Starting phenix.real_space_refine on Tue Nov 18 19:02:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9o_10419/11_2025/6t9o_10419.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9o_10419/11_2025/6t9o_10419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t9o_10419/11_2025/6t9o_10419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9o_10419/11_2025/6t9o_10419.map" model { file = "/net/cci-nas-00/data/ceres_data/6t9o_10419/11_2025/6t9o_10419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9o_10419/11_2025/6t9o_10419.cif" } resolution = 3.39 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= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 76 5.16 5 C 10924 2.51 5 N 2472 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16481 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 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: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Unusual residues: {' CA': 1, 'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 4.14, per 1000 atoms: 0.25 Number of scatterers: 16481 At special positions: 0 Unit cell: (115.056, 115.056, 111.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 76 16.00 O 3008 8.00 N 2472 7.00 C 10924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.02 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.02 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.02 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 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 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " " NAG H 1 " - " ASN D 375 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 676.1 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 61.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 215 through 241 removed outlier: 3.728A pdb=" N TYR A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.639A pdb=" N TYR A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.807A pdb=" N ILE A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.643A pdb=" N LEU A 374 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 498 removed outlier: 3.755A pdb=" N ILE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.623A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 593 through 620 Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.787A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 672 through 701 removed outlier: 4.264A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 241 removed outlier: 3.727A pdb=" N TYR B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.639A pdb=" N TYR B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.807A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.643A pdb=" N LEU B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 498 removed outlier: 3.755A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.624A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 593 through 620 Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.787A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 672 through 701 removed outlier: 4.263A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 removed outlier: 3.727A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.640A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.807A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.644A pdb=" N LEU C 374 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 498 removed outlier: 3.755A pdb=" N ILE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 528 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 548 through 573 removed outlier: 3.623A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 593 through 620 Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.787A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 Processing helix chain 'C' and resid 672 through 701 removed outlier: 4.263A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 241 removed outlier: 3.729A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.640A pdb=" N TYR D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.808A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.643A pdb=" N LEU D 374 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 498 removed outlier: 3.754A pdb=" N ILE D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 528 Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 548 through 573 removed outlier: 3.624A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 580 through 593 Processing helix chain 'D' and resid 593 through 620 Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.788A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 667 Processing helix chain 'D' and resid 672 through 701 removed outlier: 4.264A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.527A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.527A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.527A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.528A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 952 hydrogen bonds defined for protein. 