Starting phenix.real_space_refine on Sat May 10 17:24:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t23_40979/05_2025/8t23_40979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t23_40979/05_2025/8t23_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_40979/05_2025/8t23_40979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t23_40979/05_2025/8t23_40979.map" model { file = "/net/cci-nas-00/data/ceres_data/8t23_40979/05_2025/8t23_40979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t23_40979/05_2025/8t23_40979.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.88 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: 1.66 Conformation dependent library (CDL) restraints added in 933.9 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: 0.61 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: 1.45 Time building geometry restraints manager: 1.92 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 - 23.55: 3535 23.55 - 47.09: 388 47.09 - 70.64: 62 70.64 - 94.19: 10 94.19 - 117.74: 6 Dihedral angle restraints: 4001 sinusoidal: 1708 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 3998 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: 10.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.470 Find NCS groups from input model: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 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 : 19.217 117.737 2511 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.047 0.002 TRP A 168 HIS 0.008 0.001 HIS A 505 PHE 0.020 0.002 PHE B 338 TYR 0.015 0.001 TYR A 510 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.01295 ( 4) link_NAG-ASN : angle 6.53667 ( 12) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 1.35764 ( 3) hydrogen bonds : bond 0.15776 ( 173) hydrogen bonds : angle 6.45848 ( 468) link_BETA1-6 : bond 0.00809 ( 1) link_BETA1-6 : angle 1.93647 ( 3) SS BOND : bond 0.00539 ( 6) SS BOND : angle 1.15684 ( 12) covalent geometry : bond 0.00462 ( 6635) covalent geometry : angle 1.00443 ( 9012) *********************** 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 : 1.532 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: 0.5829 (mm) REVERT: A 62 MET cc_start: 0.4429 (mpp) cc_final: 0.4108 (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: 0.6390 (t80) REVERT: A 379 ILE cc_start: 0.8955 (tt) cc_final: 0.8683 (mm) REVERT: A 382 ASP cc_start: 0.8908 (t70) cc_final: 0.8393 (p0) REVERT: A 408 MET cc_start: 0.3341 (mmp) cc_final: 0.2561 (mmm) REVERT: A 474 MET cc_start: -0.1394 (ptt) cc_final: -0.2041 (ptt) REVERT: A 497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6257 (t80) REVERT: A 515 TYR cc_start: 0.6070 (m-80) cc_final: 0.5712 (m-80) REVERT: A 539 LEU cc_start: 0.6118 (tp) cc_final: 0.5859 (mp) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.1968 time to fit residues: 33.9599 Evaluate side-chains 82 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 23 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 overall best weight: 0.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4572 r_free = 0.4572 target = 0.146013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.127507 restraints weight = 41723.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.129451 restraints weight = 36307.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.130638 restraints weight = 29197.162| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5109 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6647 Z= 0.144 Angle : 0.817 18.296 9042 Z= 0.399 Chirality : 0.051 0.504 946 Planarity : 0.006 0.066 1164 Dihedral : 11.473 104.692 982 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.25 % Allowed : 26.65 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.30), residues: 775 helix: -1.21 (0.32), residues: 259 sheet: 1.82 (1.13), residues: 24 loop : -2.45 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 211 HIS 0.006 0.001 HIS A 417 PHE 0.023 0.002 PHE B 490 TYR 0.016 0.001 TYR A 180 ARG 0.005 0.001 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.01213 ( 4) link_NAG-ASN : angle 6.10587 ( 12) link_BETA1-4 : bond 0.00374 ( 1) link_BETA1-4 : angle 1.51297 ( 3) hydrogen bonds : bond 0.04018 ( 173) hydrogen bonds : angle 5.76141 ( 468) link_BETA1-6 : bond 0.01476 ( 1) link_BETA1-6 : angle 2.29532 ( 3) SS BOND : bond 0.00373 ( 6) SS BOND : angle 1.30389 ( 12) covalent geometry : bond 0.00309 ( 6635) covalent geometry : angle 0.78421 ( 9012) *********************** 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 120 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.6994 (mm) cc_final: 0.6711 (mt) REVERT: A 203 TRP cc_start: 0.6056 (t-100) cc_final: 0.4614 (m-10) REVERT: A 211 TRP cc_start: 0.5747 (p90) cc_final: 0.3102 (m100) REVERT: A 252 TYR cc_start: 0.2777 (OUTLIER) cc_final: 0.1782 (p90) REVERT: A 279 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.5036 (m-10) REVERT: A 345 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7336 (t70) REVERT: A 376 MET cc_start: 0.8852 (tpt) cc_final: 0.8010 (ptt) REVERT: A 382 ASP cc_start: 0.9116 (t70) cc_final: 0.8461 (p0) REVERT: A 400 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7688 (t80) REVERT: A 402 GLU cc_start: 0.7109 (mp0) cc_final: 0.6766 (mp0) REVERT: A 462 MET cc_start: 0.7041 (ppp) cc_final: 0.6725 (ppp) REVERT: A 539 LEU cc_start: 0.5704 (tp) cc_final: 0.5490 (mp) REVERT: A 566 TRP cc_start: 0.7457 (p-90) cc_final: 0.6990 (p-90) REVERT: A 579 MET cc_start: 0.6576 (ppp) cc_final: 0.5330 (ppp) outliers start: 29 outliers final: 14 residues processed: 112 average time/residue: 0.1769 time to fit residues: 26.9203 Evaluate side-chains 91 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 A residue 542 CYS 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 18 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4542 r_free = 0.4542 target = 0.143022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.124798 restraints weight = 41832.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.126374 restraints weight = 34672.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.127433 restraints weight = 29299.088| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.2755 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= 0.146 Angle : 0.800 18.157 9042 Z= 0.386 Chirality : 0.050 0.532 946 Planarity : 0.006 0.065 1164 Dihedral : 11.062 100.883 980 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 4.83 % Allowed : 26.94 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.30), residues: 775 helix: -0.83 (0.34), residues: 244 sheet: 1.56 (1.08), residues: 24 loop : -2.34 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS A 417 PHE 0.037 0.002 PHE A 72 TYR 0.013 0.002 TYR A 587 ARG 0.012 0.001 ARG A 572 Details of bonding type rmsd link_NAG-ASN : bond 0.01380 ( 4) link_NAG-ASN : angle 6.18513 ( 12) link_BETA1-4 : bond 0.00316 ( 1) link_BETA1-4 : angle 1.67778 ( 3) hydrogen bonds : bond 0.03829 ( 173) hydrogen bonds : angle 5.72360 ( 468) link_BETA1-6 : bond 0.01160 ( 1) link_BETA1-6 : angle 2.81991 ( 3) SS BOND : bond 0.00298 ( 6) SS BOND : angle 1.13732 ( 12) covalent geometry : bond 0.00315 ( 6635) covalent geometry : angle 0.76496 ( 9012) *********************** 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 112 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: -0.0597 (OUTLIER) cc_final: -0.1034 (pttm) REVERT: A 93 ILE cc_start: 0.6872 (mm) cc_final: 0.6331 (pt) REVERT: A 123 MET cc_start: -0.0683 (tpt) cc_final: -0.0913 (tpt) REVERT: A 171 GLU cc_start: 0.9061 (pp20) cc_final: 0.8658 (pm20) REVERT: A 203 TRP cc_start: 0.6364 (t-100) cc_final: 0.4769 (m-10) REVERT: A 211 TRP cc_start: 0.6002 (p90) cc_final: 0.3564 (m100) REVERT: A 252 TYR cc_start: 0.2878 (OUTLIER) cc_final: 0.2004 (p90) REVERT: A 279 TYR cc_start: 0.5576 (OUTLIER) cc_final: 0.4890 (m-10) REVERT: A 345 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7534 (t70) REVERT: A 376 MET cc_start: 0.9026 (tpt) cc_final: 0.8045 (ptp) REVERT: A 381 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.4113 (p90) REVERT: A 382 ASP cc_start: 0.9170 (t70) cc_final: 0.8356 (p0) REVERT: A 400 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 462 MET cc_start: 0.7334 (ppp) cc_final: 0.6933 (ppp) REVERT: A 539 LEU cc_start: 0.5375 (tp) cc_final: 0.5163 (mp) REVERT: A 544 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6094 (pt) REVERT: A 566 TRP cc_start: 0.7547 (p-90) cc_final: 0.7047 (p-90) REVERT: A 579 MET cc_start: 0.6831 (ppp) cc_final: 0.5414 (tpp) outliers start: 33 outliers final: 18 residues processed: 101 average time/residue: 0.1788 time to fit residues: 24.1706 Evaluate side-chains 101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 544 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 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 5 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4523 r_free = 0.4523 target = 0.140319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.122147 restraints weight = 42845.