Starting phenix.real_space_refine on Fri Aug 22 19:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnt_37672/08_2025/8wnt_37672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnt_37672/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wnt_37672/08_2025/8wnt_37672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnt_37672/08_2025/8wnt_37672.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wnt_37672/08_2025/8wnt_37672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnt_37672/08_2025/8wnt_37672.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.54, per 1000 atoms: 0.21 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: 0.53 Conformation dependent library (CDL) restraints added in 281.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.00 Time building geometry restraints manager: 0.71 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: 0.010 Normalize map: mean=0, sd=1: 1.230 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 212 TYR 0.026 0.001 TYR B 399 PHE 0.016 0.001 PHE B 463 TRP 0.044 0.002 TRP B 316 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7496) covalent geometry : angle 0.66788 (10201) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.40104 ( 2) hydrogen bonds : bond 0.19351 ( 384) hydrogen bonds : angle 7.57181 ( 1110) link_BETA1-4 : bond 0.00201 ( 1) link_BETA1-4 : angle 1.23603 ( 3) link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 2.39388 ( 12) *********************** 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 : 0.225 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: 0.0639 time to fit residues: 9.0478 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 : 0.313 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.179191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130086 restraints weight = 10633.264| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.28 r_work: 0.3434 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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= 0.139 Angle : 0.616 8.063 10218 Z= 0.309 Chirality : 0.042 0.243 1180 Planarity : 0.004 0.057 1269 Dihedral : 4.965 33.901 1104 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.29 % Rotamer: Outliers : 2.30 % Allowed : 22.41 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.28), residues: 928 helix: 1.39 (0.24), residues: 505 sheet: 1.58 (0.78), residues: 46 loop : -0.75 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.021 0.001 TYR B 399 PHE 0.014 0.001 PHE A 627 TRP 0.018 0.001 TRP B 316 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7496) covalent geometry : angle 0.60840 (10201) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.12962 ( 2) hydrogen bonds : bond 0.04597 ( 384) hydrogen bonds : angle 4.96836 ( 1110) link_BETA1-4 : bond 0.00349 ( 1) link_BETA1-4 : angle 1.24353 ( 3) link_NAG-ASN : bond 0.00233 ( 4) link_NAG-ASN : angle 2.82350 ( 12) *********************** 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 122 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7671 (tt) REVERT: B 194 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8062 (mtmm) REVERT: B 308 GLU cc_start: 0.8440 (pp20) cc_final: 0.8222 (pp20) REVERT: B 347 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7218 (mt-10) REVERT: B 464 PHE cc_start: 0.7352 (m-10) cc_final: 0.6861 (m-10) outliers start: 18 outliers final: 10 residues processed: 119 average time/residue: 0.0687 time to fit residues: 11.6126 Evaluate side-chains 99 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 41 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.179147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128564 restraints weight = 10484.880| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.36 r_work: 0.3418 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1347 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= 0.143 Angle : 0.617 8.192 10218 Z= 0.305 Chirality : 0.042 0.230 1180 Planarity : 0.004 0.056 1269 Dihedral : 4.633 31.513 1100 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.60 % Favored : 94.18 % Rotamer: Outliers : 3.33 % Allowed : 22.28 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.29), residues: 928 helix: 1.52 (0.24), residues: 500 sheet: 1.71 (0.78), residues: 46 loop : -0.78 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 452 TYR 0.028 0.002 TYR B 399 PHE 0.013 0.001 PHE A 524 TRP 0.014 0.001 TRP B 124 HIS 0.004 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7496) covalent geometry : angle 0.60984 (10201) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.24357 ( 2) hydrogen bonds : bond 0.04407 ( 384) hydrogen bonds : angle 4.63778 ( 1110) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 1.28782 ( 3) link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 2.68041 ( 12) *********************** 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 125 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (mmtt) REVERT: B 122 