2712 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: 2.98 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4690 1.34 - 1.45: 3558 1.45 - 1.57: 8548 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 16912 Sorted by residual: bond pdb=" C2' UMQ A 809 " pdb=" C3' UMQ A 809 " ideal model delta sigma weight residual 1.521 1.564 -0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C2' UMQ C 809 " pdb=" C3' UMQ C 809 " ideal model delta sigma weight residual 1.521 1.564 -0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C2' UMQ D 809 " pdb=" C3' UMQ D 809 " ideal model delta sigma weight residual 1.521 1.563 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" C2' UMQ B 809 " pdb=" C3' UMQ B 809 " ideal model delta sigma weight residual 1.521 1.563 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C5 UMQ B 806 " pdb=" O5 UMQ B 806 " ideal model delta sigma weight residual 1.421 1.379 0.042 2.00e-02 2.50e+03 4.44e+00 ... (remaining 16907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21743 2.10 - 4.21: 1041 4.21 - 6.31: 141 6.31 - 8.41: 15 8.41 - 10.52: 16 Bond angle restraints: 22956 Sorted by residual: angle pdb=" C1 UMQ C 806 " pdb=" O1 UMQ C 806 " pdb=" C4' UMQ C 806 " ideal model delta sigma weight residual 119.70 110.26 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" C1 UMQ B 806 " pdb=" O1 UMQ B 806 " pdb=" C4' UMQ B 806 " ideal model delta sigma weight residual 119.70 110.31 9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" C1 UMQ D 806 " pdb=" O1 UMQ D 806 " pdb=" C4' UMQ D 806 " ideal model delta sigma weight residual 119.70 110.32 9.38 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C1 UMQ A 806 " pdb=" O1 UMQ A 806 " pdb=" C4' UMQ A 806 " ideal model delta sigma weight residual 119.70 110.35 9.35 3.00e+00 1.11e-01 9.72e+00 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 126.82 -10.52 3.50e+00 8.16e-02 9.03e+00 ... (remaining 22951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.23: 9656 13.23 - 26.46: 732 26.46 - 39.69: 216 39.69 - 52.92: 80 52.92 - 66.15: 28 Dihedral angle restraints: 10712 sinusoidal: 5004 harmonic: 5708 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 344 " pdb=" CB CYS A 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.54 65.54 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.52 65.52 1 1.00e+01 1.00e-02 5.62e+01 ... (remaining 10709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2138 0.071 - 0.142: 443 0.142 - 0.213: 111 0.213 - 0.284: 16 0.284 - 0.355: 4 Chirality restraints: 2712 Sorted by residual: chirality pdb=" C1 NAG C 802 " pdb=" ND2 ASN C 362 " pdb=" C2 NAG C 802 " pdb=" O5 NAG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C1 NAG D 802 " pdb=" ND2 ASN D 362 " pdb=" C2 NAG D 802 " pdb=" O5 NAG D 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 2709 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 634 " -0.034 2.00e-02 2.50e+03 2.18e-02 8.33e+00 pdb=" CG PHE D 634 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 634 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 634 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 634 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 634 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 634 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 634 " 0.034 2.00e-02 2.50e+03 2.18e-02 8.32e+00 pdb=" CG PHE C 634 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 634 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 634 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 634 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 634 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 634 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 634 " 0.033 2.00e-02 2.50e+03 2.17e-02 8.23e+00 pdb=" CG PHE B 634 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 634 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 634 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 634 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 634 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 634 " 0.025 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1723 2.74 - 3.28: 15366 3.28 - 3.82: 26975 3.82 - 4.36: 32747 4.36 - 4.90: 57286 Nonbonded interactions: 134097 Sorted by model distance: nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLU D 491 " pdb=" OH TYR D 502 " model vdw 2.271 3.040 ... (remaining 134092 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 'A' and resid 214 through 810) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.220 Find NCS groups from input model: 0.370 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.010 0.064 16932 Z= 0.414 Angle : 1.028 10.515 23012 Z= 0.513 Chirality : 0.066 0.355 2712 Planarity : 0.006 0.054 2728 Dihedral : 11.321 66.146 7004 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.71 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.77 (0.15), residues: 1908 helix: -2.29 (0.11), residues: 1108 sheet: -2.34 (0.35), residues: 192 loop : -2.53 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.039 0.003 TYR B 249 PHE 0.034 0.003 PHE C 634 TRP 0.027 0.004 TRP A 507 HIS 0.005 0.002 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00954 (16912) covalent geometry : angle 1.00740 (22956) SS BOND : bond 0.00820 ( 4) SS BOND : angle 3.93723 ( 8) hydrogen bonds : bond 0.15137 ( 936) hydrogen bonds : angle 6.34646 ( 2712) link_BETA1-4 : bond 0.00052 ( 4) link_BETA1-4 : angle 2.05842 ( 12) link_NAG-ASN : bond 0.00841 ( 12) link_NAG-ASN : angle 4.81826 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 SER cc_start: 0.8764 (p) cc_final: 0.8254 (t) REVERT: A 367 ILE cc_start: 0.8961 (mt) cc_final: 0.8511 (pt) REVERT: A 489 VAL cc_start: 0.8598 (t) cc_final: 0.8322 (p) REVERT: A 570 TRP cc_start: 0.8517 (m100) cc_final: 0.8089 (m100) REVERT: A 625 ASP cc_start: 0.7488 (m-30) cc_final: 0.7278 (m-30) REVERT: A 648 GLU cc_start: 0.8390 (pt0) cc_final: 0.8156 (pt0) REVERT: A 650 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7407 (tt0) REVERT: B 275 SER cc_start: 0.8804 (p) cc_final: 0.8269 (t) REVERT: B 367 ILE cc_start: 0.9004 (mt) cc_final: 0.8673 (pt) REVERT: B 398 THR cc_start: 0.8485 (p) cc_final: 0.7832 (p) REVERT: B 444 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 570 TRP cc_start: 0.8436 (m100) cc_final: 0.7993 (m100) REVERT: B 650 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7646 (tt0) REVERT: C 223 GLU cc_start: 0.6938 (pt0) cc_final: 0.6696 (tp30) REVERT: C 367 ILE cc_start: 0.8970 (mt) cc_final: 0.8609 (pt) REVERT: C 398 THR cc_start: 0.8464 (p) cc_final: 0.8049 (p) REVERT: C 489 VAL cc_start: 0.8532 (t) cc_final: 0.8261 (p) REVERT: C 531 ASN cc_start: 0.7892 (t0) cc_final: 0.7678 (t0) REVERT: C 570 TRP cc_start: 0.8468 (m100) cc_final: 0.8052 (m100) REVERT: D 223 GLU cc_start: 0.6875 (pt0) cc_final: 0.6647 (tp30) REVERT: D 271 LYS cc_start: 0.8903 (mttt) cc_final: 0.8624 (mttm) REVERT: D 275 SER cc_start: 0.8755 (p) cc_final: 0.8252 (t) REVERT: D 398 THR cc_start: 0.8598 (p) cc_final: 0.8179 (t) REVERT: D 489 VAL cc_start: 0.8617 (t) cc_final: 0.8374 (p) REVERT: D 570 TRP cc_start: 0.8501 (m100) cc_final: 0.8138 (m100) REVERT: D 587 SER cc_start: 0.8468 (m) cc_final: 0.8260 (t) REVERT: D 650 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1384 time to fit residues: 88.6496 Evaluate side-chains 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 HIS A 636 GLN A 653 ASN B 255 GLN B 313 ASN B 323 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS B 636 GLN B 653 ASN C 255 GLN C 323 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 636 GLN C 653 ASN D 323 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 ASN D 550 HIS D 636 GLN D 653 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108980 restraints weight = 20726.804| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.96 r_work: 0.2909 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16932 Z= 0.164 Angle : 0.560 8.172 23012 Z= 0.297 Chirality : 0.041 0.315 2712 Planarity : 0.004 0.045 2728 Dihedral : 9.858 58.267 3564 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 2.34 % Allowed : 6.35 % Favored : 91.31 % 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: -1.49 (0.17), residues: 1908 helix: -0.21 (0.14), residues: 1100 sheet: -2.02 (0.35), residues: 200 loop : -1.86 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 592 TYR 0.020 0.001 TYR D 486 PHE 0.022 0.002 PHE C 600 TRP 0.013 0.002 TRP D 554 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00365 (16912) covalent geometry : angle 0.54623 (22956) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.97236 ( 8) hydrogen bonds : bond 0.05174 ( 936) hydrogen bonds : angle 4.61821 ( 2712) link_BETA1-4 : bond 0.00174 ( 4) link_BETA1-4 : angle 1.35931 ( 12) link_NAG-ASN : bond 0.00553 ( 12) link_NAG-ASN : angle 2.92341 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.8826 (p) cc_final: 0.8438 (t) REVERT: A 