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.123875 restraints weight = 35005.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.124787 restraints weight = 28987.553| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6647 Z= 0.162 Angle : 0.807 17.830 9042 Z= 0.393 Chirality : 0.050 0.516 946 Planarity : 0.006 0.066 1164 Dihedral : 10.439 90.509 980 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 5.86 % Allowed : 26.50 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.30), residues: 775 helix: -0.90 (0.34), residues: 246 sheet: 1.59 (1.13), residues: 24 loop : -2.31 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 168 HIS 0.010 0.001 HIS A 555 PHE 0.032 0.003 PHE A 452 TYR 0.015 0.002 TYR A 158 ARG 0.007 0.001 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.01349 ( 4) link_NAG-ASN : angle 6.25830 ( 12) link_BETA1-4 : bond 0.00104 ( 1) link_BETA1-4 : angle 2.05625 ( 3) hydrogen bonds : bond 0.03625 ( 173) hydrogen bonds : angle 5.85896 ( 468) link_BETA1-6 : bond 0.00965 ( 1) link_BETA1-6 : angle 2.72801 ( 3) SS BOND : bond 0.00311 ( 6) SS BOND : angle 0.81921 ( 12) covalent geometry : bond 0.00347 ( 6635) covalent geometry : angle 0.77181 ( 9012) *********************** 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 117 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7024 (mm) cc_final: 0.6418 (pt) REVERT: A 171 GLU cc_start: 0.8871 (pp20) cc_final: 0.8591 (pm20) REVERT: A 211 TRP cc_start: 0.5755 (p90) cc_final: 0.3447 (m100) REVERT: A 252 TYR cc_start: 0.3406 (OUTLIER) cc_final: 0.2809 (p90) REVERT: A 279 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5014 (m-10) REVERT: A 345 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7708 (t70) REVERT: A 376 MET cc_start: 0.8929 (tpt) cc_final: 0.8019 (ptp) REVERT: A 381 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4179 (p90) REVERT: A 462 MET cc_start: 0.7449 (ppp) cc_final: 0.7135 (ppp) REVERT: A 497 TYR cc_start: 0.6809 (t80) cc_final: 0.6488 (t80) REVERT: A 566 TRP cc_start: 0.7716 (p-90) cc_final: 0.7172 (p-90) REVERT: A 579 MET cc_start: 0.7055 (ppp) cc_final: 0.6454 (ppp) REVERT: B 486 PHE cc_start: 0.6993 (OUTLIER) cc_final: 0.6535 (t80) outliers start: 40 outliers final: 25 residues processed: 105 average time/residue: 0.1939 time to fit residues: 26.8019 Evaluate side-chains 100 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 125 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE 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 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 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 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 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.0070 chunk 46 optimal weight: 0.4980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4546 r_free = 0.4546 target = 0.142336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.123811 restraints weight = 41555.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.125436 restraints weight = 33841.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.126318 restraints weight = 28824.721| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6647 Z= 0.130 Angle : 0.776 18.128 9042 Z= 0.369 Chirality : 0.048 0.490 946 Planarity : 0.005 0.063 1164 Dihedral : 8.802 69.176 980 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.83 % Allowed : 28.55 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.30), residues: 775 helix: -0.87 (0.34), residues: 246 sheet: 1.84 (1.12), residues: 24 loop : -2.21 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.006 0.001 HIS A 555 PHE 0.023 0.002 PHE A 452 TYR 0.010 0.001 TYR A 41 ARG 0.006 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.01299 ( 4) link_NAG-ASN : angle 6.29460 ( 12) link_BETA1-4 : bond 0.00481 ( 1) link_BETA1-4 : angle 1.76980 ( 3) hydrogen bonds : bond 0.03277 ( 173) hydrogen bonds : angle 5.71915 ( 468) link_BETA1-6 : bond 0.01281 ( 1) link_BETA1-6 : angle 2.54195 ( 3) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.90076 ( 12) covalent geometry : bond 0.00275 ( 6635) covalent geometry : angle 0.73988 ( 9012) *********************** 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 110 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7119 (mm) cc_final: 0.6533 (pt) REVERT: A 171 GLU cc_start: 0.8936 (pp20) cc_final: 0.8642 (pm20) REVERT: A 249 MET cc_start: 0.6336 (mmm) cc_final: 0.6052 (mmt) REVERT: A 252 TYR cc_start: 0.3722 (OUTLIER) cc_final: 0.3257 (p90) REVERT: A 279 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.4809 (m-10) REVERT: A 345 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7625 (t70) REVERT: A 376 MET cc_start: 0.8904 (tpt) cc_final: 0.7931 (ptp) REVERT: A 381 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.4087 (p90) REVERT: A 462 MET cc_start: 0.7417 (ppp) cc_final: 0.7151 (ppp) REVERT: A 497 TYR cc_start: 0.6960 (t80) cc_final: 0.6647 (t80) REVERT: A 566 TRP cc_start: 0.7707 (p-90) cc_final: 0.7255 (p-90) REVERT: A 579 MET cc_start: 0.7069 (ppp) cc_final: 0.6492 (ppp) REVERT: B 486 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6681 (t80) outliers start: 33 outliers final: 20 residues processed: 99 average time/residue: 0.2078 time to fit residues: 26.7253 Evaluate side-chains 95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 308 PHE 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 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG 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 12 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 34 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4538 r_free = 0.4538 target = 0.141724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.123390 restraints weight = 41475.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.125138 restraints weight = 33463.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.126157 restraints weight = 28300.577| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6647 Z= 0.132 Angle : 0.783 18.013 9042 Z= 0.373 Chirality : 0.047 0.496 946 Planarity : 0.006 0.064 1164 Dihedral : 7.390 53.740 980 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.27 % Allowed : 28.40 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.30), residues: 775 helix: -0.81 (0.35), residues: 242 sheet: 1.47 (1.00), residues: 27 loop : -2.23 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.006 0.001 HIS A 555 PHE 0.020 0.002 PHE A 452 TYR 0.012 0.001 TYR B 351 ARG 0.014 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.01274 ( 4) link_NAG-ASN : angle 6.46994 ( 12) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 1.70628 ( 3) hydrogen bonds : bond 0.03205 ( 173) hydrogen bonds : angle 5.72853 ( 468) link_BETA1-6 : bond 0.01480 ( 1) link_BETA1-6 : angle 2.83414 ( 3) SS BOND : bond 0.00358 ( 6) SS BOND : angle 1.41553 ( 12) covalent geometry : bond 0.00284 ( 6635) covalent geometry : angle 0.74366 ( 9012) *********************** 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 109 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7085 (mm) cc_final: 0.6513 (pt) REVERT: A 171 GLU cc_start: 0.8993 (pp20) cc_final: 0.8627 (pm20) REVERT: A 172 VAL cc_start: 0.8399 (t) cc_final: 0.7917 (t) REVERT: A 249 MET cc_start: 0.6357 (mmm) cc_final: 0.6156 (mmt) REVERT: A 252 TYR cc_start: 0.4100 (OUTLIER) cc_final: 0.3466 (p90) REVERT: A 279 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.4943 (m-10) REVERT: A 376 MET cc_start: 0.8869 (tpt) cc_final: 0.7925 (ptp) REVERT: A 381 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.4119 (p90) REVERT: A 462 MET cc_start: 0.7465 (ppp) cc_final: 0.7223 (ppp) REVERT: A 464 PHE cc_start: 0.2804 (OUTLIER) cc_final: -0.0708 (t80) REVERT: A 497 TYR cc_start: 0.6900 (t80) cc_final: 0.6590 (t80) REVERT: A 566 TRP cc_start: 0.7773 (p-90) cc_final: 0.7262 (p-90) REVERT: A 579 MET cc_start: 0.7243 (ppp) cc_final: 0.6728 (ppp) REVERT: B 484 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6326 (tm-30) REVERT: B 486 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6677 (t80) outliers start: 36 outliers final: 26 residues processed: 99 average time/residue: 0.1949 time to fit residues: 25.5431 Evaluate side-chains 101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 308 PHE 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 452 PHE 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 514 ARG 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 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 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 10 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.0010 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.141970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.123629 restraints weight = 41443.