Starting phenix.real_space_refine on Tue Feb 11 20:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t23_40979/02_2025/8t23_40979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t23_40979/02_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_40979/02_2025/8t23_40979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t23_40979/02_2025/8t23_40979.map" model { file = "/net/cci-nas-00/data/ceres_data/8t23_40979/02_2025/8t23_40979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t23_40979/02_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-5592/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: 6.45, per 1000 atoms: 1.00 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: 1.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.47 Time building geometry restraints manager: 1.82 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: 8.280 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.160 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- 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 6635 Z= 0.293 Angle : 1.004 16.729 9012 Z= 0.535 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.689 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: 0.1878 time to fit residues: 31.5977 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 : 0.736 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 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: 0.1542 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.146761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.128114 restraints weight = 41088.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.129930 restraints weight = 33500.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.131113 restraints weight = 27884.034| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5100 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6635 Z= 0.202 Angle : 0.793 13.523 9012 Z= 0.397 Chirality : 0.051 0.497 946 Planarity : 0.006 0.067 1164 Dihedral : 11.621 106.110 982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.25 % Allowed : 26.50 % Favored : 69.25 % 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: -2.68 (0.30), residues: 775 helix: -1.13 (0.33), residues: 252 sheet: 1.87 (1.14), residues: 24 loop : -2.47 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 168 HIS 0.006 0.001 HIS A 417 PHE 0.024 0.002 PHE B 490 TYR 0.017 0.001 TYR A 180 ARG 0.006 0.001 ARG A 115 *********************** 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 117 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.4924 (mpp) cc_final: 0.4695 (pmm) REVERT: A 92 ILE cc_start: 0.6941 (mm) cc_final: 0.6663 (mt) REVERT: A 203 TRP cc_start: 0.6350 (t-100) cc_final: 0.4743 (m-10) REVERT: A 211 TRP cc_start: 0.5336 (p90) cc_final: 0.2754 (m100) REVERT: A 252 TYR cc_start: 0.2729 (OUTLIER) cc_final: 0.1783 (p90) REVERT: A 279 TYR cc_start: 0.5445 (OUTLIER) cc_final: 0.4930 (m-10) REVERT: A 345 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7396 (t70) REVERT: A 376 MET cc_start: 0.8902 (tpt) cc_final: 0.8044 (ptp) REVERT: A 382 ASP cc_start: 0.9119 (t70) cc_final: 0.8465 (p0) REVERT: A 400 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7868 (t80) REVERT: A 402 GLU cc_start: 0.6979 (mp0) cc_final: 0.6654 (mp0) REVERT: A 462 MET cc_start: 0.7180 (ppp) cc_final: 0.6819 (ppp) REVERT: A 474 MET cc_start: -0.1832 (ptt) cc_final: -0.2069 (ptt) REVERT: A 566 TRP cc_start: 0.7374 (p-90) cc_final: 0.6969 (p-90) REVERT: A 579 MET cc_start: 0.6568 (ppp) cc_final: 0.5329 (ppp) outliers start: 29 outliers final: 14 residues processed: 109 average time/residue: 0.1689 time to fit residues: 24.9170 Evaluate side-chains 93 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 51 optimal weight: 0.0010 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.0030 chunk 41 optimal weight: 0.0010 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.1360 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.147475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.128816 restraints weight = 41203.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.130555 restraints weight = 34346.