Starting phenix.real_space_refine on Tue Feb 3 20:09:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kra_62524/02_2026/9kra_62524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kra_62524/02_2026/9kra_62524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kra_62524/02_2026/9kra_62524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kra_62524/02_2026/9kra_62524.map" model { file = "/net/cci-nas-00/data/ceres_data/9kra_62524/02_2026/9kra_62524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kra_62524/02_2026/9kra_62524.cif" } resolution = 2.8 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= 0.005 sd= 0.145 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 42 5.16 5 C 4201 2.51 5 N 1070 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6607 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1545 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Chain: "B" Number of atoms: 4852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4852 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 26, 'TRANS': 563} 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: "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 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "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 Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6607 At special positions: 0 Unit cell: (82.612, 90.221, 120.657, 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 42 16.00 O 1294 8.00 N 1070 7.00 C 4201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 541 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 601 " - " ASN A 495 " " NAG B 901 " - " ASN B 279 " " NAG B 902 " - " ASN B 431 " " NAG C 1 " - " ASN A 418 " " NAG D 1 " - " ASN B 53 " " NAG E 1 " - " ASN B 103 " " NAG F 1 " - " ASN B 215 " " NAG G 1 " - " ASN B 386 " " NAG H 1 " - " ASN B 545 " Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 239.8 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 46.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.586A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.588A pdb=" N ALA A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 443' Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.548A pdb=" N MET A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 461 " --> pdb=" O THR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 461' Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'B' and resid 20 through 52 removed outlier: 3.650A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 80 removed outlier: 3.762A pdb=" N GLU B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.606A pdb=" N ILE B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.740A pdb=" N THR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.920A pdb=" N ASP B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.681A pdb=" N ARG B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 4.205A pdb=" N GLU B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 Processing helix chain 'B' and resid 220 through 251 Proline residue: B 234 - end of helix removed outlier: 3.732A pdb=" N LYS B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.835A pdb=" N VAL B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 removed outlier: 3.509A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B 372 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.518A pdb=" N LYS B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 3.504A pdb=" N GLU B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.634A pdb=" N ARG B 481 " --> pdb=" O TRP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 removed outlier: 3.577A pdb=" N SER B 501 " --> pdb=" O ASP B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.581A pdb=" N TYR B 514 " --> pdb=" O PHE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.777A pdb=" N PHE B 522 " --> pdb=" O THR B 518 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 527 " --> pdb=" O GLN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.638A pdb=" N LYS B 540 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.858A pdb=" N GLY B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 574 removed outlier: 3.902A pdb=" N ILE B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.506A pdb=" N TYR B 586 " --> pdb=" O PRO B 582 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 587' Processing helix chain 'B' and resid 587 through 599 removed outlier: 3.675A pdb=" N LYS B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 