333 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8397 (tp) REVERT: A 367 ILE cc_start: 0.9081 (mt) cc_final: 0.8628 (pt) REVERT: A 488 VAL cc_start: 0.8925 (t) cc_final: 0.8615 (m) REVERT: A 570 TRP cc_start: 0.8676 (m100) cc_final: 0.8275 (m100) REVERT: A 650 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7842 (tt0) REVERT: B 275 SER cc_start: 0.8886 (p) cc_final: 0.8406 (t) REVERT: B 367 ILE cc_start: 0.9091 (mt) cc_final: 0.8688 (pt) REVERT: B 531 ASN cc_start: 0.7954 (t0) cc_final: 0.7557 (t0) REVERT: B 570 TRP cc_start: 0.8652 (m100) cc_final: 0.8425 (m100) REVERT: B 650 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8005 (tt0) REVERT: C 223 GLU cc_start: 0.7346 (pt0) cc_final: 0.6776 (tp30) REVERT: C 275 SER cc_start: 0.8953 (p) cc_final: 0.8396 (t) REVERT: C 367 ILE cc_start: 0.9101 (mt) cc_final: 0.8900 (tp) REVERT: C 444 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8540 (mt-10) REVERT: C 486 TYR cc_start: 0.8469 (t80) cc_final: 0.8173 (t80) REVERT: C 531 ASN cc_start: 0.8105 (t0) cc_final: 0.7640 (t0) REVERT: C 570 TRP cc_start: 0.8665 (m100) cc_final: 0.8361 (m100) REVERT: D 223 GLU cc_start: 0.7249 (pt0) cc_final: 0.6729 (tp30) REVERT: D 275 SER cc_start: 0.8803 (p) cc_final: 0.8412 (t) REVERT: D 444 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8479 (mt-10) REVERT: D 570 TRP cc_start: 0.8683 (m100) cc_final: 0.8280 (m100) REVERT: D 650 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7858 (tt0) outliers start: 39 outliers final: 27 residues processed: 305 average time/residue: 0.1122 time to fit residues: 55.3474 Evaluate side-chains 248 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 56 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105338 restraints weight = 20876.798| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.01 r_work: 0.3053 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16932 Z= 0.119 Angle : 0.484 8.410 23012 Z= 0.256 Chirality : 0.039 0.291 2712 Planarity : 0.003 0.039 2728 Dihedral : 8.635 59.962 3564 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 2.10 % Allowed : 9.29 % Favored : 88.61 % 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: -0.55 (0.18), residues: 1908 helix: 0.68 (0.15), residues: 1096 sheet: -1.83 (0.34), residues: 200 loop : -1.67 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 592 TYR 0.018 0.001 TYR D 486 PHE 0.021 0.001 PHE C 600 TRP 0.009 0.001 TRP A 507 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00256 (16912) covalent geometry : angle 0.47401 (22956) SS BOND : bond 0.00085 ( 4) SS BOND : angle 1.19492 ( 8) hydrogen bonds : bond 0.04453 ( 936) hydrogen bonds : angle 4.22065 ( 2712) link_BETA1-4 : bond 0.00319 ( 4) link_BETA1-4 : angle 1.09652 ( 12) link_NAG-ASN : bond 0.00501 ( 12) link_NAG-ASN : angle 2.40809 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.615 Fit side-chains REVERT: A 245 ASN cc_start: 0.7857 (m-40) cc_final: 0.7652 (m-40) REVERT: A 275 SER cc_start: 0.8881 (p) cc_final: 0.8553 (t) REVERT: A 367 ILE cc_start: 0.9099 (mt) cc_final: 0.8869 (tp) REVERT: A 488 VAL cc_start: 0.8986 (t) cc_final: 0.8676 (m) REVERT: A 570 TRP cc_start: 0.8730 (m100) cc_final: 0.8368 (m100) REVERT: A 650 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7872 (tt0) REVERT: B 245 ASN cc_start: 0.7846 (m-40) cc_final: 0.7012 (p0) REVERT: B 275 SER cc_start: 0.8913 (p) cc_final: 0.8549 (t) REVERT: B 367 ILE cc_start: 0.9130 (mt) cc_final: 0.8876 (tp) REVERT: C 223 GLU cc_start: 0.7170 (pt0) cc_final: 0.6865 (tp30) REVERT: C 275 SER cc_start: 0.8977 (p) cc_final: 0.8564 (t) REVERT: C 367 ILE cc_start: 0.9134 (mt) cc_final: 0.8895 (tp) REVERT: C 444 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8539 (mt-10) REVERT: C 673 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 223 GLU cc_start: 0.7134 (pt0) cc_final: 0.6707 (tp30) REVERT: D 245 ASN cc_start: 0.7846 (m-40) cc_final: 0.7643 (m-40) REVERT: D 275 SER cc_start: 0.8913 (p) cc_final: 0.8583 (t) REVERT: D 650 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7855 (tt0) outliers start: 35 outliers final: 26 residues processed: 268 average time/residue: 0.1056 time to fit residues: 46.2594 Evaluate side-chains 244 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096472 restraints weight = 21096.368| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.10 r_work: 0.2828 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16932 Z= 0.203 Angle : 0.532 7.941 23012 Z= 0.276 Chirality : 0.041 0.276 2712 Planarity : 0.003 0.043 2728 Dihedral : 8.298 57.389 3564 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 3.48 % Allowed : 8.63 