Starting phenix.real_space_refine on Tue Aug 4 20:24:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2026/8t23_40979.cif" } resolution = 3.87 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= -0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4121 2.51 5 N 1075 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain: "B" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1467 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain breaks: 1 Chain: "G" 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 chiralities: 2 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.39, per 1000 atoms: 0.22 Number of scatterers: 6451 At special positions: 0 Unit cell: (103.23, 75.48, 135.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1218 8.00 N 1075 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG H 1 " - " FUC H 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 53 " " NAG B 601 " - " ASN B 343 " " NAG G 1 " - " ASN A 322 " " NAG H 1 " - " ASN A 216 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 407.6 milliseconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 45.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.534A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.646A pdb=" N THR A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.610A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 4.873A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.616A pdb=" N GLY A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 157 through 163 removed outlier: 4.367A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.577A pdb=" N LEU A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 248 removed outlier: 4.855A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.973A pdb=" N TYR A 252 " --> pdb=" O MET A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.388A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.956A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.628A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 446 through 452 removed outlier: 4.238A pdb=" N THR A 449 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 450 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Proline residue: A 451 - end of helix No H-bonds generated for 'chain 'A' and resid 446 through 452' Processing helix chain 'A' and resid 453 through 464 removed outlier: 4.725A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.026A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 6.677A pdb=" N PHE A 504 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS A 505 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.646A pdb=" N GLN A 522 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.946A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.840A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.536A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.588A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.008A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.941A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 396 through 403 removed outlier: 3.898A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 468 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: 0.90 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2064 1.34 - 1.46: 1660 1.46 - 1.58: 2852 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6635 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.92e+00 bond pdb=" CG PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 1.503 1.431 0.072 3.40e-02 8.65e+02 4.45e+00 bond pdb=" CA LYS A 441 " pdb=" CB LYS A 441 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.70e-02 3.46e+03 3.83e+00 bond pdb=" N PRO A 389 " pdb=" CA PRO A 389 " ideal model delta sigma weight residual 1.469 1.444 0.024 1.28e-02 6.10e+03 3.66e+00 ... (remaining 6630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 8877 3.35 - 6.69: 118 6.69 - 10.04: 10 10.04 - 13.38: 4 13.38 - 16.73: 3 Bond angle restraints: 9012 Sorted by residual: angle pdb=" CA PRO A 389 " pdb=" N PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 112.00 95.27 16.73 1.40e+00 5.10e-01 1.43e+02 angle pdb=" C ALA A 212 " pdb=" N ASP A 213 " pdb=" CA ASP A 213 " ideal model delta sigma weight residual 122.35 132.59 -10.24 1.46e+00 4.69e-01 4.92e+01 angle pdb=" N