409 removed outlier: 3.637A pdb=" N LYS A 408 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 448 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 574 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.817A pdb=" N THR A 555 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS A 511 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 553 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 552 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'B' and resid 261 through 262 removed outlier: 6.133A pdb=" N LEU B 261 " --> pdb=" O VAL B 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 346 through 351 removed outlier: 3.528A pdb=" N ARG B 356 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 636 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: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1188 1.32 - 1.45: 1881 1.45 - 1.57: 3643 1.57 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6780 Sorted by residual: bond pdb=" C ASN B 321 " pdb=" O ASN B 321 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.35e-02 5.49e+03 6.44e+00 bond pdb=" C ASN B 38 " pdb=" O ASN B 38 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" N ASN B 38 " pdb=" CA ASN B 38 " ideal model delta sigma weight residual 1.458 1.427 0.031 1.30e-02 5.92e+03 5.68e+00 bond pdb=" CA ASN B 321 " pdb=" C ASN B 321 " ideal model delta sigma weight residual 1.528 1.495 0.032 1.37e-02 5.33e+03 5.61e+00 bond pdb=" C GLY A 470 " pdb=" O GLY A 470 " ideal model delta sigma weight residual 1.234 1.204 0.030 1.36e-02 5.41e+03 4.84e+00 ... (remaining 6775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 8766 1.58 - 3.15: 373 3.15 - 4.73: 39 4.73 - 6.31: 13 6.31 - 7.89: 7 Bond angle restraints: 9198 Sorted by residual: angle pdb=" C GLN B 102 " pdb=" N ASN B 103 " pdb=" CA ASN B 103 " ideal model delta sigma weight residual 120.38 126.28 -5.90 1.37e+00 5.33e-01 1.85e+01 angle pdb=" N ASN B 103 " pdb=" CA ASN B 103 " pdb=" C ASN B 103 " ideal model delta sigma weight residual 111.33 116.18 -4.85 1.21e+00 6.83e-01 1.61e+01 angle pdb=" N ASP A 459 " pdb=" CA ASP A 459 " pdb=" C ASP A 459 " ideal model delta sigma weight residual 111.14 106.89 4.25 1.08e+00 8.57e-01 1.55e+01 angle pdb=" C LEU B 284 " pdb=" N GLU B 285 " pdb=" CA GLU B 285 " ideal model delta sigma weight residual 120.60 126.78 -6.18 1.60e+00 3.91e-01 1.49e+01 angle pdb=" C GLN B 101 " pdb=" N GLN B 102 " pdb=" CA GLN B 102 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 ... (remaining 9193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3833 17.74 - 35.48: 271 35.48 - 53.21: 104 53.21 - 70.95: 26 70.95 - 88.69: 11 Dihedral angle restraints: 4245 sinusoidal: 1920 harmonic: 2325 Sorted by residual: dihedral pdb=" CA GLN B 101 " pdb=" C GLN B 101 " pdb=" N GLN B 102 " pdb=" CA GLN B 102 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PRO B 135 " pdb=" CA PRO B 135 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET B 407 " pdb=" C MET B 407 " pdb=" N SER B 408 " pdb=" CA SER B 408 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 757 0.053 - 0.107: 220 0.107 - 0.160: 35 0.160 - 0.213: 5 0.213 - 0.266: 1 Chirality restraints: 1018 Sorted by residual: chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 431 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA GLN B 102 " pdb=" N GLN B 102 " pdb=" C GLN B 102 " pdb=" CB GLN B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1015 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 465 " 0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 466 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 394 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO A 395 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 233 " 0.041 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO B 234 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.034 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1866 2.80 - 3.33: 5215 3.33 - 3.85: 10361 3.85 - 4.38: 12264 4.38 - 4.90: 21810 Nonbonded interactions: 51516 Sorted by model distance: nonbonded pdb=" O GLY A 470 " pdb=" N ILE A 472 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR B 214 " pdb=" OE1 GLU B 570 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR A 400 " pdb=" OG1 THR A 500 " model vdw 2.339 3.040 nonbonded pdb=" O PHE B 326 " pdb=" OG SER B 330 " model vdw 2.341 3.040 nonbonded pdb=" OD1 ASN A 414 " pdb=" OG SER A 581 " model vdw 2.358 3.040 ... (remaining 51511 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.700 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 7.