Starting phenix.real_space_refine on Fri Jul 19 09:35:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnt_37672/07_2024/8wnt_37672.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnt_37672/07_2024/8wnt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnt_37672/07_2024/8wnt_37672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnt_37672/07_2024/8wnt_37672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnt_37672/07_2024/8wnt_37672.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnt_37672/07_2024/8wnt_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 Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.67, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 3 sheets defined 59.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 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: 2.02 Time building geometry restraints manager: 3.24 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: 97.77 - 105.06: 142 105.06 - 112.36: 3837 112.36 - 119.66: 2552 119.66 - 126.95: 3553 126.95 - 134.25: 117 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 2.520 nonbonded pdb=" O ILE B 53 " pdb=" N ALA B1001 " model vdw 2.234 2.520 nonbonded pdb=" OE2 GLU A 605 " pdb=" OG SER A 608 " model vdw 2.253 2.440 nonbonded pdb=" O LYS B 472 " pdb=" NE2 HIS B 477 " model vdw 2.258 2.520 nonbonded pdb=" O SER B 230 " pdb=" OG SER B 230 " model vdw 2.265 2.440 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7496 Z= 0.231 Angle : 0.668 13.133 10201 Z= 0.354 Chirality : 0.043 0.275 1180 Planarity : 0.005 0.070 1269 Dihedral : 16.761 89.998 2726 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.60 % Favored : 94.18 % Rotamer: Outliers : 0.77 % Allowed : 24.71 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 928 helix: 0.89 (0.24), residues: 494 sheet: 1.48 (0.79), residues: 46 loop : -0.83 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 316 HIS 0.004 0.001 HIS B 477 PHE 0.016 0.001 PHE B 463 TYR 0.026 0.001 TYR B 399 ARG 0.002 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.791 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: 0.1756 time to fit residues: 24.6556 Evaluate side-chains 95 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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: 0.6980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7126 ------------------------------------------------------------------------------- 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7496 Z= 0.192 Angle : 0.587 7.945 10201 Z= 0.294 Chirality : 0.041 0.236 1180 Planarity : 0.004 0.055 1269 Dihedral : 5.076 38.362 1104 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.29 % Rotamer: Outliers : 2.43 % Allowed : 23.05 % 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: 0.86 (0.29), residues: 928 helix: 1.43 (0.24), residues: 506 sheet: 1.66 (0.79), residues: 46 loop : -0.74 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 316 HIS 0.003 0.001 HIS B 477 PHE 0.014 0.001 PHE B 342 TYR 0.020 0.001 TYR B 399 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7415 (tt) REVERT: B 194 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8314 (mtmm) REVERT: B 464 PHE cc_start: 0.7262 (m-10) cc_final: 0.6887 (m-10) outliers start: 19 outliers final: 12 residues processed: 115 average time/residue: 0.1796 time to fit residues: 29.6600 Evaluate side-chains 104 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 489 VAL 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 46 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 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 211 GLN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7496 Z= 0.167 Angle : 0.566 8.022 10201 Z= 0.279 Chirality : 0.040 0.222 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.577 31.552 1100 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.28 % Favored : 94.50 % Rotamer: Outliers : 3.46 % Allowed : 22.54 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 928 helix: 1.68 (0.24), residues: 499 sheet: 1.80 (0.79), residues: 46 loop : -0.77 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.004 0.001 HIS B 477 PHE 0.012 0.001 PHE A 627 TYR 0.021 0.001 TYR B 399 ARG 0.001 0.000 ARG A 227 *********************** 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 123 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: B 122 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 194 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8465 (mtmm) REVERT: B 404 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (tt) outliers start: 27 outliers final: 15 residues processed: 117 average time/residue: 0.1754 time to fit residues: 28.3828 Evaluate side-chains 105 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 A residue 595 ASP 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 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: 0.5980 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 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 513 GLN A 543 HIS B 211 GLN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7496 Z= 0.169 Angle : 0.568 7.908 10201 Z= 0.282 Chirality : 0.040 0.219 1180 Planarity : 0.004 0.048 1269 Dihedral : 4.418 29.766 1100 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.60 % Favored : 94.29 % Rotamer: Outliers : 3.46 % Allowed : 23.18 % Favored : 73.37 % 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: 1.69 (0.24), residues: 502 sheet: 1.85 (0.78), residues: 46 loop : -0.68 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 469 HIS 0.004 0.001 HIS B 477 PHE 0.011 0.001 PHE A 542 TYR 0.021 0.001 TYR B 399 ARG 0.001 0.000 ARG A 227 *********************** 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 122 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7989 (mmtt) REVERT: A 336 GLU cc_start: 0.7368 (tp30) cc_final: 