Starting phenix.real_space_refine on Tue Mar 3 15:46:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v84_31789/03_2026/7v84_31789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v84_31789/03_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_31789/03_2026/7v84_31789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v84_31789/03_2026/7v84_31789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v84_31789/03_2026/7v84_31789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v84_31789/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 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: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.36, per 1000 atoms: 0.20 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: 0.74 Conformation dependent library (CDL) restraints added in 254.1 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: 0.15 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: 0.88 Time building geometry restraints manager: 0.89 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 - 23.59: 3897 23.59 - 47.17: 245 47.17 - 70.76: 26 70.76 - 94.35: 10 94.35 - 117.94: 15 Dihedral angle restraints: 4193 sinusoidal: 1854 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 4190 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: 4.630 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.060 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 16.314 117.936 2672 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 covalent geometry : bond 0.00304 ( 6819) covalent geometry : angle 0.53821 ( 9268) SS BOND : bond 0.00329 ( 7) SS BOND : angle 0.94537 ( 14) hydrogen bonds : bond 0.16960 ( 261) hydrogen bonds : angle 6.01990 ( 735) link_BETA1-4 : bond 0.00684 ( 5) link_BETA1-4 : angle 1.47524 ( 15) link_NAG-ASN : bond 0.00417 ( 8) link_NAG-ASN : angle 2.81682 ( 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 : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.6186 time to fit residues: 32.4742 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 : 0.244 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3118 r_free = 0.3118 target = 0.061438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050563 restraints weight = 19666.105| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.42 r_work: 0.2739 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6839 Z= 0.103 Angle : 0.590 10.210 9321 Z= 0.272 Chirality : 0.043 0.381 1009 Planarity : 0.003 0.028 1182 Dihedral : 10.307 103.780 1139 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.00 % Allowed : 6.71 % 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: 0.94 (0.29), residues: 356 sheet: 0.99 (0.78), residues: 47 loop : -1.13 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.010 0.001 TYR A 369 PHE 0.007 0.001 PHE F 369 TRP 0.010 0.001 TRP F 69 HIS 0.004 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 6819) covalent geometry : angle 0.57267 ( 9268) SS BOND : bond 0.00323 ( 7) SS BOND : angle 0.95386 ( 14) hydrogen bonds : bond 0.04269 ( 261) hydrogen bonds : angle 4.40928 ( 735) link_BETA1-4 : bond 0.00605 ( 5) link_BETA1-4 : angle 1.50576 ( 15) link_NAG-ASN : bond 0.00502 ( 8) link_NAG-ASN : angle 2.58666 ( 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: 7 poor density : 41 time to evaluate : 0.172 Fit side-chains REVERT: A 382 VAL cc_start: 0.9177 (m) cc_final: 0.8952 (p) REVERT: A 386 LYS cc_start: 0.9082 (tppp) cc_final: 0.8425 (tmmm) outliers start: 7 outliers final: 2 residues processed: 45 average time/residue: 0.6339 time to fit residues: 29.8742 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** F 401 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 = 0.3081 r_free = 0.3081 target = 0.059605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.048714 restraints weight = 19638.481| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.43 r_work: 0.2690 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6839 Z= 0.122 Angle : 0.562 9.584 9321 Z= 0.261 Chirality : 0.043 0.395 1009 Planarity : 0.003 0.029 1182 Dihedral : 7.878 97.088 1139 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.86 % Allowed : 9.43 % Favored : 89.71 % 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: 0.03 (0.29), residues: 793 helix: 1.08 (0.29), residues: 350 sheet: 1.03 (0.79), residues: 47 loop : -1.10 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 460 TYR 0.009 0.001 TYR F 385 PHE 0.011 0.001 PHE F 523 TRP 