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 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 : 0.007 0.072 6802 Z= 0.304 Angle : 0.793 12.258 9257 Z= 0.423 Chirality : 0.051 0.266 1018 Planarity : 0.008 0.083 1158 Dihedral : 15.279 88.691 2732 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.11 % Favored : 93.38 % Rotamer: Outliers : 6.11 % Allowed : 8.81 % Favored : 85.09 % 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: -4.57 (0.22), residues: 785 helix: -3.31 (0.17), residues: 374 sheet: -2.33 (0.53), residues: 70 loop : -2.69 (0.27), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 517 TYR 0.022 0.002 TYR B 384 PHE 0.013 0.002 PHE B 399 TRP 0.019 0.002 TRP B 162 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 6780) covalent geometry : angle 0.75502 ( 9198) SS BOND : bond 0.00325 ( 7) SS BOND : angle 1.09260 ( 14) hydrogen bonds : bond 0.19604 ( 219) hydrogen bonds : angle 6.31508 ( 636) link_BETA1-4 : bond 0.00751 ( 6) link_BETA1-4 : angle 3.97576 ( 18) link_NAG-ASN : bond 0.00444 ( 9) link_NAG-ASN : angle 3.17270 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.282 Fit side-chains REVERT: A 410 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8571 (tm) REVERT: A 510 GLU cc_start: 0.8835 (pt0) cc_final: 0.8494 (pt0) REVERT: B 31 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7676 (ttmm) REVERT: B 34 HIS cc_start: 0.7893 (t70) cc_final: 0.7547 (t-90) REVERT: B 149 ASP cc_start: 0.8207 (t70) cc_final: 0.7986 (t0) REVERT: B 196 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8081 (mtpp) REVERT: B 200 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8247 (t0) REVERT: B 205 ASP cc_start: 0.7793 (t70) cc_final: 0.7575 (m-30) REVERT: B 322 MET cc_start: 0.9228 (mmp) cc_final: 0.8891 (mmm) REVERT: B 362 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7791 (mtmp) REVERT: B 494 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7280 (tp30) REVERT: B 601 SER cc_start: 0.8534 (m) cc_final: 0.8003 (p) outliers start: 43 outliers final: 13 residues processed: 148 average time/residue: 0.5091 time to fit residues: 79.3298 Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 526 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN B 41 HIS B 96 GLN B 98 GLN B 136 ASN B 340 GLN B 588 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103629 restraints weight = 8336.571| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.97 r_work: 0.3188 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6802 Z= 0.141 Angle : 0.594 8.187 9257 Z= 0.299 Chirality : 0.041 0.229 1018 Planarity : 0.005 0.048 1158 Dihedral : 9.193 58.617 1208 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 5.54 % Allowed : 16.05 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.26), residues: 785 helix: -1.65 (0.25), residues: 352 sheet: -1.94 (0.55), residues: 70 loop : -2.09 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 176 TYR 0.015 0.001 TYR B 384 PHE 0.009 0.001 PHE B 522 TRP 0.017 0.001 TRP B 164 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6780) covalent geometry : angle 0.57152 ( 9198) SS BOND : bond 0.00404 ( 7) SS BOND : angle 0.49326 ( 14) hydrogen bonds : bond 0.04664 ( 219) hydrogen bonds : angle 4.36988 ( 636) link_BETA1-4 : bond 0.00318 ( 6) link_BETA1-4 : angle 2.54315 ( 18) link_NAG-ASN : bond 0.00359 ( 9) link_NAG-ASN : angle 2.30506 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.165 Fit side-chains REVERT: A 425 LEU cc_start: 0.8580 (mt) cc_final: 0.8244 (mp) REVERT: A 427 GLN cc_start: 0.7351 (mt0) cc_final: 0.6951 (mt0) REVERT: A 510 GLU cc_start: 0.9037 (pt0) cc_final: 0.8791 (pt0) REVERT: B 19 TYR cc_start: 0.6176 (OUTLIER) cc_final: 0.5395 (p90) REVERT: B 31 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7847 (ttmm) REVERT: B 34 HIS cc_start: 0.8290 (t70) cc_final: 0.8030 (t-90) REVERT: B 75 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7344 (tp30) REVERT: B 149 ASP cc_start: 0.8259 (t70) cc_final: 0.7962 (t0) REVERT: B 196 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8548 (mtpp) REVERT: B 200 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8686 (t0) REVERT: B 205 ASP cc_start: 0.8341 (t70) cc_final: 0.8021 (m-30) REVERT: B 322 MET cc_start: 0.9368 (mmp) cc_final: 0.9025 (mmm) REVERT: B 362 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7901 (mtmp) REVERT: B 403 