Starting phenix.real_space_refine on Thu Jul 2 04:46:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v84_31789/07_2026/7v84_31789.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.033 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 4238 2.51 5 N 1083 2.21 5 O 1278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6636 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.24, per 1000 atoms: 0.19 Number of scatterers: 6636 At special positions: 0 Unit cell: (102.3, 74.8, 126.5, 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 1278 8.00 N 1083 7.00 C 4238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 103 " " NAG E 1 " - " ASN F 322 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 432 " " NAG G 1 " - " ASN F 546 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 349.7 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 52.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.507A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.367A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.722A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 53 removed outlier: 4.030A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.342A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.648A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 Processing helix chain 'F' and resid 147 through 152 removed outlier: 4.084A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 175 through 193 removed outlier: 4.252A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.901A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.887A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.728A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.683A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.580A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.904A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.716A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.542A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 removed outlier: 3.517A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.590A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.637A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.864A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.532A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.606A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.552A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.782A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.598A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.663A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.981A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.58 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: 2101 1.34 - 1.46: 1769 1.46 - 1.58: 2891 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6819 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 9059 1.54 - 3.08: 169 3.08 - 4.62: 30 4.62 - 6.15: 9 6.15 - 7.69: 1 Bond angle restraints: 9268 Sorted by residual: angle pdb=" N GLY F 326 " pdb=" CA GLY F 326 " pdb=" C GLY F 326 " ideal model delta sigma weight residual 113.58 110.08 3.50 1.07e+00 8.73e-01 1.07e+01 angle pdb=" CA MET F 557 " pdb=" CB MET F 557 " pdb=" CG MET F 557 " ideal model delta sigma weight residual 114.10 119.57 -5.47 2.00e+00 2.50e-01 7.48e+00 angle pdb=" CB MET F 557 " pdb=" CG MET F 557 " pdb=" SD MET F 557 " ideal model delta sigma weight residual 112.70 120.39 -7.69 3.00e+00 1.11e-01 6.58e+00 angle pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sigma weight residual 113.21 118.73 -5.52 3.00e+00 1.11e-01 3.39e+00 angle pdb=" N ASP F 335 " pdb=" CA ASP F 335 " pdb=" C ASP F 335 " ideal model delta sigma weight residual 109.81 113.87 -4.06 2.21e+00 2.05e-01 3.37e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3477 17.40 - 34.80: 355 34.80 - 52.20: 66 52.20 - 69.60: 14 69.60 - 87.00: 8 Dihedral angle restraints: 3920 sinusoidal: 1581 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 43.92 49.08 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS F 133 " pdb=" SG CYS F 133 " pdb=" SG CYS F 141 " pdb=" CB CYS F 141 " ideal model delta sinusoidal sigma weight residual -86.00 -120.26 34.26 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA PRO F 146 " pdb=" C PRO F 146 " pdb=" N GLY F 147 " pdb=" CA GLY F 147 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 988 0.106 - 0.212: 19 