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7991 (tt) REVERT: B 194 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8252 (mtmm) REVERT: B 308 GLU cc_start: 0.8486 (pp20) cc_final: 0.8235 (pp20) REVERT: B 404 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7947 (tt) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.0807 time to fit residues: 13.3249 Evaluate side-chains 110 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 309 LYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.179688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128909 restraints weight = 10718.546| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.39 r_work: 0.3423 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7502 Z= 0.130 Angle : 0.600 8.025 10218 Z= 0.298 Chirality : 0.041 0.225 1180 Planarity : 0.004 0.056 1269 Dihedral : 4.531 29.856 1100 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 3.71 % Allowed : 22.66 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.29), residues: 928 helix: 1.55 (0.24), residues: 500 sheet: 1.76 (0.78), residues: 46 loop : -0.73 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 452 TYR 0.028 0.002 TYR B 399 PHE 0.012 0.001 PHE A 542 TRP 0.018 0.001 TRP B 469 HIS 0.003 0.000 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7496) covalent geometry : angle 0.59339 (10201) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.30817 ( 2) hydrogen bonds : bond 0.04180 ( 384) hydrogen bonds : angle 4.48929 ( 1110) link_BETA1-4 : bond 0.00411 ( 1) link_BETA1-4 : angle 1.29417 ( 3) link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 2.67416 ( 12) *********************** 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 126 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8106 (mmtt) REVERT: B 194 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8192 (mtmm) REVERT: B 233 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.5389 (t-90) REVERT: B 308 GLU cc_start: 0.8513 (pp20) cc_final: 0.8264 (pp20) REVERT: B 309 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8337 (mtpp) REVERT: B 404 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7956 (tt) REVERT: B 430 TYR cc_start: 0.7934 (t80) cc_final: 0.7561 (t80) REVERT: B 464 PHE cc_start: 0.7439 (m-10) cc_final: 0.7204 (m-10) outliers start: 29 outliers final: 16 residues processed: 120 average time/residue: 0.0733 time to fit residues: 12.1963 Evaluate side-chains 110 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 510 VAL 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 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 424 LEU 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 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.179320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131006 restraints weight = 10508.758| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.35 r_work: 0.3422 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7502 Z= 0.129 Angle : 0.591 8.307 10218 Z= 0.294 Chirality : 0.041 0.222 1180 Planarity : 0.004 0.055 1269 Dihedral : 4.489 27.399 1100 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.10 % Allowed : 22.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.29), residues: 928 helix: 1.63 (0.24), residues: 500 sheet: 1.77 (0.77), residues: 46 loop : -0.70 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.031 0.002 TYR B 399 PHE 0.011 0.001 PHE A 542 TRP 0.017 0.001 TRP A 364 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7496) covalent geometry : angle 0.58403 (10201) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.38515 ( 2) hydrogen bonds : bond 0.04015 ( 384) hydrogen bonds : angle 4.36574 ( 1110) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 1.33124 ( 3) link_NAG-ASN : bond 0.00227 ( 4) link_NAG-ASN : angle 2.62643 ( 12) *********************** 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 130 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8214 (mmtp) REVERT: A 309 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8862 (pp) REVERT: B 194 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8216 (mtmm) REVERT: B 227 MET cc_start: 0.4941 (ttt) cc_final: 0.4711 (ttt) REVERT: B 233 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.5331 (t-90) REVERT: B 260 ASP cc_start: 0.8147 (t70) cc_final: 0.7823 (t70) REVERT: B 308 GLU cc_start: 0.8587 (pp20) cc_final: 0.8353 (pp20) REVERT: B 404 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7938 (tt) outliers start: 32 outliers final: 20 residues processed: 125 average time/residue: 0.0769 time to fit residues: 13.5156 Evaluate side-chains 116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 296 GLN 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 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 455 ILE Chi-restraints excluded: chain B residue 462 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 83 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 