0.008 0.001 TRP F 165 HIS 0.004 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6819) covalent geometry : angle 0.54286 ( 9268) SS BOND : bond 0.00356 ( 7) SS BOND : angle 0.97758 ( 14) hydrogen bonds : bond 0.04379 ( 261) hydrogen bonds : angle 4.12760 ( 735) link_BETA1-4 : bond 0.00710 ( 5) link_BETA1-4 : angle 1.78255 ( 15) link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.53552 ( 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 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.289 Fit side-chains REVERT: A 386 LYS cc_start: 0.9099 (tppp) cc_final: 0.8459 (tmmm) outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.6902 time to fit residues: 30.4542 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 : 0.259 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.048126 restraints weight = 20046.529| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.52 r_work: 0.2668 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6839 Z= 0.118 Angle : 0.563 9.632 9321 Z= 0.261 Chirality : 0.043 0.387 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.163 87.317 1139 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.00 % Allowed : 11.00 % 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: 0.14 (0.30), residues: 793 helix: 1.18 (0.29), residues: 355 sheet: 1.08 (0.80), 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 0.009 0.001 TYR F 385 PHE 0.010 0.001 PHE F 369 TRP 0.008 0.001 TRP F 165 HIS 0.005 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6819) covalent geometry : angle 0.54156 ( 9268) SS BOND : bond 0.00370 ( 7) SS BOND : angle 0.98052 ( 14) hydrogen bonds : bond 0.04119 ( 261) hydrogen bonds : angle 3.97229 ( 735) link_BETA1-4 : bond 0.00559 ( 5) link_BETA1-4 : angle 2.11854 ( 15) link_NAG-ASN : bond 0.00361 ( 8) link_NAG-ASN : angle 2.54295 ( 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 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.213 Fit side-chains REVERT: A 386 LYS cc_start: 0.9176 (tppp) cc_final: 0.8392 (tmmm) REVERT: A 390 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9324 (pt) REVERT: F 249 MET cc_start: 0.8348 (ttt) cc_final: 0.8078 (mtp) REVERT: F 376 MET cc_start: 0.9281 (tpp) cc_final: 0.9079 (tpp) outliers start: 7 outliers final: 1 residues processed: 41 average time/residue: 0.6914 time to fit residues: 29.7847 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 : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU 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: 0.0010 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.048125 restraints weight = 20038.062| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.46 r_work: 0.2674 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6839 Z= 0.105 Angle : 0.553 9.786 9321 Z= 0.255 Chirality : 0.042 0.376 1009 Planarity : 0.003 0.025 1182 Dihedral : 7.005 82.295 1139 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.86 % Allowed : 12.71 % Favored : 86.43 % 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: 0.20 (0.30), residues: 793 helix: 1.24 (0.29), residues: 356 sheet: 1.10 (0.80), residues: 47 loop : -1.07 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 covalent geometry : bond 0.00239 ( 6819) covalent geometry : angle 0.53250 ( 9268) SS BOND : bond 0.00348 ( 7) SS BOND : angle 0.92815 ( 14) hydrogen bonds : bond 0.03868 ( 261) hydrogen bonds : angle 3.90860 ( 735) link_BETA1-4 : bond 0.00558 ( 5) link_BETA1-4 : angle 2.08745 ( 15) link_NAG-ASN : bond 0.00343 ( 8) link_NAG-ASN : angle 2.48117 ( 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 : 0.259 Fit side-chains REVERT: A 386 LYS cc_start: 0.9183 (tppp) cc_final: 0.8366 (tmmm) REVERT: A 390 LEU cc_start: 0.9531 (pp) cc_final: 0.9299 (pt) outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.6776 time to fit residues: 29.9053 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 : 0.260 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2957 r_free = 0.2957 target = 0.056118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.044807 restraints weight = 20337.110| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.64 r_work: 0.2542 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6839 Z= 0.197 Angle : 0.625 10.613 9321 Z= 0.297 Chirality : 0.045 0.405 1009 Planarity : 0.003 0.028 1182 Dihedral : 7.262 81.716 1139 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.43 % Allowed : 12.71 % Favored : 85.86 % 