0.212 - 0.318: 1 0.318 - 0.424: 0 0.424 - 0.530: 1 Chirality restraints: 1009 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.27 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1006 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 72 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.68e+00 pdb=" C PHE F 72 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE F 72 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU F 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 283 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO F 284 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 284 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 284 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 234 " -0.019 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO F 235 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " -0.017 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 462 2.74 - 3.28: 6514 3.28 - 3.82: 10579 3.82 - 4.36: 12110 4.36 - 4.90: 21228 Nonbonded interactions: 50893 Sorted by model distance: nonbonded pdb=" OG1 THR F 20 " pdb=" OE1 GLU F 23 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.256 3.040 nonbonded pdb=" NE1 TRP F 271 " pdb=" O SER F 502 " model vdw 2.324 3.120 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.335 3.040 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.335 3.120 ... (remaining 50888 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 : 0.003 0.065 6839 Z= 0.151 Angle : 0.560 9.242 9321 Z= 0.271 Chirality : 0.045 0.530 1009 Planarity : 0.003 0.031 1182 Dihedral : 14.424 87.003 2399 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 793 helix: 0.79 (0.29), residues: 343 sheet: 1.04 (0.79), residues: 47 loop : -1.35 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 346 TYR 0.006 0.001 TYR F 50 PHE 0.008 0.001 PHE F 369 TRP 0.010 0.001 TRP F 165 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 6819) covalent geometry : angle 0.53821 / 0.27 ( 9268) SS BOND : bond 0.00329 / 0.17 ( 7) SS BOND : angle 0.94537 / 0.57 ( 14) hydrogen bonds : bond 0.16960 / 11.39 ( 261) hydrogen bonds : angle 6.01990 / 4.16 ( 735) link_BETA1-4 : bond 0.00684 / 0.42 ( 5) link_BETA1-4 : angle 1.47524 / 1.05 ( 15) link_NAG-ASN : bond 0.00417 / 0.16 ( 8) link_NAG-ASN : angle 2.81682 / 2.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.178 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.5484 time to fit residues: 28.8143 Evaluate side-chains 38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 overall best weight: 0.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN F 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050494 restraints weight = 19717.668| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.52 r_work: 0.2729 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6839 Z= 0.104 Angle : 0.560 9.331 9321 Z= 0.264 Chirality : 0.043 0.337 1009 Planarity : 0.003 0.029 1182 Dihedral : 3.702 21.943 866 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.14 % Allowed : 6.57 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 793 helix: 0.95 (0.29), residues: 356 sheet: 0.99 (0.78), residues: 47 loop : -1.15 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 161 TYR 0.009 0.001 TYR A 369 PHE 0.007 0.001 PHE A 392 TRP 0.010 0.001 TRP F 69 HIS 0.004 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 6819) covalent geometry : angle 0.54337 / 0.26 ( 9268) SS BOND : bond 0.00309 / 0.15 ( 7) SS BOND : angle 0.94175 / 0.58 ( 14) hydrogen bonds : bond 0.04594 / 2.79 ( 261) hydrogen bonds : angle 4.45854 / 3.05 ( 735) link_BETA1-4 : bond 0.00999 / 0.63 ( 5) link_BETA1-4 : angle 1.13627 / 0.76 ( 15) link_NAG-ASN : bond 0.00546 / 0.19 ( 8) link_NAG-ASN : angle 2.50586 / 1.