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 = 0.4145 r_free = 0.4145 target = 0.178676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132096 restraints weight = 10532.293| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.24 r_work: 0.3422 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1757 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= 0.116 Angle : 0.582 8.105 10218 Z= 0.288 Chirality : 0.040 0.216 1180 Planarity : 0.004 0.056 1269 Dihedral : 4.377 27.804 1100 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.23 % Allowed : 22.66 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 928 helix: 1.73 (0.24), residues: 501 sheet: 1.79 (0.77), residues: 46 loop : -0.67 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 470 TYR 0.027 0.001 TYR B 399 PHE 0.012 0.001 PHE B 314 TRP 0.028 0.001 TRP B 469 HIS 0.004 0.000 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7496) covalent geometry : angle 0.57526 (10201) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.42509 ( 2) hydrogen bonds : bond 0.03785 ( 384) hydrogen bonds : angle 4.25942 ( 1110) link_BETA1-4 : bond 0.00291 ( 1) link_BETA1-4 : angle 1.29688 ( 3) link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 2.56986 ( 12) *********************** 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 134 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7390 (Cg_endo) REVERT: A 529 ASP cc_start: 0.8060 (t0) cc_final: 0.7798 (t0) REVERT: B 122 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8039 (tt) REVERT: B 194 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8109 (mtmm) REVERT: B 227 MET cc_start: 0.4940 (ttt) cc_final: 0.4701 (ttt) REVERT: B 233 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.5430 (t-90) REVERT: B 260 ASP cc_start: 0.8196 (t70) cc_final: 0.7873 (t70) REVERT: B 291 MET cc_start: 0.7953 (ptp) cc_final: 0.7722 (pmm) REVERT: B 308 GLU cc_start: 0.8589 (pp20) cc_final: 0.8368 (pp20) REVERT: B 316 TRP cc_start: 0.7535 (p-90) cc_final: 0.7208 (p-90) REVERT: B 404 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7970 (tt) REVERT: B 464 PHE cc_start: 0.7348 (m-10) cc_final: 0.7115 (m-10) REVERT: B 469 TRP cc_start: 0.7675 (t-100) cc_final: 0.7311 (t-100) outliers start: 33 outliers final: 22 residues processed: 129 average time/residue: 0.0642 time to fit residues: 11.5150 Evaluate side-chains 119 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 122 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 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 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 Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 overall best weight: 0.9118 ------------------------------------------------------------------------------- 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 365 GLN A 543 HIS A 557 HIS B 176 ASN B 213 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128753 restraints weight = 10558.104| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.35 r_work: 0.3408 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7502 Z= 0.141 Angle : 0.627 10.294 10218 Z= 0.305 Chirality : 0.042 0.226 1180 Planarity : 0.004 0.053 1269 Dihedral : 4.431 32.843 1100 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.84 % Allowed : 23.30 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.29), residues: 928 helix: 1.71 (0.24), residues: 501 sheet: 1.68 (0.76), residues: 46 loop : -0.69 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 452 TYR 0.031 0.002 TYR B 399 PHE 0.022 0.001 PHE B 314 TRP 0.019 0.001 TRP A 364 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7496) covalent geometry : angle 0.62061 (10201) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.38678 ( 2) hydrogen bonds : bond 0.04027 ( 384) hydrogen bonds : angle 4.31051 ( 1110) link_BETA1-4 : bond 0.00327 ( 1) link_BETA1-4 : angle 1.32672 ( 3) link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 2.56036 ( 12) *********************** 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 129 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7584 (Cg_exo) cc_final: 0.7292 (Cg_endo) REVERT: A 529 ASP cc_start: 0.8048 (t0) cc_final: 0.7791 (t0) REVERT: B 122 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8056 (tt) REVERT: B 194 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8111 (mtmm) REVERT: B 227 MET cc_start: 0.4953 (ttt) cc_final: 0.4710 (ttt) REVERT: B 233 HIS cc_start: 0.6794 (OUTLIER) cc_final: 0.5432 (t-90) REVERT: B 260 ASP cc_start: 0.8213 (t70) cc_final: 0.7872 (t70) REVERT: B 262 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8100 (ttm110) REVERT: B 291 MET cc_start: 0.8109 (ptp) cc_final: 0.7820 (pmm) REVERT: B 308 GLU cc_start: 0.8596 (pp20) cc_final: 0.8375 (pp20) REVERT: B 316 TRP cc_start: 0.7639 (p-90) cc_final: 0.7293 (p-90) REVERT: B 404 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7985 (tt) REVERT: B 469 TRP cc_start: 0.7642 (t-100) cc_final: 0.7320 (t-100) outliers start: 30 outliers final: 22 residues processed: 124 average time/residue: 0.0599 time to fit residues: 10.5067 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 : 0.226 ------------------------------------------------------------------------------- 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 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 B residue 122 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 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 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 Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 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 = 0.4164 r_free = 0.4164 target = 0.180870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133327 restraints weight = 10566.256| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.15 r_work: 0.3433 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2031 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= 0.121 Angle : 0.602 9.202 10218 Z= 0.295 Chirality : 0.041 0.217 1180 Planarity : 0.004 0.052 1269 Dihedral : 4.361 33.108 1100 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.71 % Allowed : 23.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.29), residues: 928 helix: 1.77 (0.24), residues: 501 sheet: 1.73 (0.76), residues: 46 loop : -0.66 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.025 0.002 TYR B 399 PHE 0.022 0.001 PHE B 314 TRP 0.020 0.001 TRP A 364 HIS 0.003 0.000 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7496) covalent geometry : angle 0.59635 (10201) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.46504 ( 2) hydrogen bonds : bond 0.03802 ( 384) hydrogen bonds : angle 4.20605 ( 1110) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.30682 ( 3) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 2.44880 ( 12) *********************** 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 125 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7291 (Cg_endo) REVERT: A 529 ASP cc_start: 0.8009 (t0) cc_final: 0.7749 (t0) REVERT: A 621 GLU cc_start: 0.7583 (tt0) cc_final: 0.6966 (pp20) REVERT: B 122 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 194 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8102 (mtmm) REVERT: B 233 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.5510 (t-90) REVERT: B 260 ASP cc_start: 0.8155 (t70) cc_final: 0.7818 (t70) REVERT: B 262 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8107 (ttm110) REVERT: B 291 MET cc_start: 0.7987 (ptp) cc_final: 0.7726 (pmm) REVERT: B 308 GLU cc_start: 0.8566 (pp20) cc_final: 0.8305 (pp20) REVERT: B 404 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8029 (tt) REVERT: B 469 TRP cc_start: 0.7656 (t-100) cc_final: 0.7323 (t-100) outliers start: 29 outliers final: 22 residues processed: 120 average time/residue: 0.0523 time to fit residues: 9.1629 Evaluate side-chains 116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 260 LEU 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 B residue 122 LEU Chi-restraints excluded: chain B residue 125 SER 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 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 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 Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 = 0.4161 r_free = 0.4161 target = 0.180597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130103 restraints weight = 10386.350| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.31 r_work: 0.3423 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2139 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= 0.127 Angle : 0.620 10.250 10218 Z= 0.304 Chirality : 0.041 0.216 1180 Planarity : 0.004 0.052 1269 Dihedral : 4.341 34.775 1100 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.46 % Allowed : 24.07 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.29), residues: 928 helix: 1.74 (0.24), residues: 502 sheet: 1.76 (0.75), residues: 46 loop : -0.59 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.029 0.002 TYR B 399 PHE 0.024 0.001 PHE B 314 TRP 0.021 0.001 TRP A 364 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7496) covalent geometry : angle 0.61477 (10201) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.47222 ( 2) hydrogen bonds : bond 0.03848 ( 384) hydrogen bonds : angle 4.24607 ( 1110) link_BETA1-4 : bond 0.00327 ( 1) link_BETA1-4 : angle 1.31607 ( 3) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 2.40537 ( 12) *********************** 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 123 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7596 (Cg_exo) cc_final: 0.7308 (Cg_endo) REVERT: A 529 ASP cc_start: 0.8051 (t0) cc_final: 0.7790 (t0) REVERT: A 621 GLU cc_start: 0.7645 (tt0) cc_final: 0.7039 (pt0) REVERT: B 122 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8015 (tt) REVERT: B 194 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8092 (mtmm) REVERT: B 