0.7087 (tp30) REVERT: A 339 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5640 (mm) REVERT: B 122 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 194 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8450 (mtmm) REVERT: B 404 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8029 (tt) REVERT: B 430 TYR cc_start: 0.7866 (t80) cc_final: 0.7631 (t80) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.1844 time to fit residues: 30.6672 Evaluate side-chains 113 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 202 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 176 ASN B 211 GLN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7496 Z= 0.249 Angle : 0.614 8.240 10201 Z= 0.304 Chirality : 0.042 0.226 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.569 29.814 1100 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.71 % Allowed : 23.69 % Favored : 72.60 % 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: 0.98 (0.29), residues: 928 helix: 1.60 (0.24), residues: 501 sheet: 1.76 (0.76), residues: 46 loop : -0.78 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 364 HIS 0.005 0.001 HIS A 557 PHE 0.016 0.001 PHE A 524 TYR 0.032 0.002 TYR B 399 ARG 0.002 0.000 ARG A 525 *********************** 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 124 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7920 (mmtt) REVERT: A 336 GLU cc_start: 0.7364 (tp30) cc_final: 0.7067 (tp30) REVERT: A 339 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5805 (mm) REVERT: B 122 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 194 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8428 (mtmm) REVERT: B 233 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.5594 (t-90) REVERT: B 316 TRP cc_start: 0.7426 (p-90) cc_final: 0.7158 (p-90) REVERT: B 404 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7985 (tt) outliers start: 29 outliers final: 18 residues processed: 119 average time/residue: 0.1804 time to fit residues: 30.2177 Evaluate side-chains 115 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 284 ASN 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 595 ASP Chi-restraints excluded: chain B residue 122 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7496 Z= 0.250 Angle : 0.628 11.016 10201 Z= 0.307 Chirality : 0.042 0.227 1180 Planarity : 0.004 0.050 1269 Dihedral : 4.561 29.386 1100 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.35 % Allowed : 23.82 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 928 helix: 1.58 (0.24), residues: 501 sheet: 1.65 (0.76), residues: 46 loop : -0.77 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 469 HIS 0.005 0.001 HIS A 557 PHE 0.015 0.001 PHE A 524 TYR 0.037 0.002 TYR B 399 ARG 0.002 0.000 ARG B 470 *********************** 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 fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7584 (Cg_exo) cc_final: 0.7298 (Cg_endo) REVERT: A 246 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8010 (mmtt) REVERT: A 336 GLU cc_start: 0.7331 (tp30) cc_final: 0.7083 (tp30) REVERT: A 339 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5851 (mm) REVERT: B 122 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 194 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8417 (mtmm) REVERT: B 233 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.5732 (t-90) REVERT: B 404 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7995 (tt) REVERT: B 469 TRP cc_start: 0.7364 (t-100) cc_final: 0.6985 (t-100) outliers start: 34 outliers final: 22 residues processed: 128 average time/residue: 0.1592 time to fit residues: 28.9258 Evaluate side-chains 121 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 284 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 THR 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 285 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 74 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7496 Z= 0.151 Angle : 0.591 10.062 10201 Z= 0.285 Chirality : 0.040 0.210 1180 Planarity : 0.003 0.046 1269 Dihedral : 4.279 24.114 1100 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.46 % Allowed : 25.22 % 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: 1.21 (0.29), residues: 928 helix: 1.77 (0.24), residues: 502 sheet: 1.62 (0.76), residues: 46 loop : -0.63 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 364 HIS 0.004 0.000 HIS B 477 PHE 0.012 0.001 PHE A 542 TYR 0.021 0.001 TYR B 399 ARG 0.002 0.000 ARG A 563 *********************** 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 120 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7528 (Cg_exo) cc_final: 0.7262 (Cg_endo) REVERT: A 246 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8056 (mmtt) REVERT: A 336 GLU cc_start: 0.7334 (tp30) cc_final: 0.7117 (tp30) REVERT: A 339 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5803 (mm) REVERT: A 621 GLU cc_start: 0.7607 (tt0) cc_final: 0.6726 (pt0) REVERT: B 122 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8003 (tt) REVERT: B 194 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8384 (mtmm) REVERT: B 379 MET cc_start: 0.7332 (mmm) cc_final: 0.6987 (mtt) REVERT: B 469 TRP cc_start: 0.7313 (t-100) cc_final: 0.7031 (t-100) outliers start: 27 outliers final: 18 residues processed: 114 average time/residue: 0.1677 time to fit residues: 27.1111 Evaluate side-chains 108 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 246 LYS 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 A residue 595 ASP Chi-restraints excluded: chain B residue 90 SER 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 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 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.173 Angle : 0.595 9.883 10201 Z= 0.288 Chirality : 0.041 0.214 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.225 