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.283 Fit side-chains REVERT: A 346 ARG cc_start: 0.8735 (pmm-80) cc_final: 0.8305 (pmm-80) REVERT: A 382 VAL cc_start: 0.9169 (m) cc_final: 0.8940 (p) REVERT: A 386 LYS cc_start: 0.9066 (tppp) cc_final: 0.8421 (tmmm) outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 0.6821 time to fit residues: 31.5115 Evaluate side-chains 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 522 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.047299 restraints weight = 19846.786| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.51 r_work: 0.2644 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6839 Z= 0.169 Angle : 0.587 9.557 9321 Z= 0.279 Chirality : 0.045 0.364 1009 Planarity : 0.003 0.031 1182 Dihedral : 3.919 21.011 866 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.71 % Allowed : 9.43 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.29), residues: 793 helix: 0.88 (0.29), residues: 362 sheet: 0.93 (0.77), residues: 49 loop : -1.09 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 460 TYR 0.011 0.001 TYR F 385 PHE 0.013 0.001 PHE F 523 TRP 0.008 0.001 TRP F 165 HIS 0.005 0.001 HIS F 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 6819) covalent geometry : angle 0.57102 / 0.28 ( 9268) SS BOND : bond 0.00418 / 0.21 ( 7) SS BOND : angle 1.06621 / 0.68 ( 14) hydrogen bonds : bond 0.05074 / 3.10 ( 261) hydrogen bonds : angle 4.21980 / 2.85 ( 735) link_BETA1-4 : bond 0.00637 / 0.40 ( 5) link_BETA1-4 : angle 1.15358 / 0.83 ( 15) link_NAG-ASN : bond 0.00387 / 0.13 ( 8) link_NAG-ASN : angle 2.52403 / 1.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.275 Fit side-chains REVERT: A 386 LYS cc_start: 0.9116 (tppp) cc_final: 0.8497 (tmmm) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.7493 time to fit residues: 32.2754 Evaluate side-chains 38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.047720 restraints weight = 20047.568| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.43 r_work: 0.2661 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6839 Z= 0.118 Angle : 0.557 9.552 9321 Z= 0.261 Chirality : 0.044 0.339 1009 Planarity : 0.003 0.027 1182 Dihedral : 3.887 21.058 866 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.14 % Allowed : 10.86 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 793 helix: 1.07 (0.29), residues: 355 sheet: 1.07 (0.79), residues: 47 loop : -1.10 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.009 0.001 TYR F 50 PHE 0.009 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6819) covalent geometry : angle 0.54094 / 0.26 ( 9268) SS BOND : bond 0.00473 / 0.28 ( 7) SS BOND : angle 1.01343 / 0.65 ( 14) hydrogen bonds : bond 0.04326 / 2.60 ( 261) hydrogen bonds : angle 4.06560 / 2.75 ( 735) link_BETA1-4 : bond 0.00703 / 0.44 ( 5) link_BETA1-4 : angle 1.10667 / 0.80 ( 15) link_NAG-ASN : bond 0.00333 / 0.13 ( 8) link_NAG-ASN : angle 2.44885 / 1.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.280 Fit side-chains REVERT: A 386 LYS cc_start: 0.9139 (tppp) cc_final: 0.8395 (tmmm) outliers start: 8 outliers final: 1 residues processed: 42 average time/residue: 0.7178 time to fit residues: 31.6853 Evaluate side-chains 38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.0000 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.048044 restraints weight = 20062.737| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.44 r_work: 0.2670 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6839 Z= 0.106 Angle : 0.546 9.808 9321 Z= 0.254 Chirality : 0.043 0.326 1009 Planarity : 0.003 0.026 1182 Dihedral : 3.833 20.623 866 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.86 % Allowed : 11.86 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.30), residues: 793 helix: 1.20 (0.29), residues: 355 sheet: 1.09 (0.79), residues: 47 loop : -1.08 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.007 0.001 TYR F 385 PHE 0.009 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 6819) covalent geometry : angle 0.53066 / 0.25 ( 9268) SS BOND : bond 0.00380 / 0.20 ( 7) SS BOND : angle 0.95654 / 0.62 ( 14) hydrogen bonds : bond 0.03964 / 2.37 ( 261) hydrogen bonds : angle 3.96222 / 2.67 ( 735) link_BETA1-4 : bond 0.00679 / 0.43 ( 5) link_BETA1-4 : angle 1.09252 / 0.79 ( 15) link_NAG-ASN : bond 0.00323 / 0.13 ( 8) link_NAG-ASN : angle 2.37571 / 1.