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.125457 restraints weight = 33481.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.126371 restraints weight = 28553.392| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6647 Z= 0.126 Angle : 0.754 17.867 9042 Z= 0.359 Chirality : 0.047 0.483 946 Planarity : 0.005 0.064 1164 Dihedral : 6.608 52.976 980 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.27 % Allowed : 28.84 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.31), residues: 775 helix: -0.73 (0.35), residues: 242 sheet: 2.01 (1.03), residues: 24 loop : -2.18 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.006 0.001 HIS A 555 PHE 0.020 0.002 PHE A 452 TYR 0.012 0.001 TYR B 423 ARG 0.005 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.01285 ( 4) link_NAG-ASN : angle 6.58596 ( 12) link_BETA1-4 : bond 0.00827 ( 1) link_BETA1-4 : angle 1.42299 ( 3) hydrogen bonds : bond 0.03070 ( 173) hydrogen bonds : angle 5.71723 ( 468) link_BETA1-6 : bond 0.01092 ( 1) link_BETA1-6 : angle 3.07108 ( 3) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.31580 ( 12) covalent geometry : bond 0.00278 ( 6635) covalent geometry : angle 0.71188 ( 9012) *********************** 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 114 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7203 (mm) cc_final: 0.6560 (pt) REVERT: A 171 GLU cc_start: 0.9086 (pp20) cc_final: 0.8714 (pm20) REVERT: A 172 VAL cc_start: 0.8463 (t) cc_final: 0.7883 (t) REVERT: A 252 TYR cc_start: 0.3856 (OUTLIER) cc_final: 0.3242 (p90) REVERT: A 279 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.4848 (m-10) REVERT: A 381 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.4019 (p90) REVERT: A 382 ASP cc_start: 0.9187 (t0) cc_final: 0.8788 (t0) REVERT: A 462 MET cc_start: 0.7398 (ppp) cc_final: 0.7119 (ppp) REVERT: A 566 TRP cc_start: 0.7639 (p-90) cc_final: 0.7141 (p-90) REVERT: A 579 MET cc_start: 0.7310 (ppp) cc_final: 0.6817 (ppp) REVERT: B 486 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6629 (t80) outliers start: 36 outliers final: 27 residues processed: 105 average time/residue: 0.1949 time to fit residues: 26.9322 Evaluate side-chains 100 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE 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 452 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 539 LEU 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 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4518 r_free = 0.4518 target = 0.139163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.125164 restraints weight = 41038.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.126207 restraints weight = 34778.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.126658 restraints weight = 30715.855| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.5451 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= 0.144 Angle : 0.780 17.475 9042 Z= 0.376 Chirality : 0.048 0.508 946 Planarity : 0.006 0.067 1164 Dihedral : 6.686 53.874 980 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 4.98 % Allowed : 29.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.30), residues: 775 helix: -0.70 (0.35), residues: 242 sheet: 2.06 (1.05), residues: 27 loop : -2.23 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 168 HIS 0.006 0.001 HIS A 555 PHE 0.021 0.002 PHE A 452 TYR 0.015 0.002 TYR A 158 ARG 0.012 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01306 ( 4) link_NAG-ASN : angle 6.15480 ( 12) link_BETA1-4 : bond 0.00753 ( 1) link_BETA1-4 : angle 0.83539 ( 3) hydrogen bonds : bond 0.03291 ( 173) hydrogen bonds : angle 5.86019 ( 468) link_BETA1-6 : bond 0.01125 ( 1) link_BETA1-6 : angle 2.71921 ( 3) SS BOND : bond 0.00431 ( 6) SS BOND : angle 1.31157 ( 12) covalent geometry : bond 0.00315 ( 6635) covalent geometry : angle 0.74547 ( 9012) *********************** 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 104 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7307 (mm) cc_final: 0.6681 (pt) REVERT: A 168 TRP cc_start: 0.7362 (m100) cc_final: 0.7083 (m100) REVERT: A 171 GLU cc_start: 0.8964 (pp20) cc_final: 0.8683 (pm20) REVERT: A 172 VAL cc_start: 0.8354 (t) cc_final: 0.6073 (t) REVERT: A 249 MET cc_start: 0.5973 (mmm) cc_final: 0.5544 (mmt) REVERT: A 252 TYR cc_start: 0.4466 (OUTLIER) cc_final: 