PRO A 389 " pdb=" CD PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 103.20 94.54 8.66 1.50e+00 4.44e-01 3.33e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.71 108.86 4.85 9.50e-01 1.11e+00 2.61e+01 angle pdb=" CA LEU A 45 " pdb=" CB LEU A 45 " pdb=" CG LEU A 45 " ideal model delta sigma weight residual 116.30 132.29 -15.99 3.50e+00 8.16e-02 2.09e+01 ... (remaining 9007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3228 17.99 - 35.97: 494 35.97 - 53.96: 129 53.96 - 71.94: 18 71.94 - 89.93: 10 Dihedral angle restraints: 3879 sinusoidal: 1586 harmonic: 2293 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 168.30 -75.30 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 167.32 -74.32 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.83 48.17 1 1.00e+01 1.00e-02 3.20e+01 ... (remaining 3876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 828 0.077 - 0.154: 113 0.154 - 0.231: 3 0.231 - 0.308: 1 0.308 - 0.385: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 216 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB VAL A 318 " pdb=" CA VAL A 318 " pdb=" CG1 VAL A 318 " pdb=" CG2 VAL A 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 943 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.144 5.00e-02 4.00e+02 2.00e-01 6.39e+01 pdb=" N PRO A 389 " -0.344 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " -0.017 2.00e-02 2.50e+03 1.96e-02 9.57e+00 pdb=" CG TRP A 168 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 564 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO A 565 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.039 5.00e-02 4.00e+02 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 191 2.69 - 3.24: 6608 3.24 - 3.79: 9892 3.79 - 4.35: 12329 4.35 - 4.90: 18650 Nonbonded interactions: 47670 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O THR A 496 " model vdw 2.136 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.226 3.040 nonbonded pdb=" O GLU A 166 " pdb=" OG SER A 170 " model vdw 2.228 3.040 nonbonded pdb=" O ARG A 305 " pdb=" NZ LYS A 309 " model vdw 2.233 3.120 nonbonded pdb=" NH2 ARG B 355 " pdb=" OD2 ASP B 398 " model vdw 2.239 3.120 ... (remaining 47665 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 Found NCS groups: ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.740 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4822 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 : 0.005 0.149 6647 Z= 0.209 Angle : 1.032 19.045 9042 Z= 0.540 Chirality : 0.051 0.385 946 Planarity : 0.009 0.200 1164 Dihedral : 18.281 89.928 2389 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 0.59 % Allowed : 31.48 % Favored : 67.94 % 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 are not related in a simple way. whole: -3.06 (0.28), residues: 775 helix: -1.63 (0.31), residues: 257 sheet: 2.48 (1.14), residues: 24 loop : -2.66 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.015 0.001 TYR A 510 PHE 0.020 0.002 PHE B 338 TRP 0.047 0.002 TRP A 168 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 ( 6635) covalent geometry : angle 1.00443 / 0.53 ( 9012) SS BOND : bond 0.00539 / 0.30 ( 6) SS BOND : angle 1.15684 / 0.68 ( 12) hydrogen bonds : bond 0.15776 / 10.28 ( 173) hydrogen bonds : angle 6.45848 / 4.57 ( 468) link_BETA1-4 : bond 0.00233 / 0.12 ( 1) link_BETA1-4 : angle 1.35764 / 0.70 ( 3) link_BETA1-6 : bond 0.00809 / 0.43 ( 1) link_BETA1-6 : angle 1.93647 / 1.01 ( 3) link_NAG-ASN : bond 0.01295 / 0.62 ( 4) link_NAG-ASN : angle 6.53667 / 3.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6107 (mt) cc_final: 0.5497 (mm) REVERT: A 62 MET cc_start: 0.4429 (mpp) cc_final: 0.4110 (pmm) REVERT: A 123 MET cc_start: -0.0391 (tpt) cc_final: -0.0686 (tpt) REVERT: A 202 TYR cc_start: 0.7222 (m-10) cc_final: 0.6389 (t80) REVERT: A 379 ILE cc_start: 0.8955 (tt) cc_final: 0.8682 (mm) REVERT: A 382 ASP cc_start: 0.8908 (t70) cc_final: 0.8392 (p0) REVERT: A 408 MET cc_start: 0.3341 (mmp) cc_final: 0.2562 (mmm) REVERT: A 474 MET cc_start: -0.1393 (ptt) cc_final: -0.2040 (ptt) REVERT: A 497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6258 (t80) REVERT: A 539 LEU cc_start: 0.6117 (tp) cc_final: 0.5861 (mp) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.0788 time to fit residues: 13.5724 Evaluate side-chains 81 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.141785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.129285 restraints weight = 40829.