233 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.5540 (t-90) REVERT: B 260 ASP cc_start: 0.8216 (t70) cc_final: 0.7902 (t0) REVERT: B 262 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8127 (ttm110) REVERT: B 291 MET cc_start: 0.8076 (ptp) cc_final: 0.7830 (pmm) REVERT: B 308 GLU cc_start: 0.8580 (pp20) cc_final: 0.8316 (pp20) REVERT: B 404 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8006 (tt) REVERT: B 469 TRP cc_start: 0.7744 (t-100) cc_final: 0.7389 (t-100) outliers start: 27 outliers final: 22 residues processed: 119 average time/residue: 0.0597 time to fit residues: 10.2742 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 : 0.287 ------------------------------------------------------------------------------- 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 260 LEU 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 618 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 SER 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 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 455 ILE Chi-restraints excluded: chain B residue 486 TRP Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 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 = 0.4161 r_free = 0.4161 target = 0.180752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130135 restraints weight = 10468.230| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.32 r_work: 0.3435 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7502 Z= 0.119 Angle : 0.635 16.168 10218 Z= 0.305 Chirality : 0.040 0.213 1180 Planarity : 0.004 0.051 1269 Dihedral : 4.274 35.138 1100 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.20 % Allowed : 24.46 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 928 helix: 1.84 (0.24), residues: 499 sheet: 1.76 (0.74), residues: 46 loop : -0.61 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 212 TYR 0.027 0.001 TYR B 399 PHE 0.022 0.001 PHE B 314 TRP 0.021 0.001 TRP A 364 HIS 0.004 0.000 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7496) covalent geometry : angle 0.63025 (10201) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.47920 ( 2) hydrogen bonds : bond 0.03729 ( 384) hydrogen bonds : angle 4.21653 ( 1110) link_BETA1-4 : bond 0.00381 ( 1) link_BETA1-4 : angle 1.29566 ( 3) link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 2.28127 ( 12) ********************** 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 120 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7597 (Cg_exo) cc_final: 0.7313 (Cg_endo) REVERT: A 621 GLU cc_start: 0.7615 (tt0) cc_final: 0.7020 (pt0) REVERT: B 122 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 194 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8052 (mtmm) REVERT: B 233 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.5506 (t-90) REVERT: B 260 ASP cc_start: 0.8147 (t70) cc_final: 0.7834 (t0) REVERT: B 262 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8110 (ttm110) REVERT: B 308 GLU cc_start: 0.8626 (pp20) cc_final: 0.8416 (pp20) REVERT: B 379 MET cc_start: 0.7257 (mmm) cc_final: 0.6794 (mtt) REVERT: B 469 TRP cc_start: 0.7692 (t-100) cc_final: 0.7324 (t-100) outliers start: 25 outliers final: 19 residues processed: 116 average time/residue: 0.0603 time to fit residues: 10.2008 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 : 0.210 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 SER 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 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Chi-restraints excluded: chain B residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 0.0060 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 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 = 0.4164 r_free = 0.4164 target = 0.181039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131218 restraints weight = 10436.045| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.18 r_work: 0.3453 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7502 Z= 0.120 Angle : 0.656 16.173 10218 Z= 0.311 Chirality : 0.041 0.213 1180 Planarity : 0.004 0.051 1269 Dihedral : 4.238 35.657 1100 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.20 % Allowed : 24.84 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 928 helix: 1.82 (0.24), residues: 504 sheet: 1.87 (0.74), residues: 46 loop : -0.61 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 212 TYR 0.027 0.001 TYR B 399 PHE 0.026 0.001 PHE B 314 TRP 0.026 0.001 TRP A 364 HIS 0.003 0.000 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7496) covalent geometry : angle 0.65172 (10201) SS BOND : bond 0.00181 ( 1) SS BOND : angle 0.52885 ( 2) hydrogen bonds : bond 0.03701 ( 384) hydrogen bonds : angle 4.18166 ( 1110) link_BETA1-4 : bond 0.00358 ( 1) link_BETA1-4 : angle 1.29593 ( 3) link_NAG-ASN : bond 0.00270 ( 4) link_NAG-ASN : angle 2.26089 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.06 seconds wall clock time: 27 minutes 12.99 seconds (1632.99 seconds total)