23.238 1100 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.59 % Allowed : 25.74 % Favored : 70.68 % 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: 1.22 (0.29), residues: 928 helix: 1.79 (0.24), residues: 502 sheet: 1.60 (0.74), residues: 46 loop : -0.62 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 364 HIS 0.004 0.001 HIS B 477 PHE 0.023 0.001 PHE B 314 TYR 0.025 0.001 TYR B 399 ARG 0.001 0.000 ARG A 430 *********************** 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 122 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7544 (Cg_exo) cc_final: 0.7278 (Cg_endo) REVERT: A 246 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7986 (mmtt) REVERT: A 339 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5866 (mm) REVERT: A 621 GLU cc_start: 0.7563 (tt0) cc_final: 0.6677 (pt0) REVERT: B 122 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8029 (tt) REVERT: B 194 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8343 (mtmm) REVERT: B 262 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8106 (ttm110) REVERT: B 379 MET cc_start: 0.7369 (mmm) cc_final: 0.7092 (mtt) REVERT: B 469 TRP cc_start: 0.7360 (t-100) cc_final: 0.7048 (t-100) outliers start: 28 outliers final: 20 residues processed: 118 average time/residue: 0.1599 time to fit residues: 27.0246 Evaluate side-chains 114 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 A residue 595 ASP Chi-restraints excluded: chain B residue 90 SER 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 276 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 64 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7496 Z= 0.173 Angle : 0.592 10.620 10201 Z= 0.288 Chirality : 0.040 0.214 1180 Planarity : 0.004 0.045 1269 Dihedral : 4.157 22.935 1100 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.71 % Allowed : 25.22 % 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: 1.23 (0.29), residues: 928 helix: 1.82 (0.24), residues: 499 sheet: 1.60 (0.73), residues: 46 loop : -0.63 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 364 HIS 0.003 0.001 HIS B 477 PHE 0.025 0.001 PHE B 314 TYR 0.027 0.001 TYR B 399 ARG 0.001 0.000 ARG A 525 *********************** 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 122 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7561 (Cg_exo) cc_final: 0.7295 (Cg_endo) REVERT: A 246 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (mmtt) REVERT: A 339 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5880 (mm) REVERT: A 621 GLU cc_start: 0.7546 (tt0) cc_final: 0.6665 (pt0) REVERT: B 122 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8040 (tt) REVERT: B 194 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8320 (mtmm) REVERT: B 262 ARG cc_start: 0.8486 (mtt90) cc_final: 0.8106 (ttm110) REVERT: B 469 TRP cc_start: 0.7427 (t-100) cc_final: 0.7127 (t-100) outliers start: 29 outliers final: 20 residues processed: 116 average time/residue: 0.1703 time to fit residues: 27.8793 Evaluate side-chains 113 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 A residue 595 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 291 MET 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 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.0050 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.170 Angle : 0.615 14.270 10201 Z= 0.292 Chirality : 0.040 0.211 1180 Planarity : 0.004 0.047 1269 Dihedral : 4.090 22.989 1100 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.94 % Allowed : 25.74 % 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: 1.28 (0.29), residues: 928 helix: 1.85 (0.24), residues: 500 sheet: 1.64 (0.74), residues: 46 loop : -0.60 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 364 HIS 0.004 0.001 HIS B 68 PHE 0.025 0.001 PHE B 314 TYR 0.024 0.001 TYR B 399 ARG 0.001 0.000 ARG A 212 ********************** 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 117 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 177 PRO cc_start: 0.7675 (Cg_exo) cc_final: 0.7402 (Cg_endo) REVERT: A 246 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8003 (mmtt) REVERT: A 339 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5941 (mm) REVERT: A 621 GLU cc_start: 0.7509 (tt0) cc_final: 0.6645 (pt0) REVERT: B 122 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 194 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8264 (mtmm) REVERT: B 262 ARG cc_start: 0.8451 (mtt90) cc_final: 0.8091 (ttm110) REVERT: B 469 TRP cc_start: 0.7421 (t-100) cc_final: 0.7115 (t-100) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.1906 time to fit residues: 29.9376 Evaluate side-chains 115 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 246 LYS 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 A residue 595 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 291 MET 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 455 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.179804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129526 restraints weight = 10292.124| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.27 r_work: 0.3428 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7496 Z= 0.179 Angle : 0.617 14.691 10201 Z= 0.293 Chirality : 0.040 0.213 1180 Planarity : 0.004 0.046 1269 Dihedral : 4.080 23.321 1100 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.33 % Allowed : 25.74 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 928 helix: 1.83 (0.24), residues: 500 sheet: 1.60 (0.74), residues: 46 loop : -0.60 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 364 HIS 0.004 0.001 HIS B 68 PHE 0.025 0.001 PHE B 314 TYR 0.026 0.001 TYR B 399 ARG 0.001 0.000 ARG A 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1795.14 seconds wall clock time: 32 minutes 56.87 seconds (1976.87 seconds total)