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.19), residues: 1908 helix: 0.95 (0.15), residues: 1104 sheet: -1.77 (0.34), residues: 200 loop : -1.44 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 592 TYR 0.021 0.002 TYR A 486 PHE 0.023 0.002 PHE C 600 TRP 0.012 0.002 TRP D 554 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00475 (16912) covalent geometry : angle 0.52377 (22956) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.82069 ( 8) hydrogen bonds : bond 0.04698 ( 936) hydrogen bonds : angle 4.17654 ( 2712) link_BETA1-4 : bond 0.00354 ( 4) link_BETA1-4 : angle 1.34964 ( 12) link_NAG-ASN : bond 0.00456 ( 12) link_NAG-ASN : angle 2.25054 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.551 Fit side-chains REVERT: A 275 SER cc_start: 0.8882 (p) cc_final: 0.8562 (t) REVERT: A 570 TRP cc_start: 0.8754 (m100) cc_final: 0.8365 (m100) REVERT: A 650 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8006 (tt0) REVERT: B 245 ASN cc_start: 0.7955 (m-40) cc_final: 0.7746 (m-40) REVERT: B 275 SER cc_start: 0.8904 (p) cc_final: 0.8578 (t) REVERT: B 650 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8035 (tt0) REVERT: C 223 GLU cc_start: 0.7197 (pt0) cc_final: 0.6776 (tp30) REVERT: C 245 ASN cc_start: 0.7937 (m-40) cc_final: 0.7082 (p0) REVERT: C 275 SER cc_start: 0.8971 (p) cc_final: 0.8603 (t) REVERT: C 444 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8678 (mt-10) REVERT: C 673 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8761 (mp) REVERT: D 223 GLU cc_start: 0.7129 (pt0) cc_final: 0.6692 (tp30) REVERT: D 275 SER cc_start: 0.8855 (p) cc_final: 0.8638 (t) REVERT: D 650 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7970 (tt0) REVERT: D 673 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8618 (mp) outliers start: 58 outliers final: 49 residues processed: 266 average time/residue: 0.1044 time to fit residues: 46.3443 Evaluate side-chains 257 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 102 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN B 255 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN C 255 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN C 636 GLN D 430 ASN D 636 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108297 restraints weight = 20700.386| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.95 r_work: 0.2917 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16932 Z= 0.128 Angle : 0.474 8.712 23012 Z= 0.246 Chirality : 0.039 0.268 2712 Planarity : 0.003 0.037 2728 Dihedral : 7.856 57.958 3564 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.30 % Favored : 96.49 % Rotamer: Outliers : 2.64 % Allowed : 10.85 % Favored : 86.51 % 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: 0.18 (0.19), residues: 1908 helix: 1.22 (0.15), residues: 1104 sheet: -1.52 (0.34), residues: 200 loop : -1.30 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.018 0.001 TYR A 486 PHE 0.021 0.001 PHE B 600 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00286 (16912) covalent geometry : angle 0.46704 (22956) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.71144 ( 8) hydrogen bonds : bond 0.04315 ( 936) hydrogen bonds : angle 4.00745 ( 2712) link_BETA1-4 : bond 0.00224 ( 4) link_BETA1-4 : angle 1.24998 ( 12) link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 2.00662 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.602 Fit side-chains REVERT: A 245 ASN cc_start: 0.7720 (m-40) cc_final: 0.6920 (p0) REVERT: A 275 SER cc_start: 0.8857 (p) cc_final: 0.8628 (t) REVERT: A 312 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 488 VAL cc_start: 0.8955 (t) cc_final: 0.8683 (m) REVERT: A 570 TRP cc_start: 0.8769 (m100) cc_final: 0.8466 (m100) REVERT: A 650 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7974 (tt0) REVERT: B 245 ASN cc_start: 0.7792 (m-40) cc_final: 0.7023 (p0) REVERT: B 275 SER cc_start: 0.8869 (p) cc_final: 0.8573 (t) REVERT: C 223 GLU cc_start: 0.7155 (pt0) cc_final: 0.6759 (tp30) REVERT: C 245 ASN cc_start: 0.7767 (m-40) cc_final: 0.7074 (p0) REVERT: C 275 SER cc_start: 0.8960 (p) cc_final: 0.8639 (t) REVERT: C 444 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8552 (mt-10) REVERT: C 673 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (mp) REVERT: D 223 GLU cc_start: 0.7055 (pt0) cc_final: 0.6663 (tp30) REVERT: D 245 ASN cc_start: 0.7681 (m-40) cc_final: 0.7013 (p0) REVERT: D 650 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 673 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8705 (mp) outliers start: 44 outliers final: 36 residues processed: 252 average time/residue: 0.1048 time to fit residues: 43.5723 Evaluate