluate side-chains 115 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 269 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 SER 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 195 LEU 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 320 VAL 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 486 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 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: 0.9980 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 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 = 0.4133 r_free = 0.4133 target = 0.177745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126943 restraints weight = 10417.765| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.30 r_work: 0.3397 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7502 Z= 0.134 Angle : 0.612 9.375 10218 Z= 0.301 Chirality : 0.041 0.223 1180 Planarity : 0.004 0.048 1269 Dihedral : 4.550 36.647 1100 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.35 % Allowed : 24.33 % Favored : 71.32 % 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: 1.60 (0.24), residues: 500 sheet: 1.39 (0.75), residues: 46 loop : -0.73 (0.33), residues: 382 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 0.003 0.000 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 4) link_NAG-ASN : angle 2.51428 ( 12) link_BETA1-4 : bond 0.00292 ( 1) link_BETA1-4 : angle 1.36874 ( 3) hydrogen bonds : bond 0.04057 ( 384) hydrogen bonds : angle 4.33810 ( 1110) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.53030 ( 2) covalent geometry : bond 0.00307 ( 7496) covalent geometry : angle 0.60629 (10201) *********************** 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 131 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7666 (Cg_exo) cc_final: 0.7398 (Cg_endo) REVERT: A 339 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6060 (mm) REVERT: A 529 ASP cc_start: 0.8109 (t0) cc_final: 0.7880 (t0) REVERT: B 122 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8046 (tt) REVERT: B 194 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8077 (mtmm) REVERT: B 233 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.5588 (t-90) REVERT: B 260 ASP cc_start: 0.8221 (t70) cc_final: 0.7905 (t70) REVERT: B 308 GLU cc_start: 0.8555 (pp20) cc_final: 0.8260 (pp20) REVERT: B 404 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7958 (tt) REVERT: B 464 PHE cc_start: 0.7480 (m-10) cc_final: 0.7011 (m-10) REVERT: B 477 HIS cc_start: 0.7917 (m-70) cc_final: 0.7413 (m-70) outliers start: 34 outliers final: 25 residues processed: 125 average time/residue: 0.1519 time to fit residues: 27.3018 Evaluate side-chains 118 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 296 GLN 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 510 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 SER 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 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 310 LEU Chi-restraints excluded: chain B residue 320 VAL 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 462 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: 9.9990 chunk 29 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.177576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129103 restraints weight = 10483.436| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.39 r_work: 0.3387 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7502 Z= 0.142 Angle : 0.631 9.775 10218 Z= 0.310 Chirality : 0.042 0.223 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.570 37.386 1100 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.35 % Allowed : 24.33 % Favored : 71.32 % 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: 0.96 (0.29), residues: 928 helix: 1.59 (0.24), residues: 500 sheet: 1.26 (0.74), residues: 46 loop : -0.72 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 364 HIS 0.003 0.001 HIS A 557 PHE 0.014 0.001 PHE B 314 TYR 0.029 0.002 TYR B 399 ARG 0.001 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 2.46034 ( 12) link_BETA1-4 : bond 0.00273 ( 1) link_BETA1-4 : angle 1.36563 ( 3) hydrogen bonds : bond 0.04113 ( 384) hydrogen bonds : angle 4.35479 ( 1110) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.49534 ( 2) covalent geometry : bond 0.00329 ( 7496) covalent geometry : angle 0.62569 (10201) *********************** 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 127 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7693 (Cg_exo) cc_final: 0.7427 (Cg_endo) REVERT: A 339 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5992 (mm) REVERT: A 529 ASP cc_start: 0.8135 (t0) cc_final: 0.7881 (t0) REVERT: A 621 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7133 (pt0) REVERT: B 122 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8031 (tt) REVERT: B 194 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8080 (mtmm) REVERT: B 233 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.5669 (t-90) REVERT: B 260 ASP cc_start: 0.8230 (t70) cc_final: 0.7917 (t0) REVERT: B 262 ARG cc_start: 0.8616 (mtt90) cc_final: 0.8104 (ttm110) REVERT: B 308 GLU cc_start: 0.8558 (pp20) cc_final: 0.8270 (pp20) REVERT: B 379 MET cc_start: 0.7524 (mmm) cc_final: 0.6826 (mtt) REVERT: B 404 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 477 HIS cc_start: 0.7926 (m-70) cc_final: 0.7422 (m-70) outliers start: 34 outliers final: 25 residues processed: 120 average time/residue: 0.1660 time to fit residues: 28.3730 Evaluate side-chains 125 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 275 GLN Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 296 GLN 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 510 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 SER 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 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 310 LEU Chi-restraints excluded: chain B residue 320 VAL 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 486 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.0060 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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 = 0.179524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131296 restraints weight = 10558.533| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.35 r_work: 0.3407 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7502 Z= 