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.129365 restraints weight = 37904.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.129619 restraints weight = 36178.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.129890 restraints weight = 34164.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.129949 restraints weight = 32484.706| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5019 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6647 Z= 0.163 Angle : 0.837 18.107 9042 Z= 0.413 Chirality : 0.051 0.527 946 Planarity : 0.006 0.066 1164 Dihedral : 6.494 40.178 860 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 4.39 % Allowed : 26.79 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.30), residues: 775 helix: -1.21 (0.32), residues: 258 sheet: 1.73 (1.15), residues: 24 loop : -2.46 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 115 TYR 0.019 0.002 TYR A 180 PHE 0.026 0.002 PHE A 588 TRP 0.019 0.002 TRP A 211 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 6635) covalent geometry : angle 0.80455 / 0.41 ( 9012) SS BOND : bond 0.00787 / 0.40 ( 6) SS BOND : angle 1.52391 / 0.78 ( 12) hydrogen bonds : bond 0.04058 / 2.63 ( 173) hydrogen bonds : angle 5.94112 / 4.28 ( 468) link_BETA1-4 : bond 0.00227 / 0.12 ( 1) link_BETA1-4 : angle 0.98785 / 0.51 ( 3) link_BETA1-6 : bond 0.00940 / 0.49 ( 1) link_BETA1-6 : angle 2.24537 / 1.16 ( 3) link_NAG-ASN : bond 0.01294 / 0.62 ( 4) link_NAG-ASN : angle 6.14807 / 3.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.6934 (mm) cc_final: 0.6691 (mt) REVERT: A 211 TRP cc_start: 0.4513 (p90) cc_final: 0.2762 (m100) REVERT: A 252 TYR cc_start: 0.2925 (OUTLIER) cc_final: 0.2003 (p90) REVERT: A 279 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.4727 (m-10) REVERT: A 345 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7411 (t70) REVERT: A 376 MET cc_start: 0.8834 (tpt) cc_final: 0.8057 (ptp) REVERT: A 382 ASP cc_start: 0.9143 (t70) cc_final: 0.8480 (p0) REVERT: A 417 HIS cc_start: 0.8683 (t-90) cc_final: 0.8443 (t-90) REVERT: A 462 MET cc_start: 0.7186 (ppp) cc_final: 0.6821 (ppp) REVERT: A 474 MET cc_start: -0.1265 (ptt) cc_final: -0.1725 (ptt) REVERT: A 497 TYR cc_start: 0.6766 (t80) cc_final: 0.6534 (t80) REVERT: A 566 TRP cc_start: 0.7696 (p-90) cc_final: 0.7104 (p-90) REVERT: A 579 MET cc_start: 0.6596 (ppp) cc_final: 0.5349 (ppp) REVERT: B 410 ILE cc_start: 0.7922 (mm) cc_final: 0.7448 (mm) outliers start: 30 outliers final: 14 residues processed: 116 average time/residue: 0.0795 time to fit residues: 12.4622 Evaluate side-chains 92 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 0.0070 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.143598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.125359 restraints weight = 41701.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.127297 restraints weight = 33734.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.128275 restraints weight = 27747.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.129939 restraints weight = 23935.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.130197 restraints weight = 20512.784| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5198 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6647 Z= 0.137 Angle : 0.784 18.397 9042 Z= 0.384 Chirality : 0.050 0.504 946 Planarity : 0.006 0.065 1164 Dihedral : 6.003 27.478 858 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.69 % Allowed : 26.94 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.30), residues: 775 helix: -0.82 (0.34), residues: 244 sheet: 1.59 (1.11), residues: 24 loop : -2.37 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 572 TYR 0.018 0.002 TYR A 515 PHE 0.016 0.002 PHE B 490 TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 6635) covalent geometry : angle 0.75051 / 0.38 ( 9012) SS BOND : bond 0.00341 / 0.20 ( 6) SS BOND : angle 1.13882 / 0.63 ( 12) hydrogen bonds : bond 0.03844 / 2.52 ( 173) hydrogen bonds : angle 5.78779 / 4.16 ( 468) link_BETA1-4 : bond 0.00260 / 0.14 ( 1) link_BETA1-4 : angle 1.03267 / 0.53 ( 3) link_BETA1-6 : bond 0.00395 / 0.21 ( 1) link_BETA1-6 : angle 1.47568 / 0.78 ( 3) link_NAG-ASN : bond 0.01351 / 0.65 ( 4) link_NAG-ASN : angle 6.17835 / 3.