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: -0.01 (0.29), residues: 793 helix: 1.06 (0.29), residues: 356 sheet: 0.95 (0.77), residues: 49 loop : -1.17 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.014 0.001 TYR F 385 PHE 0.014 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 covalent geometry : bond 0.00459 ( 6819) covalent geometry : angle 0.60452 ( 9268) SS BOND : bond 0.00513 ( 7) SS BOND : angle 1.07174 ( 14) hydrogen bonds : bond 0.05264 ( 261) hydrogen bonds : angle 4.07572 ( 735) link_BETA1-4 : bond 0.00558 ( 5) link_BETA1-4 : angle 2.12153 ( 15) link_NAG-ASN : bond 0.00336 ( 8) link_NAG-ASN : angle 2.67307 ( 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 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.267 Fit side-chains REVERT: A 386 LYS cc_start: 0.9118 (tppp) cc_final: 0.8357 (tmmm) REVERT: F 249 MET cc_start: 0.8322 (ttt) cc_final: 0.8045 (mtp) outliers start: 10 outliers final: 2 residues processed: 46 average time/residue: 0.6147 time to fit residues: 30.0200 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 : 0.255 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.044759 restraints weight = 20164.400| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.61 r_work: 0.2541 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6839 Z= 0.184 Angle : 0.615 10.176 9321 Z= 0.291 Chirality : 0.045 0.391 1009 Planarity : 0.003 0.025 1182 Dihedral : 7.234 80.009 1139 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.14 % Allowed : 13.57 % Favored : 85.29 % 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: -0.13 (0.29), residues: 793 helix: 0.89 (0.28), residues: 373 sheet: 0.89 (0.76), residues: 51 loop : -1.27 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.011 0.001 TYR A 453 PHE 0.012 0.001 PHE F 369 TRP 0.010 0.001 TRP F 477 HIS 0.005 0.001 HIS F 505 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6819) covalent geometry : angle 0.59251 ( 9268) SS BOND : bond 0.00447 ( 7) SS BOND : angle 1.34668 ( 14) hydrogen bonds : bond 0.04960 ( 261) hydrogen bonds : angle 4.10687 ( 735) link_BETA1-4 : bond 0.00515 ( 5) link_BETA1-4 : angle 2.15464 ( 15) link_NAG-ASN : bond 0.00282 ( 8) link_NAG-ASN : angle 2.69907 ( 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 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.247 Fit side-chains REVERT: A 386 LYS cc_start: 0.9127 (tppp) cc_final: 0.8479 (tmmm) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 0.5918 time to fit residues: 29.1996 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.057105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.045794 restraints weight = 20142.074| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.61 r_work: 0.2568 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6839 Z= 0.124 Angle : 0.595 10.555 9321 Z= 0.279 Chirality : 0.043 0.371 1009 Planarity : 0.003 0.036 1182 Dihedral : 7.115 77.610 1139 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.71 % Allowed : 14.14 % 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: 0.04 (0.30), residues: 793 helix: 1.08 (0.29), residues: 361 sheet: 1.05 (0.78), residues: 49 loop : -1.16 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.008 0.001 TYR F 50 PHE 0.010 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6819) covalent geometry : angle 0.57241 ( 9268) SS BOND : bond 0.00442 ( 7) SS BOND : angle 1.22587 ( 14) hydrogen bonds : bond 0.04299 ( 261) hydrogen bonds : angle 3.98730 ( 735) link_BETA1-4 : bond 0.00535 ( 5) link_BETA1-4 : angle 2.22084 ( 15) link_NAG-ASN : bond 0.00287 ( 8) link_NAG-ASN : angle 2.61321 ( 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 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.251 Fit side-chains REVERT: A 346 ARG cc_start: 0.8659 (pmm-80) cc_final: 0.8183 (pmm-80) REVERT: A 386 LYS cc_start: 0.9135 (tppp) cc_final: 0.8375 (tmmm) REVERT: F 249 MET cc_start: 0.8233 (ttt) cc_final: 0.7497 (tmm) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.6334 time to fit residues: 28.7220 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.055790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.044537 restraints weight = 20462.213| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.63 r_work: 0.2533 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6839 Z= 0.186 Angle : 0.631 10.828 9321 Z= 0.300 Chirality : 0.045 0.389 1009 Planarity : 0.003 0.030 1182 Dihedral : 7.263 77.546 