side-chains 238 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109270 restraints weight = 20770.141| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.96 r_work: 0.2935 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16932 Z= 0.105 Angle : 0.454 9.458 23012 Z= 0.234 Chirality : 0.038 0.256 2712 Planarity : 0.003 0.035 2728 Dihedral : 7.366 58.873 3564 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.67 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 10.97 % Favored : 86.39 % 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: 0.53 (0.19), residues: 1908 helix: 1.47 (0.15), residues: 1100 sheet: -1.31 (0.35), residues: 200 loop : -1.08 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 464 TYR 0.018 0.001 TYR A 486 PHE 0.021 0.001 PHE C 600 TRP 0.007 0.001 TRP D 554 HIS 0.002 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00223 (16912) covalent geometry : angle 0.44833 (22956) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.57093 ( 8) hydrogen bonds : bond 0.04083 ( 936) hydrogen bonds : angle 3.87352 ( 2712) link_BETA1-4 : bond 0.00283 ( 4) link_BETA1-4 : angle 1.17539 ( 12) link_NAG-ASN : bond 0.00398 ( 12) link_NAG-ASN : angle 1.82633 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.634 Fit side-chains REVERT: A 245 ASN cc_start: 0.7777 (m-40) cc_final: 0.7010 (p0) REVERT: A 488 VAL cc_start: 0.8933 (t) cc_final: 0.8648 (m) REVERT: A 673 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 245 ASN cc_start: 0.7802 (m-40) cc_final: 0.7053 (p0) REVERT: B 275 SER cc_start: 0.8872 (p) cc_final: 0.8647 (t) REVERT: C 223 GLU cc_start: 0.7116 (pt0) cc_final: 0.6788 (tp30) REVERT: C 245 ASN cc_start: 0.7747 (m-40) cc_final: 0.7087 (p0) REVERT: C 275 SER cc_start: 0.8916 (p) cc_final: 0.8645 (t) REVERT: C 673 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8802 (mp) REVERT: D 223 GLU cc_start: 0.7083 (pt0) cc_final: 0.6695 (tp30) REVERT: D 245 ASN cc_start: 0.7730 (m-40) cc_final: 0.7082 (p0) REVERT: D 312 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 337 LEU cc_start: 0.8124 (mt) cc_final: 0.7738 (mt) REVERT: D 650 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7871 (tt0) REVERT: D 673 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8748 (mp) outliers start: 44 outliers final: 37 residues processed: 254 average time/residue: 0.0981 time to fit residues: 42.6453 Evaluate side-chains 243 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108926 restraints weight = 20734.917| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.94 r_work: 0.2912 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.148 Angle : 0.480 10.096 23012 Z= 0.245 Chirality : 0.039 0.251 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.319 59.678 3564 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.73 % Favored : 97.06 % Rotamer: Outliers : 3.06 % Allowed : 11.63 % Favored : 85.31 % 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: 0.60 (0.19), residues: 1908 helix: 1.53 (0.15), residues: 1100 sheet: -1.28 (0.35), residues: 200 loop : -1.06 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.016 0.001 TYR A 486 PHE 0.022 0.001 PHE C 600 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00340 (16912) covalent geometry : angle 0.47396 (22956) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.56084 ( 8) hydrogen bonds : bond 0.04224 ( 936) hydrogen bonds : angle 3.88551 ( 2712) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 1.30520 ( 12) link_NAG-ASN : bond 0.00377 ( 12) link_NAG-ASN : angle 1.78946 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.477 Fit side-chains REVERT: A 245 ASN cc_start: 0.7787 (m-40) cc_final: 0.6978 (p0) REVERT: A 488 VAL cc_start: 0.8930 (t) cc_final: 0.8643 (m) REVERT: A 673 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 245 ASN cc_start: 0.7877 (m-40) cc_final: 0.7083 (p0) REVERT: B 275 SER cc_start: 0.8894 (p) cc_final: 0.8661 (t) REVERT: C 223 GLU cc_start: 0.7121 (pt0) cc_final: 0.6801 (tp30) REVERT: C 245 ASN cc_start: 0.7793 (m-40) cc_final: 0.7099 (p0) REVERT: C 275 SER cc_start: 0.8930 (p) cc_final: 0.8655 (t) REVERT: C 673 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8822 (mp) REVERT: D 223 GLU cc_start: 0.7038 (pt0) cc_final: 0.6785 (tp30) REVERT: D 245 ASN cc_start: 0.7780 (m-40) cc_final: 0.7108 (p0) REVERT: D 312 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8415 (mm-30) REVERT: D 488 VAL cc_start: 0.8909 (t) cc_final: 0.8643 (m) REVERT: D 650 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7913 (tt0) REVERT: D 673 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8754 (mp) outliers start: 51 outliers final: 42 