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: -0.0956 (OUTLIER) cc_final: -0.1306 (pttm) REVERT: A 150 ASP cc_start: 0.9106 (p0) cc_final: 0.8139 (t0) REVERT: A 171 GLU cc_start: 0.9124 (pp20) cc_final: 0.8667 (pm20) REVERT: A 252 TYR cc_start: 0.2737 (OUTLIER) cc_final: 0.2084 (p90) REVERT: A 279 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.4946 (m-10) REVERT: A 345 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7627 (t70) REVERT: A 376 MET cc_start: 0.9088 (tpt) cc_final: 0.8066 (ptp) REVERT: A 381 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.4195 (p90) REVERT: A 382 ASP cc_start: 0.9161 (t70) cc_final: 0.8341 (p0) REVERT: A 400 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7965 (t80) REVERT: A 462 MET cc_start: 0.7467 (ppp) cc_final: 0.7075 (ppp) REVERT: A 474 MET cc_start: -0.1599 (ptt) cc_final: -0.1827 (ptt) REVERT: A 579 MET cc_start: 0.6707 (ppp) cc_final: 0.5459 (tpp) outliers start: 32 outliers final: 20 residues processed: 104 average time/residue: 0.0789 time to fit residues: 11.0418 Evaluate side-chains 99 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 15 optimal weight: 0.0030 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.0020 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.143460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.125028 restraints weight = 41691.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.126382 restraints weight = 34130.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.127549 restraints weight = 28225.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.129438 restraints weight = 24235.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.129689 restraints weight = 20225.908| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5128 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6647 Z= 0.129 Angle : 0.742 17.733 9042 Z= 0.364 Chirality : 0.049 0.511 946 Planarity : 0.005 0.065 1164 Dihedral : 5.849 25.791 858 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 5.42 % Allowed : 27.82 % Favored : 66.76 % 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 are not related in a simple way. whole: -2.50 (0.30), residues: 775 helix: -1.02 (0.33), residues: 253 sheet: 1.67 (1.14), residues: 24 loop : -2.32 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 177 TYR 0.012 0.001 TYR A 41 PHE 0.018 0.002 PHE A 438 TRP 0.022 0.001 TRP A 566 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6635) covalent geometry : angle 0.70819 / 0.36 ( 9012) SS BOND : bond 0.00286 / 0.17 ( 6) SS BOND : angle 0.92624 / 0.51 ( 12) hydrogen bonds : bond 0.03546 / 2.30 ( 173) hydrogen bonds : angle 5.78392 / 4.16 ( 468) link_BETA1-4 : bond 0.00037 / 0.02 ( 1) link_BETA1-4 : angle 1.03998 / 0.54 ( 3) link_BETA1-6 : bond 0.00411 / 0.22 ( 1) link_BETA1-6 : angle 1.71032 / 0.88 ( 3) link_NAG-ASN : bond 0.01268 / 0.61 ( 4) link_NAG-ASN : angle 6.04652 / 3.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9227 (pp20) cc_final: 0.8834 (pm20) REVERT: A 252 TYR cc_start: 0.2924 (OUTLIER) cc_final: 0.2510 (p90) REVERT: A 279 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.4770 (m-10) REVERT: A 345 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7683 (t70) REVERT: A 376 MET cc_start: 0.9027 (tpt) cc_final: 0.8031 (ptp) REVERT: A 381 TYR cc_start: 0.5758 (OUTLIER) cc_final: 0.3995 (p90) REVERT: A 382 ASP cc_start: 0.9118 (t70) cc_final: 0.8317 (p0) REVERT: A 400 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 462 MET cc_start: 0.7513 (ppp) cc_final: 0.7123 (ppp) REVERT: A 579 MET cc_start: 0.6847 (ppp) cc_final: 0.5487 (tpp) REVERT: B 410 ILE cc_start: 0.8012 (mm) cc_final: 0.7658 (mm) REVERT: B 486 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6444 (t80) outliers start: 37 outliers final: 24 residues processed: 105 average time/residue: 0.0724 time to fit residues: 10.4319 Evaluate side-chains 103 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.121628 restraints weight = 42546.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.123145 restraints weight = 34889.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.124150 restraints weight = 29378.