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.131856 restraints weight = 29082.724| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5172 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6635 Z= 0.179 Angle : 0.746 16.119 9012 Z= 0.368 Chirality : 0.049 0.504 946 Planarity : 0.006 0.064 1164 Dihedral : 10.715 102.438 980 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.10 % Allowed : 27.53 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.49 (0.30), residues: 775 helix: -0.84 (0.34), residues: 245 sheet: 1.73 (1.06), residues: 24 loop : -2.40 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.008 0.001 HIS A 417 PHE 0.037 0.002 PHE A 72 TYR 0.016 0.001 TYR A 217 ARG 0.006 0.001 ARG A 177 *********************** 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 113 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: -0.0590 (OUTLIER) cc_final: -0.1272 (pttm) REVERT: A 93 ILE cc_start: 0.6771 (mm) cc_final: 0.6242 (pt) REVERT: A 123 MET cc_start: -0.0657 (tpt) cc_final: -0.1050 (tpt) REVERT: A 150 ASP cc_start: 0.9148 (p0) cc_final: 0.8166 (t0) REVERT: A 171 GLU cc_start: 0.8944 (pp20) cc_final: 0.8474 (pm20) REVERT: A 252 TYR cc_start: 0.2485 (OUTLIER) cc_final: 0.1671 (p90) REVERT: A 279 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.4938 (m-10) REVERT: A 345 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7506 (t70) REVERT: A 376 MET cc_start: 0.8943 (tpt) cc_final: 0.7969 (ptp) REVERT: A 381 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.4114 (p90) REVERT: A 382 ASP cc_start: 0.9134 (t70) cc_final: 0.8336 (p0) REVERT: A 400 PHE cc_start: 0.8347 (t80) cc_final: 0.7947 (t80) REVERT: A 462 MET cc_start: 0.7353 (ppp) cc_final: 0.6952 (ppp) REVERT: A 579 MET cc_start: 0.6689 (ppp) cc_final: 0.5893 (ppp) outliers start: 28 outliers final: 16 residues processed: 103 average time/residue: 0.2042 time to fit residues: 27.8147 Evaluate side-chains 93 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.142876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.124536 restraints weight = 42683.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.126410 restraints weight = 35326.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.127591 restraints weight = 29406.932| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6635 Z= 0.202 Angle : 0.739 11.849 9012 Z= 0.367 Chirality : 0.049 0.522 946 Planarity : 0.006 0.063 1164 Dihedral : 10.202 94.206 980 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 4.39 % Allowed : 27.53 % Favored : 68.08 % 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: -2.35 (0.30), residues: 775 helix: -0.90 (0.35), residues: 247 sheet: 1.87 (1.04), residues: 24 loop : -2.22 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 168 HIS 0.007 0.001 HIS A 555 PHE 0.033 0.002 PHE A 452 TYR 0.013 0.002 TYR A 41 ARG 0.005 0.001 ARG A 169 *********************** 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 108 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.6978 (mm) cc_final: 0.6357 (pt) REVERT: A 171 GLU cc_start: 0.9041 (pp20) cc_final: 0.8623 (pm20) REVERT: A 203 TRP cc_start: 0.6571 (t-100) cc_final: 0.4868 (m-10) REVERT: A 252 TYR cc_start: 0.3299 (OUTLIER) cc_final: 0.2259 (p90) REVERT: A 279 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.4898 (m-10) REVERT: A 345 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7710 (t70) REVERT: A 376 MET cc_start: 0.9014 (tpt) cc_final: 0.8014 (ptp) REVERT: A 382 ASP cc_start: 0.9103 (t70) cc_final: 0.8467 (p0) REVERT: A 462 MET cc_start: 0.7477 (ppp) cc_final: 0.6990 (ppp) REVERT: A 579 MET cc_start: 0.6850 (ppp) cc_final: 0.5429 (tpp) REVERT: B 486 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6403 (t80) outliers start: 30 outliers final: 20 residues processed: 98 average time/residue: 0.2038 time to fit residues: 26.6160 Evaluate side-chains 99 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR 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 503 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 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.0050 chunk 74 optimal weight: 0.0980 chunk 11 optimal weight: 0.2980 chunk 46 optimal weight: 0.0070 overall best weight: 0.0354 ------------------------------------------------------------------------------- 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 526 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 = 0.4578 r_free = 0.4578 target = 0.146028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.127483 restraints weight = 41523.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.128995 restraints weight = 34208.