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8121 (t) REVERT: B 494 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7533 (tp30) REVERT: B 526 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: B 579 ASP cc_start: 0.8054 (p0) cc_final: 0.7221 (t0) REVERT: B 601 SER cc_start: 0.8812 (m) cc_final: 0.8161 (p) outliers start: 39 outliers final: 13 residues processed: 120 average time/residue: 0.5669 time to fit residues: 71.5065 Evaluate side-chains 104 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 526 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103118 restraints weight = 8296.960| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.97 r_work: 0.3172 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6802 Z= 0.145 Angle : 0.567 7.521 9257 Z= 0.282 Chirality : 0.041 0.219 1018 Planarity : 0.004 0.044 1158 Dihedral : 8.380 58.951 1203 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.26 % Allowed : 17.61 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.28), residues: 785 helix: -0.86 (0.27), residues: 357 sheet: -1.80 (0.56), residues: 70 loop : -1.86 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.013 0.001 TYR B 384 PHE 0.009 0.001 PHE B 522 TRP 0.015 0.001 TRP B 164 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6780) covalent geometry : angle 0.54576 ( 9198) SS BOND : bond 0.00761 ( 7) SS BOND : angle 0.64061 ( 14) hydrogen bonds : bond 0.04253 ( 219) hydrogen bonds : angle 4.08070 ( 636) link_BETA1-4 : bond 0.00358 ( 6) link_BETA1-4 : angle 2.38257 ( 18) link_NAG-ASN : bond 0.00336 ( 9) link_NAG-ASN : angle 2.17233 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.270 Fit side-chains REVERT: A 410 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8036 (tm) REVERT: A 425 LEU cc_start: 0.8595 (mt) cc_final: 0.8245 (mp) REVERT: A 501 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8170 (ttmm) REVERT: A 510 GLU cc_start: 0.9008 (pt0) cc_final: 0.8741 (pt0) REVERT: B 19 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5382 (p90) REVERT: B 34 HIS cc_start: 0.8279 (t70) cc_final: 0.8017 (t-90) REVERT: B 75 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7386 (tp30) REVERT: B 149 ASP cc_start: 0.8198 (t70) cc_final: 0.7940 (t0) REVERT: B 159 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: B 196 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8577 (mtpp) REVERT: B 205 ASP cc_start: 0.8324 (t70) cc_final: 0.8007 (m-30) REVERT: B 322 MET cc_start: 0.9379 (mmp) cc_final: 0.9036 (mmm) REVERT: B 352 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7846 (mtpt) REVERT: B 362 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7921 (mtmp) REVERT: B 365 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7153 (tpt) REVERT: B 494 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7551 (tp30) REVERT: B 526 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: B 579 ASP cc_start: 0.7888 (p0) cc_final: 0.7153 (t0) REVERT: B 601 SER cc_start: 0.8928 (m) cc_final: 0.8388 (p) outliers start: 30 outliers final: 14 residues processed: 109 average time/residue: 0.5699 time to fit residues: 65.5264 Evaluate side-chains 105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 526 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103000 restraints weight = 8408.846| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.99 r_work: 0.3136 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6802 Z= 0.141 Angle : 0.542 6.982 9257 Z= 0.266 Chirality : 0.041 0.218 1018 Planarity : 0.004 0.044 1158 Dihedral : 7.381 59.599 1195 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.83 % Allowed : 17.33 % Favored : 77.84 % 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: -1.67 (0.28), residues: 785 helix: -0.39 (0.28), residues: 357 sheet: -1.67 (0.59), residues: 66 loop : -1.68 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 409 TYR 0.012 0.001 TYR B 384 PHE 0.009 0.001 PHE B 522 TRP 0.013 0.001 TRP B 164 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6780) covalent geometry : angle 0.52157 ( 9198) SS BOND : bond 0.00310 ( 7) SS BOND : angle 0.53956 ( 14) hydrogen bonds : bond 0.04044 ( 219) hydrogen bonds : angle 3.90639 ( 636) link_BETA1-4 : bond 0.00368 ( 6) link_BETA1-4 : angle 2.24474 ( 18) link_NAG-ASN : bond 0.00324 ( 9) link_NAG-ASN : angle 2.10850 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.191 Fit side-chains REVERT: A 425 LEU cc_start: 0.8626 (mt) cc_final: 0.8266 (mp) REVERT: A 501 