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.267 Fit side-chains REVERT: A 386 LYS cc_start: 0.9168 (tppp) cc_final: 0.8567 (tmmm) REVERT: F 249 MET cc_start: 0.8355 (ttt) cc_final: 0.7545 (tmm) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.7062 time to fit residues: 31.9158 Evaluate side-chains 38 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS F 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.047378 restraints weight = 20128.853| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.63 r_work: 0.2597 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6839 Z= 0.111 Angle : 0.556 9.945 9321 Z= 0.258 Chirality : 0.043 0.323 1009 Planarity : 0.003 0.026 1182 Dihedral : 3.816 20.524 866 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.00 % Allowed : 12.71 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.30), residues: 793 helix: 1.26 (0.29), residues: 354 sheet: 1.12 (0.79), residues: 47 loop : -1.09 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.007 0.001 TYR F 385 PHE 0.009 0.001 PHE F 369 TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6819) covalent geometry : angle 0.54138 / 0.26 ( 9268) SS BOND : bond 0.00443 / 0.26 ( 7) SS BOND : angle 0.94308 / 0.60 ( 14) hydrogen bonds : bond 0.03930 / 2.35 ( 261) hydrogen bonds : angle 3.90010 / 2.63 ( 735) link_BETA1-4 : bond 0.00697 / 0.44 ( 5) link_BETA1-4 : angle 1.11715 / 0.81 ( 15) link_NAG-ASN : bond 0.00302 / 0.12 ( 8) link_NAG-ASN : angle 2.34015 / 1.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.178 Fit side-chains REVERT: A 386 LYS cc_start: 0.9117 (tppp) cc_final: 0.8364 (tmmm) REVERT: F 323 MET cc_start: 0.6935 (mtp) cc_final: 0.6657 (mtm) outliers start: 7 outliers final: 2 residues processed: 43 average time/residue: 0.6555 time to fit residues: 29.7383 Evaluate side-chains 39 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS F 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.058830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.047539 restraints weight = 19949.105| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.62 r_work: 0.2605 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6839 Z= 0.107 Angle : 0.562 10.535 9321 Z= 0.261 Chirality : 0.043 0.315 1009 Planarity : 0.003 0.026 1182 Dihedral : 3.784 20.228 866 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.71 % Allowed : 13.29 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.30), residues: 793 helix: 1.27 (0.29), residues: 353 sheet: 1.13 (0.79), residues: 47 loop : -1.09 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.007 0.001 TYR F 50 PHE 0.009 0.001 PHE F 369 TRP 0.008 0.001 TRP F 165 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6819) covalent geometry : angle 0.54823 / 0.26 ( 9268) SS BOND : bond 0.00354 / 0.17 ( 7) SS BOND : angle 0.93207 / 0.61 ( 14) hydrogen bonds : bond 0.03781 / 2.26 ( 261) hydrogen bonds : angle 3.87867 / 2.62 ( 735) link_BETA1-4 : bond 0.00697 / 0.43 ( 5) link_BETA1-4 : angle 1.11716 / 0.80 ( 15) link_NAG-ASN : bond 0.00304 / 0.13 ( 8) link_NAG-ASN : angle 2.29974 / 1.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.266 Fit side-chains REVERT: A 346 ARG cc_start: 0.8593 (pmm-80) cc_final: 0.8098 (pmm-80) REVERT: A 386 LYS cc_start: 0.9136 (tppp) cc_final: 0.8500 (tmmm) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.6524 time to fit residues: 28.9418 Evaluate side-chains 39 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 46 optimal weight: 0.0010 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.047711 restraints weight = 20084.797| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.63 r_work: 0.2610 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6839 Z= 0.105 Angle : 0.566 10.576 9321 Z= 0.262 Chirality : 0.043 0.310 1009 Planarity : 0.003 0.026 1182 Dihedral : 3.756 20.172 866 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.86 % Allowed : 13.43 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.30), residues: 793 helix: 1.28 (0.29), residues: 354 sheet: 1.13 (0.79), residues: 47 loop : -1.06 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.007 0.001 TYR F 385 PHE 0.009 0.001 PHE F 369 TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 6819) covalent geometry : angle 0.55271 / 0.26 ( 9268) SS BOND : bond 0.00355 / 0.17 ( 7) SS BOND : angle 0.90915 / 0.58 ( 14) hydrogen bonds : bond 0.03669 / 2.19 ( 261) hydrogen bonds : angle 3.84487 / 2.59 ( 735) link_BETA1-4 : bond 0.00688 / 0.43 ( 5) link_BETA1-4 : angle 1.11574 / 0.81 ( 15) link_NAG-ASN : bond 0.00296 / 0.12 ( 8) link_NAG-ASN : angle 2.27381 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.270 Fit side-chains REVERT: A 386 LYS cc_start: 0.9132 (tppp) cc_final: 0.8396 (tmmm) REVERT: A 390 LEU cc_start: 0.9529 (pp) cc_final: 0.9306 (pt) REVERT: F 249 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7866 (mtp) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 0.6800 time to fit residues: 30.1411 Evaluate side-chains 