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.130229 restraints weight = 29336.117| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5316 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6635 Z= 0.168 Angle : 0.708 10.933 9012 Z= 0.348 Chirality : 0.048 0.479 946 Planarity : 0.005 0.064 1164 Dihedral : 8.606 85.241 980 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.54 % Allowed : 27.96 % Favored : 67.50 % 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: -2.30 (0.30), residues: 775 helix: -0.92 (0.34), residues: 254 sheet: 2.01 (1.02), residues: 24 loop : -2.17 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 566 HIS 0.006 0.001 HIS A 555 PHE 0.040 0.002 PHE A 72 TYR 0.011 0.001 TYR A 41 ARG 0.003 0.000 ARG A 273 *********************** 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 111 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.6867 (mm) cc_final: 0.6286 (pt) REVERT: A 171 GLU cc_start: 0.8985 (pp20) cc_final: 0.8604 (pm20) REVERT: A 203 TRP cc_start: 0.6458 (t-100) cc_final: 0.4759 (m-10) REVERT: A 252 TYR cc_start: 0.2807 (OUTLIER) cc_final: 0.2353 (p90) REVERT: A 279 TYR cc_start: 0.5699 (OUTLIER) cc_final: 0.4777 (m-10) REVERT: A 376 MET cc_start: 0.8962 (tpt) cc_final: 0.7909 (ptp) REVERT: A 381 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.4031 (p90) REVERT: A 382 ASP cc_start: 0.9084 (t70) cc_final: 0.8288 (p0) REVERT: A 400 PHE cc_start: 0.8341 (t80) cc_final: 0.8098 (t80) REVERT: A 462 MET cc_start: 0.7462 (ppp) cc_final: 0.7136 (ppp) REVERT: A 579 MET cc_start: 0.6708 (ppp) cc_final: 0.5115 (tpp) REVERT: B 486 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6603 (t80) outliers start: 31 outliers final: 20 residues processed: 101 average time/residue: 0.1928 time to fit residues: 25.9070 Evaluate side-chains 97 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 ILE 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 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 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN 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: 1.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 373 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 493 GLN B 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.131201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.114196 restraints weight = 43410.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.115785 restraints weight = 35014.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.116699 restraints weight = 29255.448| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 6635 Z= 0.436 Angle : 1.073 16.249 9012 Z= 0.552 Chirality : 0.059 0.570 946 Planarity : 0.009 0.099 1164 Dihedral : 9.303 66.759 980 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 5.86 % Allowed : 28.84 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.94 (0.29), residues: 775 helix: -1.41 (0.32), residues: 247 sheet: 0.99 (0.90), residues: 27 loop : -2.57 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 566 HIS 0.017 0.003 HIS A 345 PHE 0.030 0.004 PHE A 72 TYR 0.042 0.004 TYR A 50 ARG 0.008 0.001 ARG B 454 *********************** 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 113 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 73 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7673 (pttt) cc_final: 0.7040 (tptt) REVERT: A 93 ILE cc_start: 0.7380 (mm) cc_final: 0.6774 (pt) REVERT: A 211 TRP cc_start: 0.6436 (p90) cc_final: 0.3840 (t-100) REVERT: A 252 TYR cc_start: 0.4831 (OUTLIER) cc_final: 0.3784 (p90) REVERT: A 279 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.4923 (m-10) REVERT: A 464 PHE cc_start: 0.2847 (OUTLIER) cc_final: -0.0397 (t80) REVERT: A 497 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6459 (t80) REVERT: A 579 MET cc_start: 0.7456 (ppp) cc_final: 0.5952 (tpp) REVERT: B 484 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6233 (tm-30) REVERT: B 486 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6750 (t80) REVERT: B 489 TYR cc_start: 0.4735 (p90) cc_final: 0.3437 (m-10) outliers start: 40 outliers final: 22 residues processed: 104 average time/residue: 0.2000 time to fit residues: 28.0343 Evaluate side-chains 89 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 ILE 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 365 THR Chi-restraints excluded: chain A residue 381 TYR 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 497 TYR 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 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 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.0020 chunk 55 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 300 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.137768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.119907 restraints weight = 42055.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.121815 restraints weight = 33621.