residues processed: 258 average time/residue: 0.0999 time to fit residues: 43.5036 Evaluate side-chains 246 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 5 optimal weight: 0.3980 chunk 122 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105242 restraints weight = 20878.795| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.93 r_work: 0.2875 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16932 Z= 0.217 Angle : 0.544 10.989 23012 Z= 0.275 Chirality : 0.041 0.247 2712 Planarity : 0.003 0.038 2728 Dihedral : 7.589 59.785 3564 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 3.24 % Allowed : 11.87 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.19), residues: 1908 helix: 1.43 (0.15), residues: 1108 sheet: -1.34 (0.35), residues: 200 loop : -1.07 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 464 TYR 0.016 0.002 TYR A 486 PHE 0.022 0.002 PHE C 600 TRP 0.010 0.001 TRP A 554 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00512 (16912) covalent geometry : angle 0.53819 (22956) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.61682 ( 8) hydrogen bonds : bond 0.04568 ( 936) hydrogen bonds : angle 3.98953 ( 2712) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.57280 ( 12) link_NAG-ASN : bond 0.00364 ( 12) link_NAG-ASN : angle 1.80941 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.656 Fit side-chains REVERT: A 245 ASN cc_start: 0.7792 (m-40) cc_final: 0.6969 (p0) REVERT: A 488 VAL cc_start: 0.8952 (t) cc_final: 0.8658 (m) REVERT: A 650 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8083 (tt0) REVERT: A 673 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 245 ASN cc_start: 0.7905 (m-40) cc_final: 0.7024 (p0) REVERT: B 275 SER cc_start: 0.8927 (p) cc_final: 0.8659 (t) REVERT: B 650 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8063 (tt0) REVERT: C 223 GLU cc_start: 0.7124 (pt0) cc_final: 0.6830 (tp30) REVERT: C 245 ASN cc_start: 0.7897 (m-40) cc_final: 0.7179 (p0) REVERT: C 275 SER cc_start: 0.8960 (p) cc_final: 0.8650 (t) REVERT: C 673 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8869 (mp) REVERT: D 223 GLU cc_start: 0.7006 (pt0) cc_final: 0.6746 (tp30) REVERT: D 245 ASN cc_start: 0.7738 (m-40) cc_final: 0.7023 (p0) REVERT: D 488 VAL cc_start: 0.8934 (t) cc_final: 0.8641 (m) REVERT: D 650 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8048 (tt0) REVERT: D 673 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8792 (mp) outliers start: 54 outliers final: 45 residues processed: 257 average time/residue: 0.1051 time to fit residues: 45.0613 Evaluate side-chains 253 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN B 585 GLN B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN D 542 GLN D 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107905 restraints weight = 20685.803| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.93 r_work: 0.2906 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16932 Z= 0.157 Angle : 0.499 10.370 23012 Z= 0.254 Chirality : 0.039 0.246 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.406 58.682 3564 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.88 % Favored : 96.91 % Rotamer: Outliers : 3.18 % Allowed : 12.41 % Favored : 84.41 % 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: 0.64 (0.19), residues: 1908 helix: 1.53 (0.15), residues: 1108 sheet: -1.23 (0.35), residues: 200 loop : -1.03 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 464 TYR 0.017 0.001 TYR D 486 PHE 0.023 0.001 PHE B 600 TRP 0.008 0.001 TRP A 414 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00362 (16912) covalent geometry : angle 0.49346 (22956) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.55934 ( 8) hydrogen bonds : bond 0.04338 ( 936) hydrogen bonds : angle 3.89999 ( 2712) link_BETA1-4 : bond 0.00276 ( 4) link_BETA1-4 : angle 1.41999 ( 12) link_NAG-ASN : bond 0.00370 ( 12) link_NAG-ASN : angle 1.74428 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.624 Fit side-chains REVERT: A 245 ASN cc_start: 0.7812 (m-40) cc_final: 0.7016 (p0) REVERT: A 488 VAL cc_start: 0.8953 (t) cc_final: 0.8659 (m) REVERT: A 650 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8050 (tt0) REVERT: A 673 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 245 ASN cc_start: 0.7916 (m-40) cc_final: 0.7107 (p0) REVERT: B 275 SER cc_start: 0.8918 (p) cc_final: 0.8646 (t) REVERT: B 650 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8014 (tt0) REVERT: C 223 GLU cc_start: 0.7136 (pt0) cc_final: 0.6832 (tp30) REVERT: C 245 ASN cc_start: 0.7830 (m-40) cc_final: 0.7161 (p0) REVERT: C 275 SER cc_start: 0.8948 (p) cc_final: 0.8636 (t) REVERT: C 673 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8817 (mp) REVERT: D 223 GLU cc_start: 0.6973 (pt0) cc_final: 0.6725 (tp30) REVERT: D 245 ASN cc_start: 0.7783 (m-40) cc_final: 0.7100 (p0) REVERT: D 488 VAL cc_start: 0.8956 (t) cc_final: 0.8663 (m) REVERT: D 650 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8003 (tt0) REVERT: D 673 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8763 (mp) outliers start: 53 outliers final: 48 residues processed: 256 average time/residue: 0.1137 time to fit residues: 47.1129 Evaluate side-chains 259 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 143 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 GLN D 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104863 restraints weight = 20797.318| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.04 r_work: 0.2883 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.147 Angle : 0.494 10.397 23012 Z= 0.250 Chirality : 0.039 0.239 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.175 59.606 3564 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.78 % Favored : 97.01 % Rotamer: Outliers : 3.00 % Allowed : 12.77 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.19), residues: 1908 helix: 1.59 (0.15), residues: 1108 sheet: -1.17 (0.35), residues: 200 loop : -1.01 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 464 TYR 0.017 0.001 TYR A 486 PHE 0.022 0.001 PHE B 600 TRP 0.008 0.001 TRP D 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00338 (16912) covalent geometry : angle 0.48926 (22956) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.54089 ( 8) hydrogen bonds : bond 0.04265 ( 936) hydrogen bonds : angle 3.86783 ( 2712) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.38047 ( 12) link_NAG-ASN : bond 0.00359 ( 12) link_NAG-ASN : angle 1.65578 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.631 Fit side-chains REVERT: A 245 ASN cc_start: 0.7804 (m-40) cc_final: 0.7055 (p0) REVERT: A 312 GLU cc_start: 0.8637 (tp30) cc_final: 0.8413 (mm-30) REVERT: A 488 VAL cc_start: 0.8915 (t) cc_final: 0.8619 (m) REVERT: A 650 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8035 (tt0) REVERT: A 673 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 245 ASN cc_start: 0.7888 (m-40) cc_final: 0.7077 (p0) REVERT: B 275 SER cc_start: 0.8896 (p) cc_final: 0.8670 (t) REVERT: B 650 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7996 (tt0) REVERT: C 223 GLU cc_start: 0.7089 (pt0) cc_final: 0.6781 (tp30) REVERT: C 245 ASN cc_start: 0.7811 (m-40) cc_final: 0.7189 (p0) REVERT: C 275 SER cc_start: 0.8968 (p) cc_final: 0.8703 (t) REVERT: C 312 GLU cc_start: 0.8677 (tp30) cc_final: 0.8226 (mm-30) REVERT: C 673 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8838 (mp) REVERT: D 223 GLU cc_start: 0.7056 (pt0) cc_final: 0.6629 (tp30) REVERT: D 245 ASN cc_start: 0.7764 (m-40) cc_final: 0.7086 (p0) REVERT: D 312 GLU cc_start: 0.8689 (tp30) cc_final: 0.8319 (mm-30) REVERT: D 488 VAL cc_start: 0.8927 (t) cc_final: 0.8627 (m) REVERT: D 650 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8010 (tt0) REVERT: D 673 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8782 (mp) outliers start: 50 outliers final: 46 residues processed: 253 average time/residue: 0.1094 time to fit residues: 44.8091 Evaluate side-chains 252 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108884 restraints weight = 20634.062| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.92 r_work: 0.2933 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16932 Z= 0.108 Angle : 0.467 9.863 23012 Z= 0.237 Chirality : 0.038 0.235 2712 Planarity : 0.003 0.035 2728 Dihedral : 6.807 58.676 3564 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.46 % Favored : 97.33 % Rotamer: Outliers : 2.70 % Allowed : 13.13 % Favored : 84.17 % 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: 0.91 (0.19), residues: 1908 helix: 1.73 (0.15), residues: 1108 sheet: -1.01 (0.35), residues: 200 loop : -0.91 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 464 TYR 0.017 0.001 TYR D 486 PHE 0.020 0.001 PHE B 600 TRP 0.007 0.001 TRP B 414 HIS 0.001 0.000 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00235 (16912) covalent geometry : angle 0.46254 (22956) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.46711 ( 8) hydrogen bonds : bond 0.04024 ( 936) hydrogen bonds : angle 3.77701 ( 2712) link_BETA1-4 : bond 0.00276 ( 4) link_BETA1-4 : angle 1.24648 ( 12) link_NAG-ASN : bond 0.00348 ( 12) link_NAG-ASN : angle 1.54753 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3731.81 seconds wall clock time: 64 minutes 50.23 seconds (3890.23 seconds total)