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.125439 restraints weight = 25255.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.125696 restraints weight = 22206.921| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5264 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6647 Z= 0.151 Angle : 0.773 18.476 9042 Z= 0.378 Chirality : 0.050 0.523 946 Planarity : 0.006 0.066 1164 Dihedral : 5.953 26.705 858 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 6.00 % Allowed : 27.96 % Favored : 66.03 % 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 are not related in a simple way. whole: -2.45 (0.30), residues: 775 helix: -1.06 (0.34), residues: 241 sheet: 1.61 (1.06), residues: 24 loop : -2.21 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 245 TYR 0.013 0.002 TYR A 158 PHE 0.038 0.002 PHE A 72 TRP 0.024 0.002 TRP A 566 HIS 0.008 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6635) covalent geometry : angle 0.74038 / 0.37 ( 9012) SS BOND : bond 0.00306 / 0.18 ( 6) SS BOND : angle 0.88245 / 0.51 ( 12) hydrogen bonds : bond 0.03689 / 2.36 ( 173) hydrogen bonds : angle 5.89325 / 4.24 ( 468) link_BETA1-4 : bond 0.00058 / 0.03 ( 1) link_BETA1-4 : angle 1.30262 / 0.66 ( 3) link_BETA1-6 : bond 0.00405 / 0.21 ( 1) link_BETA1-6 : angle 1.75791 / 0.90 ( 3) link_NAG-ASN : bond 0.01274 / 0.61 ( 4) link_NAG-ASN : angle 6.06247 / 3.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6429 (mp0) cc_final: 0.6174 (mp0) REVERT: A 171 GLU cc_start: 0.9168 (pp20) cc_final: 0.8794 (pm20) REVERT: A 211 TRP cc_start: 0.5601 (p90) cc_final: 0.5292 (p90) REVERT: A 252 TYR cc_start: 0.3022 (OUTLIER) cc_final: 0.2544 (p90) REVERT: A 279 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4703 (m-10) REVERT: A 328 TRP cc_start: 0.6932 (m100) cc_final: 0.6594 (m100) REVERT: A 345 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7753 (t70) REVERT: A 376 MET cc_start: 0.8885 (tpt) cc_final: 0.7949 (ptp) REVERT: A 381 TYR cc_start: 0.5694 (OUTLIER) cc_final: 0.3825 (p90) REVERT: A 382 ASP cc_start: 0.9046 (t70) cc_final: 0.8210 (p0) REVERT: A 400 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 462 MET cc_start: 0.7428 (ppp) cc_final: 0.7131 (ppp) REVERT: A 497 TYR cc_start: 0.6934 (t80) cc_final: 0.6593 (t80) REVERT: A 579 MET cc_start: 0.7034 (ppp) cc_final: 0.6464 (ppp) REVERT: B 484 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6431 (tm-30) REVERT: B 486 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6602 (t80) outliers start: 41 outliers final: 26 residues processed: 107 average time/residue: 0.0769 time to fit residues: 10.9197 Evaluate side-chains 101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 56 optimal weight: 0.0980 chunk 26 optimal weight: 0.0060 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.143075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.124248 restraints weight = 42316.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.126152 restraints weight = 33837.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.126931 restraints weight = 28589.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.128401 restraints weight = 24571.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.128693 restraints weight = 21419.559| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6647 Z= 0.127 Angle : 0.742 17.830 9042 Z= 0.363 Chirality : 0.049 0.490 946 Planarity : 0.005 0.065 1164 Dihedral : 5.716 28.763 858 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.27 % Allowed : 29.58 % Favored : 65.15 % 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 are not related in a simple way. whole: -2.39 (0.30), residues: 775 helix: -0.99 (0.34), residues: 250 sheet: 1.61 (1.03), residues: 24 loop : -2.20 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.011 0.001 TYR A 516 PHE 0.013 0.001 PHE B 490 TRP 0.026 0.001 TRP A 566 HIS 0.006 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 6635) covalent geometry : angle 0.70692 / 0.35 ( 9012) SS BOND : bond 0.00358 / 0.21 ( 6) SS BOND : angle 1.59326 / 0.83 ( 12) hydrogen bonds : bond 0.03311 / 2.14 ( 173) hydrogen bonds : angle 5.83013 / 4.20 ( 468) link_BETA1-4 : bond 0.00208 / 0.11 ( 1) link_BETA1-4 : angle 1.12369 / 0.58 ( 3) link_BETA1-6 : bond 0.00508 / 0.27 ( 1) link_BETA1-6 : angle 1.46610 / 0.78 ( 3) link_NAG-ASN : bond 0.01326 / 0.64 ( 4) link_NAG-ASN : angle 6.02426 / 3.