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (ttmm) REVERT: A 510 GLU cc_start: 0.8985 (pt0) cc_final: 0.8714 (pt0) REVERT: A 574 GLN cc_start: 0.7670 (tp40) cc_final: 0.7039 (tp40) REVERT: B 19 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5394 (p90) REVERT: B 34 HIS cc_start: 0.8292 (t70) cc_final: 0.8044 (t-90) REVERT: B 75 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7386 (tp30) REVERT: B 149 ASP cc_start: 0.8134 (t70) cc_final: 0.7870 (t0) REVERT: B 150 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (mt) REVERT: B 159 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: B 196 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8623 (mtpp) REVERT: B 205 ASP cc_start: 0.8403 (t70) cc_final: 0.8004 (m-30) REVERT: B 322 MET cc_start: 0.9386 (mmp) cc_final: 0.9118 (mmm) REVERT: B 352 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8023 (mtpt) REVERT: B 362 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7996 (mtmp) REVERT: B 365 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7121 (tpt) REVERT: B 494 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7403 (tp30) REVERT: B 526 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: B 579 ASP cc_start: 0.7830 (p0) cc_final: 0.7207 (t0) outliers start: 34 outliers final: 14 residues processed: 103 average time/residue: 0.4874 time to fit residues: 53.3363 Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 526 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096768 restraints weight = 8542.306| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.93 r_work: 0.3067 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6802 Z= 0.235 Angle : 0.603 7.432 9257 Z= 0.296 Chirality : 0.044 0.224 1018 Planarity : 0.004 0.046 1158 Dihedral : 7.333 57.288 1194 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.55 % Allowed : 17.61 % Favored : 77.84 % 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: -1.56 (0.28), residues: 785 helix: -0.36 (0.28), residues: 360 sheet: -1.50 (0.60), residues: 70 loop : -1.58 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 409 TYR 0.015 0.002 TYR B 384 PHE 0.014 0.002 PHE A 481 TRP 0.012 0.001 TRP B 164 HIS 0.007 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 6780) covalent geometry : angle 0.58330 ( 9198) SS BOND : bond 0.00317 ( 7) SS BOND : angle 0.78600 ( 14) hydrogen bonds : bond 0.04951 ( 219) hydrogen bonds : angle 4.00267 ( 636) link_BETA1-4 : bond 0.00334 ( 6) link_BETA1-4 : angle 2.27574 ( 18) link_NAG-ASN : bond 0.00412 ( 9) link_NAG-ASN : angle 2.18718 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.272 Fit side-chains REVERT: A 425 LEU cc_start: 0.8530 (mt) cc_final: 0.8191 (mp) REVERT: A 501 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8256 (ttmm) REVERT: A 510 GLU cc_start: 0.8981 (pt0) cc_final: 0.8709 (pt0) REVERT: A 574 GLN cc_start: 0.7680 (tp40) cc_final: 0.7120 (tp40) REVERT: B 19 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.5207 (p90) REVERT: B 149 ASP cc_start: 0.7931 (t70) cc_final: 0.7689 (t0) REVERT: B 159 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: B 196 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8516 (mtpp) REVERT: B 205 ASP cc_start: 0.8405 (t70) cc_final: 0.7965 (m-30) REVERT: B 211 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: B 322 MET cc_start: 0.9445 (mmp) cc_final: 0.9009 (mmm) REVERT: B 352 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8058 (mppt) REVERT: B 362 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7747 (mtmp) REVERT: B 365 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.6963 (tpt) REVERT: B 375 MET cc_start: 0.8286 (ttm) cc_final: 0.8046 (ttp) REVERT: B 494 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7514 (tp30) REVERT: B 526 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: B 579 ASP cc_start: 0.7671 (p0) cc_final: 0.6981 (t0) outliers start: 32 outliers final: 19 residues processed: 101 average time/residue: 0.4679 time to fit residues: 50.0824 Evaluate side-chains 100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 592 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 34 HIS B 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099791 restraints weight = 8480.001| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.94 r_work: 0.3059 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6802 Z= 0.121 Angle : 0.538 6.934 9257 Z= 0.264 Chirality : 0.040 0.214 1018 Planarity : 0.004 0.049 1158 Dihedral : 6.789 57.792 1194 