0.121 Angle : 0.608 8.717 10218 Z= 0.300 Chirality : 0.041 0.215 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.426 37.530 1100 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.84 % Allowed : 24.84 % Favored : 71.32 % 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: 1.06 (0.29), residues: 928 helix: 1.66 (0.24), residues: 501 sheet: 1.29 (0.74), residues: 46 loop : -0.67 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 364 HIS 0.004 0.001 HIS B 361 PHE 0.023 0.001 PHE B 314 TYR 0.029 0.002 TYR B 399 ARG 0.001 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 2.35185 ( 12) link_BETA1-4 : bond 0.00346 ( 1) link_BETA1-4 : angle 1.33326 ( 3) hydrogen bonds : bond 0.03794 ( 384) hydrogen bonds : angle 4.25465 ( 1110) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.53327 ( 2) covalent geometry : bond 0.00275 ( 7496) covalent geometry : angle 0.60311 (10201) *********************** 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 125 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7772 (Cg_exo) cc_final: 0.7501 (Cg_endo) REVERT: A 339 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5929 (mm) REVERT: A 621 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7103 (pt0) REVERT: B 122 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 194 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8017 (mtmm) REVERT: B 233 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.5721 (t-90) REVERT: B 260 ASP cc_start: 0.8197 (t70) cc_final: 0.7886 (t0) REVERT: B 262 ARG cc_start: 0.8594 (mtt90) cc_final: 0.8115 (ttm110) REVERT: B 308 GLU cc_start: 0.8502 (pp20) cc_final: 0.8238 (pp20) REVERT: B 375 THR cc_start: 0.8166 (m) cc_final: 0.7831 (m) REVERT: B 379 MET cc_start: 0.7360 (mmm) cc_final: 0.6888 (mtt) REVERT: B 404 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8026 (tt) REVERT: B 477 HIS cc_start: 0.7964 (m-70) cc_final: 0.7472 (m-70) outliers start: 30 outliers final: 20 residues processed: 118 average time/residue: 0.1585 time to fit residues: 26.9138 Evaluate side-chains 115 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 339 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 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 291 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 320 VAL 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 442 PHE 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: 0.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.179750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128950 restraints weight = 10646.918| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.34 r_work: 0.3413 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7502 Z= 0.131 Angle : 0.649 12.812 10218 Z= 0.314 Chirality : 0.042 0.219 1180 Planarity : 0.004 0.049 1269 Dihedral : 4.401 38.016 1100 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.97 % Allowed : 24.84 % 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: 1.09 (0.29), residues: 928 helix: 1.73 (0.24), residues: 498 sheet: 1.32 (0.74), residues: 46 loop : -0.70 (0.33), residues: 384 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 0.030 0.002 TYR B 399 ARG 0.002 0.000 ARG B 470 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 2.33507 ( 12) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.33979 ( 3) hydrogen bonds : bond 0.03901 ( 384) hydrogen bonds : angle 4.29610 ( 1110) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.52488 ( 2) covalent geometry : bond 0.00301 ( 7496) covalent geometry : angle 0.64371 (10201) ********************** 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 123 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7795 (Cg_exo) cc_final: 0.7562 (Cg_endo) REVERT: A 339 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5996 (mm) REVERT: A 621 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: B 122 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8065 (tt) REVERT: B 194 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8022 (mtmm) REVERT: B 233 HIS cc_start: 0.6884 (OUTLIER) cc_final: 0.5706 (t-90) REVERT: B 260 ASP cc_start: 0.8198 (t70) cc_final: 0.7904 (t0) REVERT: B 262 ARG cc_start: 0.8591 (mtt90) cc_final: 0.8135 (ttm110) REVERT: B 308 GLU cc_start: 0.8482 (pp20) cc_final: 0.8224 (pp20) REVERT: B 404 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 464 PHE cc_start: 0.7357 (m-10) cc_final: 0.6938 (m-10) REVERT: B 477 HIS cc_start: 0.7938 (m-70) cc_final: 0.7416 (m-70) outliers start: 31 outliers final: 25 residues processed: 118 average time/residue: 0.1464 time to fit residues: 25.1322 Evaluate side-chains 120 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 339 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 86 THR 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 285 ILE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 320 VAL 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 436 PHE Chi-restraints excluded: chain B residue 442 PHE 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: 0.4980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.179918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129393 restraints weight = 10411.908| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.32 r_work: 0.3425 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7502 Z= 0.121 Angle : 0.625 13.886 10218 Z= 0.305 Chirality : 0.041 0.215 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.314 38.178 1100 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.46 % Allowed : 25.48 % Favored : 71.06 % 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: 1.74 (0.24), residues: 498 sheet: 1.35 (0.74), residues: 46 loop : -0.67 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 364 HIS 0.004 0.000 HIS B 361 PHE 0.019 0.001 PHE B 314 TYR 0.028 0.001 TYR B 399 ARG 0.001 0.000 ARG A 430 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 4) link_NAG-ASN : angle 2.26552 ( 12) link_BETA1-4 : bond 0.00342 ( 1) link_BETA1-4 : angle 1.29819 ( 3) hydrogen bonds : bond 0.03731 ( 384) hydrogen bonds : angle 4.23836 ( 1110) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.52607 ( 2) covalent geometry : bond 0.00275 ( 7496) covalent geometry : angle 0.61990 (10201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3559.17 seconds wall clock time: 62 minutes 23.91 seconds (3743.91 seconds total)