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6282 (mp0) cc_final: 0.6057 (mp0) REVERT: A 171 GLU cc_start: 0.9256 (pp20) cc_final: 0.8879 (pm20) REVERT: A 252 TYR cc_start: 0.3769 (OUTLIER) cc_final: 0.2849 (p90) REVERT: A 279 TYR cc_start: 0.5999 (OUTLIER) cc_final: 0.4824 (m-10) REVERT: A 328 TRP cc_start: 0.7198 (m100) cc_final: 0.6828 (m-10) REVERT: A 376 MET cc_start: 0.8879 (tpt) cc_final: 0.7898 (ptp) REVERT: A 381 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.4011 (p90) REVERT: A 382 ASP cc_start: 0.9047 (t70) cc_final: 0.8534 (t0) REVERT: A 400 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 462 MET cc_start: 0.7554 (ppp) cc_final: 0.7223 (ppp) REVERT: A 497 TYR cc_start: 0.6865 (t80) cc_final: 0.6531 (t80) REVERT: A 514 ARG cc_start: 0.2140 (OUTLIER) cc_final: 0.1710 (ptt180) REVERT: A 579 MET cc_start: 0.7061 (ppp) cc_final: 0.5677 (tpp) outliers start: 36 outliers final: 25 residues processed: 104 average time/residue: 0.0790 time to fit residues: 10.9330 Evaluate side-chains 95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 0.0670 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 16 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.6836 > 50:) chunk 51 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.141451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.122991 restraints weight = 42017.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.124675 restraints weight = 33618.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.125450 restraints weight = 28839.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.126851 restraints weight = 24890.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.127034 restraints weight = 21857.729| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6647 Z= 0.134 Angle : 0.760 17.684 9042 Z= 0.372 Chirality : 0.050 0.511 946 Planarity : 0.005 0.065 1164 Dihedral : 5.746 29.233 858 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 5.27 % Allowed : 29.87 % Favored : 64.86 % 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 are not related in a simple way. whole: -2.36 (0.31), residues: 775 helix: -0.94 (0.34), residues: 243 sheet: 1.48 (0.97), residues: 27 loop : -2.19 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.013 0.002 TYR A 521 PHE 0.011 0.002 PHE B 515 TRP 0.030 0.002 TRP A 566 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6635) covalent geometry : angle 0.72739 / 0.36 ( 9012) SS BOND : bond 0.00325 / 0.18 ( 6) SS BOND : angle 1.23289 / 0.62 ( 12) hydrogen bonds : bond 0.03261 / 2.07 ( 173) hydrogen bonds : angle 5.81721 / 4.18 ( 468) link_BETA1-4 : bond 0.00202 / 0.11 ( 1) link_BETA1-4 : angle 0.98586 / 0.50 ( 3) link_BETA1-6 : bond 0.00484 / 0.25 ( 1) link_BETA1-6 : angle 1.61472 / 0.84 ( 3) link_NAG-ASN : bond 0.01288 / 0.62 ( 4) link_NAG-ASN : angle 5.94627 / 3.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9207 (pp20) cc_final: 0.8835 (pm20) REVERT: A 252 TYR cc_start: 0.3753 (OUTLIER) cc_final: 0.2853 (p90) REVERT: A 279 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.4934 (m-10) REVERT: A 376 MET cc_start: 0.8860 (tpt) cc_final: 0.7923 (ptp) REVERT: A 381 TYR cc_start: 0.5792 (OUTLIER) cc_final: 0.3883 (p90) REVERT: A 382 ASP cc_start: 0.9040 (t70) cc_final: 0.8489 (t0) REVERT: A 464 PHE cc_start: 0.1878 (OUTLIER) cc_final: -0.1728 (t80) REVERT: A 579 MET cc_start: 0.7271 (ppp) cc_final: 0.6784 (ppp) REVERT: B 486 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6569 (t80) outliers start: 36 outliers final: 26 residues processed: 102 average time/residue: 0.0781 time to fit residues: 10.9211 Evaluate side-chains 96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.140018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.121724 restraints weight = 42213.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.123635 restraints weight = 33829.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.124513 restraints weight = 28819.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.125191 restraints weight = 24683.