0.3717 (p90) REVERT: A 279 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4766 (m-10) REVERT: A 332 MET cc_start: 0.7601 (pmm) cc_final: 0.6699 (tpp) REVERT: A 353 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7909 (ttpt) REVERT: A 381 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.3595 (p90) REVERT: A 462 MET cc_start: 0.7569 (ppp) cc_final: 0.7335 (ppp) REVERT: A 464 PHE cc_start: 0.2276 (OUTLIER) cc_final: -0.1153 (t80) REVERT: A 566 TRP cc_start: 0.7870 (p-90) cc_final: 0.7257 (p-90) REVERT: A 579 MET cc_start: 0.7482 (ppp) cc_final: 0.6911 (ppp) REVERT: B 486 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6520 (t80) outliers start: 34 outliers final: 27 residues processed: 96 average time/residue: 0.1884 time to fit residues: 24.0712 Evaluate side-chains 96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE 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 499 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 539 LEU 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 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 48 optimal weight: 0.0970 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4522 r_free = 0.4522 target = 0.139400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.121029 restraints weight = 42398.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.122990 restraints weight = 33403.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.123766 restraints weight = 28526.412| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6647 Z= 0.132 Angle : 0.767 17.610 9042 Z= 0.368 Chirality : 0.048 0.494 946 Planarity : 0.005 0.064 1164 Dihedral : 6.622 53.557 980 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 4.83 % Allowed : 30.75 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.30), residues: 775 helix: -0.59 (0.35), residues: 242 sheet: 1.78 (1.06), residues: 27 loop : -2.26 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.006 0.001 HIS A 555 PHE 0.037 0.002 PHE A 452 TYR 0.015 0.001 TYR A 202 ARG 0.004 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.01286 ( 4) link_NAG-ASN : angle 6.14318 ( 12) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 0.83631 ( 3) hydrogen bonds : bond 0.03153 ( 173) hydrogen bonds : angle 5.82639 ( 468) link_BETA1-6 : bond 0.01122 ( 1) link_BETA1-6 : angle 2.78603 ( 3) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.88933 ( 12) covalent geometry : bond 0.00287 ( 6635) covalent geometry : angle 0.73251 ( 9012) *********************** 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 101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7458 (mm) cc_final: 0.6898 (pt) REVERT: A 118 THR cc_start: 0.5577 (m) cc_final: 0.5260 (m) REVERT: A 155 SER cc_start: 0.6343 (t) cc_final: 0.6067 (m) REVERT: A 168 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.7141 (m100) REVERT: A 171 GLU cc_start: 0.9072 (pp20) cc_final: 0.8783 (pm20) REVERT: A 249 MET cc_start: 0.6157 (mmm) cc_final: 0.5795 (mmt) REVERT: A 252 TYR cc_start: 0.4346 (OUTLIER) cc_final: 0.3644 (p90) REVERT: A 270 MET cc_start: 0.7667 (mtm) cc_final: 0.7330 (ttp) REVERT: A 279 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.4909 (m-10) REVERT: A 332 MET cc_start: 0.7822 (pmm) cc_final: 0.6607 (tpp) REVERT: A 353 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7869 (ttpt) REVERT: A 376 MET cc_start: 0.8957 (tpt) cc_final: 0.8105 (ptp) REVERT: A 381 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.3672 (p90) REVERT: A 462 MET cc_start: 0.7587 (ppp) cc_final: 0.7332 (ppp) REVERT: A 464 PHE cc_start: 0.2095 (OUTLIER) cc_final: -0.1550 (t80) REVERT: A 579 MET cc_start: 0.7292 (ppp) cc_final: 0.6771 (ppp) REVERT: B 484 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6292 (tm-30) REVERT: B 486 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6653 (t80) outliers start: 33 outliers final: 24 residues processed: 93 average time/residue: 0.1904 time to fit residues: 23.6093 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 : 0.725 ------------------------------------------------------------------------------- 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 168 TRP 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 308 PHE 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 499 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 539 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.137661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.119059 restraints weight = 42695.