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 249 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.056450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.045156 restraints weight = 20445.284| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.64 r_work: 0.2551 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6839 Z= 0.183 Angle : 0.628 11.060 9321 Z= 0.298 Chirality : 0.045 0.338 1009 Planarity : 0.003 0.026 1182 Dihedral : 4.081 19.625 866 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.71 % Allowed : 13.71 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 793 helix: 1.12 (0.29), residues: 354 sheet: 0.94 (0.77), residues: 49 loop : -1.15 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.012 0.001 TYR A 453 PHE 0.012 0.001 PHE F 523 TRP 0.008 0.001 TRP F 165 HIS 0.005 0.001 HIS F 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 6819) covalent geometry : angle 0.61371 / 0.29 ( 9268) SS BOND : bond 0.00472 / 0.24 ( 7) SS BOND : angle 1.03217 / 0.66 ( 14) hydrogen bonds : bond 0.04951 / 3.02 ( 261) hydrogen bonds : angle 4.03089 / 2.72 ( 735) link_BETA1-4 : bond 0.00679 / 0.43 ( 5) link_BETA1-4 : angle 1.18373 / 0.90 ( 15) link_NAG-ASN : bond 0.00293 / 0.11 ( 8) link_NAG-ASN : angle 2.47556 / 1.76 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.215 Fit side-chains REVERT: A 346 ARG cc_start: 0.8652 (pmm-80) cc_final: 0.8169 (pmm-80) REVERT: A 386 LYS cc_start: 0.9157 (tppp) cc_final: 0.8412 (tmmm) REVERT: F 249 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7908 (mtp) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.5949 time to fit residues: 28.2421 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.046122 restraints weight = 20035.041| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.60 r_work: 0.2580 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6839 Z= 0.132 Angle : 0.608 10.623 9321 Z= 0.285 Chirality : 0.044 0.317 1009 Planarity : 0.003 0.046 1182 Dihedral : 4.074 25.765 866 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.57 % Allowed : 14.29 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.29), residues: 793 helix: 1.18 (0.29), residues: 354 sheet: 1.12 (0.78), residues: 49 loop : -1.10 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.008 0.001 TYR F 385 PHE 0.010 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6819) covalent geometry : angle 0.59267 / 0.28 ( 9268) SS BOND : bond 0.00406 / 0.20 ( 7) SS BOND : angle 1.41928 / 0.92 ( 14) hydrogen bonds : bond 0.04314 / 2.58 ( 261) hydrogen bonds : angle 3.97797 / 2.69 ( 735) link_BETA1-4 : bond 0.00642 / 0.41 ( 5) link_BETA1-4 : angle 1.11924 / 0.83 ( 15) link_NAG-ASN : bond 0.00273 / 0.12 ( 8) link_NAG-ASN : angle 2.42228 / 1.73 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.293 Fit side-chains REVERT: A 346 ARG cc_start: 0.8632 (pmm-80) cc_final: 0.8133 (pmm-80) REVERT: A 386 LYS cc_start: 0.9156 (tppp) cc_final: 0.8567 (tmmm) REVERT: F 249 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7832 (mtp) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.6839 time to fit residues: 29.6144 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.046423 restraints weight = 19946.365| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.59 r_work: 0.2587 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6839 Z= 0.126 Angle : 0.600 10.994 9321 Z= 0.279 Chirality : 0.044 0.311 1009 Planarity : 0.003 0.039 1182 Dihedral : 4.030 25.432 866 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.57 % Allowed : 13.86 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.30), residues: 793 helix: 1.21 (0.29), residues: 354 sheet: 1.09 (0.78), residues: 49 loop : -1.04 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.008 0.001 TYR F 385 PHE 0.009 0.001 PHE F 369 TRP 0.008 0.001 TRP F 165 HIS 0.003 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6819) covalent geometry : angle 0.58515 / 0.28 ( 9268) SS BOND : bond 0.00393 / 0.19 ( 7) SS BOND : angle 1.21537 / 0.80 ( 14) hydrogen bonds : bond 0.04103 / 2.46 ( 261) hydrogen bonds : angle 3.93511 / 2.66 ( 735) link_BETA1-4 : bond 0.00663 / 0.42 ( 5) link_BETA1-4 : angle 1.14833 / 0.85 ( 15) link_NAG-ASN : bond 0.00284 / 0.12 ( 8) link_NAG-ASN : angle 2.38508 / 1.72 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.68 seconds wall clock time: 32 minutes 12.83 seconds (1932.83 seconds total)