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.69 % Allowed : 18.89 % Favored : 77.41 % 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: -1.17 (0.29), residues: 785 helix: -0.03 (0.28), residues: 359 sheet: -1.35 (0.62), residues: 70 loop : -1.37 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 409 TYR 0.010 0.001 TYR A 559 PHE 0.011 0.001 PHE A 481 TRP 0.013 0.001 TRP B 164 HIS 0.007 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6780) covalent geometry : angle 0.51921 ( 9198) SS BOND : bond 0.00187 ( 7) SS BOND : angle 0.49505 ( 14) hydrogen bonds : bond 0.03738 ( 219) hydrogen bonds : angle 3.79062 ( 636) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 2.17322 ( 18) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 2.07015 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.271 Fit side-chains REVERT: A 425 LEU cc_start: 0.8516 (mt) cc_final: 0.8164 (mp) REVERT: A 501 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8165 (ttmm) REVERT: A 510 GLU cc_start: 0.8923 (pt0) cc_final: 0.8652 (pt0) REVERT: A 574 GLN cc_start: 0.7597 (tp40) cc_final: 0.7025 (tp40) REVERT: B 19 TYR cc_start: 0.5951 (OUTLIER) cc_final: 0.5114 (p90) REVERT: B 75 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7259 (tp30) REVERT: B 149 ASP cc_start: 0.7820 (t70) cc_final: 0.7586 (t0) REVERT: B 196 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8477 (mtpp) REVERT: B 205 ASP cc_start: 0.8353 (t70) cc_final: 0.7894 (m-30) REVERT: B 322 MET cc_start: 0.9449 (mmp) cc_final: 0.9073 (mmm) REVERT: B 362 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7667 (mtmp) REVERT: B 365 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6838 (tpt) REVERT: B 479 MET cc_start: 0.7963 (mtp) cc_final: 0.7712 (mtt) REVERT: B 494 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7416 (tp30) REVERT: B 579 ASP cc_start: 0.7663 (p0) cc_final: 0.7069 (t0) outliers start: 26 outliers final: 15 residues processed: 95 average time/residue: 0.4992 time to fit residues: 50.2768 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 462 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099190 restraints weight = 8386.456| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.92 r_work: 0.3089 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6802 Z= 0.144 Angle : 0.546 6.617 9257 Z= 0.268 Chirality : 0.041 0.214 1018 Planarity : 0.004 0.041 1158 Dihedral : 6.069 51.846 1182 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.98 % Allowed : 20.17 % Favored : 76.85 % 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: -0.90 (0.29), residues: 785 helix: 0.21 (0.29), residues: 355 sheet: -1.24 (0.63), residues: 70 loop : -1.22 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 409 TYR 0.011 0.001 TYR B 384 PHE 0.010 0.001 PHE B 522 TRP 0.012 0.001 TRP B 164 HIS 0.007 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6780) covalent geometry : angle 0.52756 ( 9198) SS BOND : bond 0.00219 ( 7) SS BOND : angle 0.53615 ( 14) hydrogen bonds : bond 0.03985 ( 219) hydrogen bonds : angle 3.76859 ( 636) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 2.16001 ( 18) link_NAG-ASN : bond 0.00316 ( 9) link_NAG-ASN : angle 2.03440 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.160 Fit side-chains REVERT: A 425 LEU cc_start: 0.8534 (mt) cc_final: 0.8215 (mp) REVERT: A 427 GLN cc_start: 0.7082 (mt0) cc_final: 0.6541 (mt0) REVERT: A 501 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8212 (ttmm) REVERT: A 510 GLU cc_start: 0.8950 (pt0) cc_final: 0.8697 (pt0) REVERT: A 574 GLN cc_start: 0.7622 (tp40) cc_final: 0.7243 (tp-100) REVERT: B 19 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.5145 (p90) REVERT: B 75 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7349 (tp30) REVERT: B 149 ASP cc_start: 0.7890 (t70) cc_final: 0.7647 (t0) REVERT: B 196 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8525 (mtpp) REVERT: B 205 ASP cc_start: 0.8342 (t70) cc_final: 0.7907 (m-30) REVERT: B 322 MET cc_start: 0.9401 (mmp) cc_final: 0.9072 (mmm) REVERT: B 362 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7671 (mtmp) REVERT: B 365 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.6924 (tpt) REVERT: B 494 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7529 (tp30) REVERT: B 579 ASP cc_start: 0.7685 (p0) cc_final: 0.7170 (t0) outliers start: 21 outliers final: 15 residues processed: 95 average time/residue: 0.4619 time to fit residues: 46.3859 Evaluate side-chains 