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.122904 restraints weight = 27768.892| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6635 Z= 0.203 Angle : 0.797 18.284 9012 Z= 0.399 Chirality : 0.050 0.481 946 Planarity : 0.006 0.064 1164 Dihedral : 7.965 53.520 980 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.25 % Allowed : 31.63 % Favored : 64.13 % 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: -2.66 (0.29), residues: 775 helix: -1.03 (0.34), residues: 243 sheet: 1.47 (0.99), residues: 27 loop : -2.49 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 211 HIS 0.006 0.001 HIS A 555 PHE 0.027 0.002 PHE A 452 TYR 0.015 0.002 TYR A 158 ARG 0.008 0.001 ARG A 245 *********************** 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 101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7663 (m-70) cc_final: 0.7082 (t-90) REVERT: A 93 ILE cc_start: 0.7480 (mm) cc_final: 0.6867 (pt) REVERT: A 155 SER cc_start: 0.6303 (t) cc_final: 0.5975 (m) REVERT: A 171 GLU cc_start: 0.8964 (pp20) cc_final: 0.8612 (pm20) REVERT: A 211 TRP cc_start: 0.6046 (p90) cc_final: 0.3403 (t-100) REVERT: A 252 TYR cc_start: 0.4387 (OUTLIER) cc_final: 0.3722 (p90) REVERT: A 279 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5032 (m-10) REVERT: A 366 MET cc_start: 0.7383 (ppp) cc_final: 0.6867 (mtt) REVERT: A 381 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.3797 (p90) REVERT: A 462 MET cc_start: 0.7601 (ppp) cc_final: 0.7401 (ppp) REVERT: A 579 MET cc_start: 0.7456 (ppp) cc_final: 0.6808 (ppp) REVERT: B 484 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6496 (tm-30) REVERT: B 486 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6840 (t80) outliers start: 29 outliers final: 18 residues processed: 91 average time/residue: 0.2002 time to fit residues: 24.0691 Evaluate side-chains 86 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 230 PHE 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 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 418 ILE Chi-restraints excluded: chain B residue 433 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.137888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.119808 restraints weight = 42422.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.122054 restraints weight = 33741.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.122926 restraints weight = 27395.278| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6635 Z= 0.194 Angle : 0.768 19.665 9012 Z= 0.385 Chirality : 0.049 0.511 946 Planarity : 0.006 0.065 1164 Dihedral : 7.291 53.116 980 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 3.51 % Allowed : 31.48 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.29), residues: 775 helix: -0.94 (0.34), residues: 237 sheet: 1.26 (1.01), residues: 27 loop : -2.49 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 566 HIS 0.006 0.001 HIS A 555 PHE 0.037 0.002 PHE A 452 TYR 0.014 0.002 TYR A 50 ARG 0.007 0.001 ARG A 204 *********************** 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 92 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7705 (m-70) cc_final: 0.7102 (t-90) REVERT: A 93 ILE cc_start: 0.7376 (mm) cc_final: 0.6759 (pt) REVERT: A 155 SER cc_start: 0.6313 (t) cc_final: 0.5979 (m) REVERT: A 252 TYR cc_start: 0.4423 (OUTLIER) cc_final: 0.3772 (p90) REVERT: A 279 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5005 (m-10) REVERT: A 366 MET cc_start: 0.7357 (ppp) cc_final: 0.6965 (mtt) REVERT: A 376 MET cc_start: 0.8997 (tpt) cc_final: 0.8083 (ptp) REVERT: A 381 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.3782 (p90) REVERT: A 382 ASP cc_start: 0.8970 (t70) cc_final: 0.8370 (t0) REVERT: A 462 MET cc_start: 0.7470 (ppp) cc_final: 0.7137 (ppp) REVERT: A 579 MET cc_start: 0.7474 (ppp) cc_final: 0.6849 (ppp) outliers start: 24 outliers final: 20 residues processed: 86 average time/residue: 0.2260 time to fit residues: 25.6045 Evaluate side-chains 85 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP 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 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.0020 chunk 57 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.138930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.120675 restraints weight = 42656.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.122985 restraints weight = 34027.