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.125629 restraints weight = 22655.271| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6647 Z= 0.141 Angle : 0.766 17.211 9042 Z= 0.375 Chirality : 0.050 0.513 946 Planarity : 0.006 0.065 1164 Dihedral : 5.770 28.712 858 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 5.56 % Allowed : 29.58 % Favored : 64.86 % 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 are not related in a simple way. whole: -2.33 (0.30), residues: 775 helix: -0.89 (0.35), residues: 242 sheet: 1.45 (0.92), residues: 27 loop : -2.19 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.017 0.002 TYR A 521 PHE 0.011 0.002 PHE A 452 TRP 0.033 0.002 TRP A 566 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6635) covalent geometry : angle 0.73377 / 0.37 ( 9012) SS BOND : bond 0.00328 / 0.19 ( 6) SS BOND : angle 1.08814 / 0.58 ( 12) hydrogen bonds : bond 0.03366 / 2.09 ( 173) hydrogen bonds : angle 5.90556 / 4.24 ( 468) link_BETA1-4 : bond 0.00283 / 0.15 ( 1) link_BETA1-4 : angle 1.14465 / 0.59 ( 3) link_BETA1-6 : bond 0.00340 / 0.18 ( 1) link_BETA1-6 : angle 1.56595 / 0.82 ( 3) link_NAG-ASN : bond 0.01333 / 0.64 ( 4) link_NAG-ASN : angle 5.93703 / 3.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9150 (pp20) cc_final: 0.8789 (pm20) REVERT: A 252 TYR cc_start: 0.4294 (OUTLIER) cc_final: 0.3192 (p90) REVERT: A 279 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.4981 (m-10) REVERT: A 376 MET cc_start: 0.8883 (tpt) cc_final: 0.7973 (ptp) REVERT: A 378 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6799 (t-90) REVERT: A 381 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.3798 (p90) REVERT: A 382 ASP cc_start: 0.8993 (t70) cc_final: 0.8435 (t0) REVERT: A 464 PHE cc_start: 0.2720 (OUTLIER) cc_final: -0.0609 (t80) REVERT: A 579 MET cc_start: 0.7439 (ppp) cc_final: 0.6884 (ppp) REVERT: B 456 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.3512 (p90) REVERT: B 486 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6587 (t80) outliers start: 38 outliers final: 28 residues processed: 100 average time/residue: 0.0766 time to fit residues: 10.5413 Evaluate side-chains 105 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.0050 chunk 16 optimal weight: 0.0040 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.141560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.122894 restraints weight = 42539.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.124806 restraints weight = 34042.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.125729 restraints weight = 29191.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.126403 restraints weight = 25130.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.127055 restraints weight = 23026.837| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6647 Z= 0.127 Angle : 0.748 17.256 9042 Z= 0.366 Chirality : 0.049 0.483 946 Planarity : 0.005 0.063 1164 Dihedral : 5.610 28.199 858 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 4.69 % Allowed : 30.01 % Favored : 65.30 % 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 are not related in a simple way. whole: -2.31 (0.30), residues: 775 helix: -0.83 (0.35), residues: 244 sheet: 1.39 (0.94), residues: 27 loop : -2.20 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.017 0.001 TYR A 202 PHE 0.015 0.001 PHE A 400 TRP 0.027 0.002 TRP A 566 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6635) covalent geometry : angle 0.71649 / 0.36 ( 9012) SS BOND : bond 0.00338 / 0.20 ( 6) SS BOND : angle 0.88939 / 0.48 ( 12) hydrogen bonds : bond 0.03227 / 2.02 ( 173) hydrogen bonds : angle 5.78434 / 4.15 ( 468) link_BETA1-4 : bond 0.00361 / 0.19 ( 1) link_BETA1-4 : angle 1.04009 / 0.54 ( 3) link_BETA1-6 : bond 0.00413 / 0.22 ( 1) link_BETA1-6 : angle 1.48225 / 0.79 ( 3) link_NAG-ASN : bond 0.01290 / 0.62 ( 4) link_NAG-ASN : angle 5.86889 / 3.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9132 (pp20) cc_final: 0.8830 (pm20) REVERT: A 203 TRP cc_start: 0.7406 (t60) cc_final: 0.7202 (t60) REVERT: A 252 TYR cc_start: 0.4215 (OUTLIER) cc_final: 0.3406 (p90) REVERT: A 279 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.5081 (m-10) REVERT: A 376 MET cc_start: 0.8870 (tpt) cc_final: 0.7972 (ptp) REVERT: A 382 ASP cc_start: 0.8944 (t70) cc_final: 0.8563 (t0) REVERT: A 579 MET cc_start: 0.7504 (ppp) cc_final: 0.6093 (tpp) REVERT: B 456 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.3492 (p90) outliers start: 32 outliers final: 26 residues processed: 96 average time/residue: 0.0747 time to fit residues: 9.9243 Evaluate side-chains 99 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.0030 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.140778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.127521 restraints weight = 40645.