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.121146 restraints weight = 33634.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.121920 restraints weight = 27898.479| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6647 Z= 0.152 Angle : 0.795 17.332 9042 Z= 0.387 Chirality : 0.049 0.515 946 Planarity : 0.006 0.066 1164 Dihedral : 6.771 54.116 980 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 4.39 % Allowed : 31.33 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.30), residues: 775 helix: -0.58 (0.36), residues: 236 sheet: 1.40 (1.10), residues: 27 loop : -2.33 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 566 HIS 0.006 0.002 HIS A 555 PHE 0.027 0.002 PHE A 452 TYR 0.019 0.002 TYR A 158 ARG 0.013 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01330 ( 4) link_NAG-ASN : angle 6.07351 ( 12) link_BETA1-4 : bond 0.00682 ( 1) link_BETA1-4 : angle 0.99539 ( 3) hydrogen bonds : bond 0.03341 ( 173) hydrogen bonds : angle 5.98856 ( 468) link_BETA1-6 : bond 0.01005 ( 1) link_BETA1-6 : angle 2.64407 ( 3) SS BOND : bond 0.00370 ( 6) SS BOND : angle 1.08125 ( 12) covalent geometry : bond 0.00333 ( 6635) covalent geometry : angle 0.76204 ( 9012) ********************** 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 97 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7533 (mm) cc_final: 0.6965 (pt) REVERT: A 118 THR cc_start: 0.5725 (m) cc_final: 0.5388 (m) REVERT: A 155 SER cc_start: 0.6569 (t) cc_final: 0.6342 (m) REVERT: A 168 TRP cc_start: 0.7527 (m100) cc_final: 0.7140 (m100) REVERT: A 171 GLU cc_start: 0.9085 (pp20) cc_final: 0.8808 (pm20) REVERT: A 249 MET cc_start: 0.6079 (mmm) cc_final: 0.5725 (mmt) REVERT: A 252 TYR cc_start: 0.4739 (OUTLIER) cc_final: 0.3945 (p90) REVERT: A 270 MET cc_start: 0.7667 (mtm) cc_final: 0.7413 (ttm) REVERT: A 279 TYR cc_start: 0.6342 (OUTLIER) cc_final: 0.4878 (m-10) REVERT: A 313 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8657 (mmmt) REVERT: A 332 MET cc_start: 0.7760 (pmm) cc_final: 0.6398 (tpp) REVERT: A 353 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7912 (ttpt) REVERT: A 366 MET cc_start: 0.7457 (ppp) cc_final: 0.6926 (mtt) REVERT: A 376 MET cc_start: 0.8998 (tpt) cc_final: 0.8209 (ptp) REVERT: A 381 TYR cc_start: 0.5832 (OUTLIER) cc_final: 0.3912 (p90) REVERT: A 464 PHE cc_start: 0.2588 (OUTLIER) cc_final: -0.0884 (t80) REVERT: A 474 MET cc_start: -0.2753 (ptt) cc_final: -0.3163 (ptt) REVERT: A 579 MET cc_start: 0.7375 (ppp) cc_final: 0.6767 (ppp) REVERT: B 486 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6627 (t80) outliers start: 30 outliers final: 24 residues processed: 91 average time/residue: 0.1874 time to fit residues: 22.7296 Evaluate side-chains 92 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 308 PHE 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 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 539 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.120186 restraints weight = 43032.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.122516 restraints weight = 33578.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.123360 restraints weight = 27249.347| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.6315 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= 0.135 Angle : 0.781 17.359 9042 Z= 0.378 Chirality : 0.048 0.492 946 Planarity : 0.006 0.065 1164 Dihedral : 6.745 53.720 980 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.10 % Allowed : 32.36 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.30), residues: 775 helix: -0.62 (0.35), residues: 237 sheet: 1.37 (1.12), residues: 27 loop : -2.34 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 566 HIS 0.006 0.001 HIS A 555 PHE 0.028 0.002 PHE A 452 TYR 0.015 0.002 TYR B 351 ARG 0.008 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01282 ( 4) link_NAG-ASN : angle 6.04093 ( 12) link_BETA1-4 : bond 0.00486 ( 1) link_BETA1-4 : angle 0.90584 ( 3) hydrogen bonds : bond 0.03243 ( 173) hydrogen bonds : angle 5.98180 ( 468) link_BETA1-6 : bond 0.01231 ( 1) link_BETA1-6 : angle 2.64986 ( 3) SS BOND : bond 0.00371 ( 6) SS BOND : angle 1.00546 ( 12) covalent geometry : bond 0.00297 ( 6635) covalent geometry : angle 0.74810 ( 9012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.87 seconds wall clock time: 52 minutes 8.01 seconds (3128.01 seconds total)