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.123974 restraints weight = 27453.992| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6635 Z= 0.183 Angle : 0.742 13.702 9012 Z= 0.374 Chirality : 0.049 0.507 946 Planarity : 0.005 0.064 1164 Dihedral : 7.237 55.181 980 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.66 % Allowed : 32.06 % 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: -2.63 (0.29), residues: 775 helix: -0.94 (0.34), residues: 237 sheet: 1.23 (1.03), residues: 27 loop : -2.48 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 203 HIS 0.006 0.001 HIS A 555 PHE 0.027 0.002 PHE A 452 TYR 0.011 0.002 TYR A 202 ARG 0.006 0.000 ARG A 204 *********************** 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 91 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7715 (m-70) cc_final: 0.7076 (t-90) REVERT: A 93 ILE cc_start: 0.7605 (mm) cc_final: 0.7038 (pt) REVERT: A 155 SER cc_start: 0.6313 (t) cc_final: 0.5987 (m) REVERT: A 249 MET cc_start: 0.5583 (mmt) cc_final: 0.5160 (mmm) REVERT: A 252 TYR cc_start: 0.4464 (OUTLIER) cc_final: 0.3869 (p90) REVERT: A 279 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5122 (m-10) REVERT: A 366 MET cc_start: 0.7335 (ppp) cc_final: 0.6977 (mtt) REVERT: A 376 MET cc_start: 0.9003 (tpt) cc_final: 0.8067 (ptp) REVERT: A 381 TYR cc_start: 0.5745 (OUTLIER) cc_final: 0.3747 (p90) REVERT: A 382 ASP cc_start: 0.8965 (t70) cc_final: 0.8362 (t0) REVERT: A 462 MET cc_start: 0.7400 (ppp) cc_final: 0.7077 (ppp) REVERT: A 474 MET cc_start: -0.3155 (ptt) cc_final: -0.3512 (ptt) REVERT: A 579 MET cc_start: 0.7494 (ppp) cc_final: 0.6860 (ppp) outliers start: 25 outliers final: 20 residues processed: 84 average time/residue: 0.1992 time to fit residues: 22.1258 Evaluate side-chains 85 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE 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 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4496 r_free = 0.4496 target = 0.137070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.119142 restraints weight = 42948.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.121695 restraints weight = 33975.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.122534 restraints weight = 26528.916| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6635 Z= 0.205 Angle : 0.755 10.770 9012 Z= 0.383 Chirality : 0.049 0.532 946 Planarity : 0.006 0.065 1164 Dihedral : 7.384 59.934 980 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 3.66 % Allowed : 32.06 % 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: -2.62 (0.29), residues: 775 helix: -0.97 (0.34), residues: 236 sheet: 1.23 (1.06), residues: 27 loop : -2.45 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 566 HIS 0.006 0.001 HIS A 555 PHE 0.026 0.002 PHE A 452 TYR 0.017 0.002 TYR A 158 ARG 0.004 0.001 ARG A 514 ********************** 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 90 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7718 (m-70) cc_final: 0.7088 (t-90) REVERT: A 93 ILE cc_start: 0.7567 (mm) cc_final: 0.6996 (pt) REVERT: A 155 SER cc_start: 0.6433 (t) cc_final: 0.6195 (m) REVERT: A 249 MET cc_start: 0.5587 (mmt) cc_final: 0.5167 (mmm) REVERT: A 252 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.4072 (p90) REVERT: A 279 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5062 (m-10) REVERT: A 366 MET cc_start: 0.7431 (ppp) cc_final: 0.7077 (mtt) REVERT: A 376 MET cc_start: 0.8978 (tpt) cc_final: 0.7948 (ptp) REVERT: A 381 TYR cc_start: 0.5809 (OUTLIER) cc_final: 0.3827 (p90) REVERT: A 382 ASP cc_start: 0.8898 (t70) cc_final: 0.8243 (t0) REVERT: A 462 MET cc_start: 0.7399 (ppp) cc_final: 0.7013 (ppp) REVERT: A 474 MET cc_start: -0.2821 (ptt) cc_final: -0.3145 (ptt) REVERT: A 579 MET cc_start: 0.7540 (ppp) cc_final: 0.6859 (ppp) outliers start: 25 outliers final: 20 residues processed: 83 average time/residue: 0.2085 time to fit residues: 23.0294 Evaluate side-chains 85 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE 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 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 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 = 0.4489 r_free = 0.4489 target = 0.136134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.117558 restraints weight = 43672.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.119620 restraints weight = 32895.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.121119 restraints weight = 26525.262| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6635 Z= 0.215 Angle : 0.763 14.397 9012 Z= 0.386 Chirality : 0.050 0.542 946 Planarity : 0.006 0.064 1164 Dihedral : 7.503 59.409 980 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 3.81 % Allowed : 31.63 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.30), residues: 775 helix: -0.98 (0.34), residues: 237 sheet: 1.25 (1.12), residues: 27 loop : -2.45 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 566 HIS 0.006 0.001 HIS A 555 PHE 0.027 0.002 PHE A 452 TYR 0.018 0.002 TYR A 158 ARG 0.004 0.001 ARG A 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.97 seconds wall clock time: 53 minutes 14.55 seconds (3194.55 seconds total)