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 462 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS B 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100488 restraints weight = 8453.024| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.93 r_work: 0.3108 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6802 Z= 0.112 Angle : 0.520 7.428 9257 Z= 0.252 Chirality : 0.040 0.209 1018 Planarity : 0.004 0.040 1158 Dihedral : 5.791 51.707 1182 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.55 % Allowed : 20.45 % Favored : 75.99 % 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: -0.63 (0.30), residues: 785 helix: 0.48 (0.29), residues: 355 sheet: -1.16 (0.64), residues: 70 loop : -1.13 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 409 TYR 0.010 0.001 TYR A 559 PHE 0.010 0.001 PHE A 481 TRP 0.013 0.001 TRP B 164 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6780) covalent geometry : angle 0.50170 ( 9198) SS BOND : bond 0.00179 ( 7) SS BOND : angle 0.45875 ( 14) hydrogen bonds : bond 0.03562 ( 219) hydrogen bonds : angle 3.65929 ( 636) link_BETA1-4 : bond 0.00409 ( 6) link_BETA1-4 : angle 2.10819 ( 18) link_NAG-ASN : bond 0.00313 ( 9) link_NAG-ASN : angle 1.98163 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.268 Fit side-chains REVERT: A 410 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7973 (tm) REVERT: A 425 LEU cc_start: 0.8567 (mt) cc_final: 0.8246 (mp) REVERT: A 501 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8200 (ttmm) REVERT: A 510 GLU cc_start: 0.8931 (pt0) cc_final: 0.8678 (pt0) REVERT: A 574 GLN cc_start: 0.7626 (tp40) cc_final: 0.7068 (tp40) REVERT: B 19 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.5071 (p90) REVERT: B 62 MET cc_start: 0.7534 (ttt) cc_final: 0.7168 (ptm) REVERT: B 75 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7362 (tp30) REVERT: B 113 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7677 (ttm110) REVERT: B 149 ASP cc_start: 0.7843 (t70) cc_final: 0.7643 (t0) REVERT: B 196 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8577 (mtpp) REVERT: B 205 ASP cc_start: 0.8328 (t70) cc_final: 0.7894 (m-30) REVERT: B 211 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: B 322 MET cc_start: 0.9402 (mmp) cc_final: 0.9117 (mmm) REVERT: B 494 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7522 (tp30) REVERT: B 579 ASP cc_start: 0.7603 (p0) cc_final: 0.7149 (t0) outliers start: 25 outliers final: 15 residues processed: 92 average time/residue: 0.5105 time to fit residues: 49.6616 Evaluate side-chains 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 592 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100168 restraints weight = 8436.791| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.93 r_work: 0.3036 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6802 Z= 0.117 Angle : 0.515 6.610 9257 Z= 0.250 Chirality : 0.040 0.207 1018 Planarity : 0.003 0.040 1158 Dihedral : 5.710 51.231 1182 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.55 % Allowed : 20.60 % Favored : 75.85 % 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: -0.49 (0.30), residues: 785 helix: 0.53 (0.29), residues: 362 sheet: -1.10 (0.65), residues: 70 loop : -1.00 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.010 0.001 TYR A 559 PHE 0.009 0.001 PHE A 481 TRP 0.012 0.001 TRP B 164 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6780) covalent geometry : angle 0.49703 ( 9198) SS BOND : bond 0.00221 ( 7) SS BOND : angle 0.47527 ( 14) hydrogen bonds : bond 0.03639 ( 219) hydrogen bonds : angle 3.65144 ( 636) link_BETA1-4 : bond 0.00399 ( 6) link_BETA1-4 : angle 2.09378 ( 18) link_NAG-ASN : bond 0.00296 ( 9) link_NAG-ASN : angle 1.94863 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.170 Fit side-chains REVERT: A 410 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7823 (tm) REVERT: A 425 LEU cc_start: 0.8509 (mt) cc_final: 0.8185 (mp) REVERT: A 501 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8154 (ttmm) REVERT: A 510 GLU cc_start: 0.8888 (pt0) cc_final: 0.8632 (pt0) REVERT: A 574 GLN cc_start: 0.7624 (tp40) cc_final: 0.7118 (tp40) REVERT: B 19 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.4998 (p90) REVERT: B 62 MET cc_start: 0.7424 (ttt) cc_final: 0.7078 (ptm) REVERT: B 75 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7246 (tp30) REVERT: B 196 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8487 (mtpp) REVERT: B 205 ASP cc_start: 0.8321 (t70) cc_final: 