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.127625 restraints weight = 37907.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.128080 restraints weight = 36767.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.128226 restraints weight = 33885.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.128388 restraints weight = 32644.932| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6647 Z= 0.134 Angle : 0.770 17.039 9042 Z= 0.373 Chirality : 0.049 0.502 946 Planarity : 0.005 0.065 1164 Dihedral : 5.627 29.380 858 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 4.39 % Allowed : 30.16 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.30), residues: 775 helix: -0.81 (0.35), residues: 244 sheet: 1.44 (0.96), residues: 27 loop : -2.22 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.016 0.002 TYR A 202 PHE 0.015 0.002 PHE A 400 TRP 0.027 0.002 TRP A 566 HIS 0.008 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6635) covalent geometry : angle 0.73917 / 0.37 ( 9012) SS BOND : bond 0.00324 / 0.19 ( 6) SS BOND : angle 0.86556 / 0.47 ( 12) hydrogen bonds : bond 0.03242 / 2.01 ( 173) hydrogen bonds : angle 5.77987 / 4.13 ( 468) link_BETA1-4 : bond 0.00315 / 0.17 ( 1) link_BETA1-4 : angle 1.09529 / 0.56 ( 3) link_BETA1-6 : bond 0.00404 / 0.21 ( 1) link_BETA1-6 : angle 1.58158 / 0.83 ( 3) link_NAG-ASN : bond 0.01283 / 0.62 ( 4) link_NAG-ASN : angle 5.85739 / 3.37 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6525 (mp0) cc_final: 0.6292 (mp0) REVERT: A 155 SER cc_start: 0.6143 (t) cc_final: 0.5765 (m) REVERT: A 252 TYR cc_start: 0.4405 (OUTLIER) cc_final: 0.3629 (p90) REVERT: A 279 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.4762 (m-10) REVERT: A 376 MET cc_start: 0.8811 (tpt) cc_final: 0.7838 (ptp) REVERT: A 464 PHE cc_start: 0.1761 (OUTLIER) cc_final: -0.1653 (t80) REVERT: A 474 MET cc_start: -0.3440 (ptt) cc_final: -0.3774 (ptt) REVERT: A 579 MET cc_start: 0.7514 (ppp) cc_final: 0.6095 (tpp) outliers start: 30 outliers final: 27 residues processed: 96 average time/residue: 0.0700 time to fit residues: 9.4663 Evaluate side-chains 96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.137175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.118777 restraints weight = 42887.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.120570 restraints weight = 34103.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.121065 restraints weight = 29515.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.122111 restraints weight = 26335.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.122969 restraints weight = 23488.600| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5564 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6647 Z= 0.171 Angle : 0.827 16.895 9042 Z= 0.411 Chirality : 0.052 0.536 946 Planarity : 0.006 0.067 1164 Dihedral : 5.999 30.406 858 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 4.54 % Allowed : 30.16 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -2.44 (0.30), residues: 775 helix: -0.82 (0.35), residues: 237 sheet: 1.27 (1.04), residues: 27 loop : -2.33 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 204 TYR 0.021 0.002 TYR A 158 PHE 0.016 0.002 PHE B 497 TRP 0.040 0.003 TRP A 203 HIS 0.007 0.002 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 6635) covalent geometry : angle 0.79715 / 0.40 ( 9012) SS BOND : bond 0.00374 / 0.21 ( 6) SS BOND : angle 1.06626 / 0.58 ( 12) hydrogen bonds : bond 0.03665 / 2.32 ( 173) hydrogen bonds : angle 6.07169 / 4.35 ( 468) link_BETA1-4 : bond 0.00405 / 0.21 ( 1) link_BETA1-4 : angle 1.36585 / 0.70 ( 3) link_BETA1-6 : bond 0.00122 / 0.06 ( 1) link_BETA1-6 : angle 1.69192 / 0.88 ( 3) link_NAG-ASN : bond 0.01309 / 0.63 ( 4) link_NAG-ASN : angle 5.93934 / 3.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.94 seconds wall clock time: 29 minutes 1.13 seconds (1741.13 seconds total)