1139 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.43 % Allowed : 14.86 % Favored : 84.71 % 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: -0.11 (0.29), residues: 793 helix: 0.93 (0.28), residues: 367 sheet: 0.92 (0.76), residues: 51 loop : -1.25 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.012 0.001 TYR A 453 PHE 0.011 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.005 0.001 HIS F 505 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6819) covalent geometry : angle 0.60936 ( 9268) SS BOND : bond 0.00474 ( 7) SS BOND : angle 1.26845 ( 14) hydrogen bonds : bond 0.05017 ( 261) hydrogen bonds : angle 4.08834 ( 735) link_BETA1-4 : bond 0.00507 ( 5) link_BETA1-4 : angle 2.22830 ( 15) link_NAG-ASN : bond 0.00295 ( 8) link_NAG-ASN : angle 2.70972 ( 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 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.202 Fit side-chains REVERT: A 386 LYS cc_start: 0.9127 (tppp) cc_final: 0.8452 (tmmm) REVERT: F 249 MET cc_start: 0.8380 (ttt) cc_final: 0.7634 (tmm) REVERT: F 455 MET cc_start: 0.8749 (tmm) cc_final: 0.8401 (tmm) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.6467 time to fit residues: 27.1579 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 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: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.056763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.045490 restraints weight = 20018.326| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.60 r_work: 0.2562 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6839 Z= 0.133 Angle : 0.602 10.305 9321 Z= 0.283 Chirality : 0.044 0.369 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.122 75.018 1139 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.57 % Allowed : 14.57 % Favored : 84.86 % 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: 0.01 (0.30), residues: 793 helix: 1.02 (0.28), residues: 367 sheet: 1.10 (0.78), residues: 49 loop : -1.19 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.008 0.001 TYR A 453 PHE 0.010 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 505 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6819) covalent geometry : angle 0.57951 ( 9268) SS BOND : bond 0.00425 ( 7) SS BOND : angle 1.17658 ( 14) hydrogen bonds : bond 0.04353 ( 261) hydrogen bonds : angle 4.00477 ( 735) link_BETA1-4 : bond 0.00513 ( 5) link_BETA1-4 : angle 2.27022 ( 15) link_NAG-ASN : bond 0.00287 ( 8) link_NAG-ASN : angle 2.62373 ( 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 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.265 Fit side-chains REVERT: A 346 ARG cc_start: 0.8655 (pmm-80) cc_final: 0.8177 (pmm-80) REVERT: A 386 LYS cc_start: 0.9123 (tppp) cc_final: 0.8324 (tmmm) REVERT: F 249 MET cc_start: 0.8382 (ttt) cc_final: 0.7648 (tmm) REVERT: F 332 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8670 (ttp) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.6810 time to fit residues: 28.5892 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 : 0.253 ------------------------------------------------------------------------------- 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 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.046632 restraints weight = 19848.620| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.58 r_work: 0.2582 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6839 Z= 0.108 Angle : 0.587 11.108 9321 Z= 0.272 Chirality : 0.043 0.357 1009 Planarity : 0.003 0.026 1182 Dihedral : 6.894 69.768 1139 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.57 % Allowed : 14.86 % Favored : 84.57 % 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: 0.21 (0.30), residues: 793 helix: 1.27 (0.29), residues: 354 sheet: 1.16 (0.78), residues: 49 loop : -1.08 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 460 TYR 0.007 0.001 TYR F 183 PHE 0.008 0.001 PHE F 369 TRP 0.009 0.001 TRP F 477 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6819) covalent geometry : angle 0.56528 ( 9268) SS BOND : bond 0.00395 ( 7) SS BOND : angle 1.11946 ( 14) hydrogen bonds : bond 0.03756 ( 261) hydrogen bonds : angle 3.91437 ( 735) link_BETA1-4 : bond 0.00513 ( 5) link_BETA1-4 : angle 2.36277 ( 15) link_NAG-ASN : bond 0.00322 ( 8) link_NAG-ASN : angle 2.52449 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.38 seconds wall clock time: 30 minutes 50.26 seconds (1850.26 seconds total)