0.7851 (m-30) REVERT: B 211 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: B 322 MET cc_start: 0.9487 (mmp) cc_final: 0.9019 (mmp) REVERT: B 362 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7487 (mtmp) REVERT: B 464 GLU cc_start: 0.7581 (tt0) cc_final: 0.7314 (tt0) REVERT: B 494 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7444 (tp30) REVERT: B 579 ASP cc_start: 0.7456 (p0) cc_final: 0.7058 (t0) REVERT: B 581 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7363 (mmmt) outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 0.4786 time to fit residues: 47.4015 Evaluate side-chains 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 592 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100380 restraints weight = 8370.248| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.92 r_work: 0.3067 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6802 Z= 0.118 Angle : 0.522 7.243 9257 Z= 0.252 Chirality : 0.040 0.206 1018 Planarity : 0.003 0.039 1158 Dihedral : 5.670 50.991 1182 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.84 % Allowed : 21.16 % Favored : 75.99 % 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: -0.39 (0.30), residues: 785 helix: 0.63 (0.29), residues: 362 sheet: -1.10 (0.65), residues: 70 loop : -0.95 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.011 0.001 TYR B 389 PHE 0.009 0.001 PHE A 481 TRP 0.012 0.001 TRP B 164 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6780) covalent geometry : angle 0.50403 ( 9198) SS BOND : bond 0.00196 ( 7) SS BOND : angle 0.45142 ( 14) hydrogen bonds : bond 0.03633 ( 219) hydrogen bonds : angle 3.62893 ( 636) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 2.07364 ( 18) link_NAG-ASN : bond 0.00289 ( 9) link_NAG-ASN : angle 1.97867 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.270 Fit side-chains REVERT: A 410 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7871 (tm) REVERT: A 425 LEU cc_start: 0.8526 (mt) cc_final: 0.8200 (mp) REVERT: A 427 GLN cc_start: 0.6911 (mt0) cc_final: 0.6572 (mt0) REVERT: A 501 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8173 (ttmm) REVERT: A 510 GLU cc_start: 0.8907 (pt0) cc_final: 0.8654 (pt0) REVERT: A 574 GLN cc_start: 0.7743 (tp40) cc_final: 0.7241 (tp40) REVERT: B 19 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.4966 (p90) REVERT: B 62 MET cc_start: 0.7482 (ttt) cc_final: 0.7116 (ptm) REVERT: B 75 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7291 (tp30) REVERT: B 196 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8512 (mtpp) REVERT: B 205 ASP cc_start: 0.8310 (t70) cc_final: 0.7848 (m-30) REVERT: B 211 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: B 322 MET cc_start: 0.9489 (mmp) cc_final: 0.9023 (mmp) REVERT: B 362 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7418 (mtmp) REVERT: B 464 GLU cc_start: 0.7604 (tt0) cc_final: 0.7336 (tt0) REVERT: B 494 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7478 (tp30) REVERT: B 579 ASP cc_start: 0.7474 (p0) cc_final: 0.7081 (t0) REVERT: B 581 LYS cc_start: 0.7605 (mtmt) cc_final: 0.7401 (mmmt) outliers start: 20 outliers final: 16 residues processed: 92 average time/residue: 0.5400 time to fit residues: 52.3557 Evaluate side-chains 98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100624 restraints weight = 8360.387| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.92 r_work: 0.3073 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6802 Z= 0.112 Angle : 0.519 7.547 9257 Z= 0.253 Chirality : 0.040 0.205 1018 Planarity : 0.003 0.040 1158 Dihedral : 5.583 50.766 1180 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.84 % Allowed : 21.45 % Favored : 75.71 % 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: -0.31 (0.30), residues: 785 helix: 0.70 (0.29), residues: 363 sheet: -1.09 (0.65), residues: 70 loop : -0.92 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.011 0.001 TYR B 389 PHE 0.009 0.001 PHE A 481 TRP 0.012 0.001 TRP B 164 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6780) covalent geometry : angle 0.50120 ( 9198) SS BOND : bond 0.00186 ( 7) SS BOND : angle 0.43260 ( 14) hydrogen bonds : bond 0.03529 ( 219) hydrogen bonds : angle 3.60723 ( 636) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 2.06074 ( 18) link_NAG-ASN : bond 0.00287 ( 9) link_NAG-ASN : angle 1.96125 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.39 seconds wall clock time: 37 minutes 1.62 seconds (2221.62 seconds total)