Starting phenix.real_space_refine on Thu Jun 4 14:32:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1m_70012/06_2026/9o1m_70012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1m_70012/06_2026/9o1m_70012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o1m_70012/06_2026/9o1m_70012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1m_70012/06_2026/9o1m_70012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o1m_70012/06_2026/9o1m_70012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1m_70012/06_2026/9o1m_70012.map" } resolution = 2.92 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= 0.003 sd= 0.043 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 10 5.49 5 S 82 5.16 5 C 8744 2.51 5 N 2090 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13322 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6475 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 36, 'TRANS': 752} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 186 Unusual residues: {' CA': 3, 'PGW': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: A Time building chain proxies: 6.45, per 1000 atoms: 0.48 Number of scatterers: 13322 At special positions: 0 Unit cell: (83.325, 132.825, 120.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 82 16.00 P 10 15.00 O 2390 8.00 N 2090 7.00 C 8744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 518.7 milliseconds 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 10 sheets defined 61.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 90 through 103 removed outlier: 5.833A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 removed outlier: 4.002A pdb=" N HIS B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.816A pdb=" N MET B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.766A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.894A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.601A pdb=" N CYS B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.642A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.812A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 458 through 489 removed outlier: 3.706A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 539 removed outlier: 3.700A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.466A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.572A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.814A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.661A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 796 through 802 removed outlier: 3.808A pdb=" N ILE B 799 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 886 removed outlier: 3.538A pdb=" N LYS B 869 " --> pdb=" O LYS B 865 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 removed outlier: 5.833A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.003A pdb=" N HIS A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.816A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.766A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.894A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.601A pdb=" N CYS A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.643A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.812A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.706A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 539 removed outlier: 3.700A pdb=" N SER A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.467A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.572A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.813A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.661A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.809A pdb=" N ILE A 799 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 886 removed outlier: 3.537A pdb=" N LYS A 869 " --> pdb=" O LYS A 865 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.315A pdb=" N GLU B 51 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG B 116 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 removed outlier: 6.448A pdb=" N PHE B 183 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AA4, first strand: chain 'B' and resid 429 through 433 removed outlier: 3.899A pdb=" N ASN B 433 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 438 " --> pdb=" O ASN B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 782 through 785 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.315A pdb=" N GLU A 51 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG A 116 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 149 removed outlier: 6.448A pdb=" N PHE A 183 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 433 removed outlier: 3.899A pdb=" N ASN A 433 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 438 " --> pdb=" O ASN A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 782 through 785 724 hydrogen bonds defined for protein. 2112 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: 2.18 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2054 1.31 - 1.44: 3906 1.44 - 1.57: 7556 1.57 - 1.70: 22 1.70 - 1.83: 124 Bond restraints: 13662 Sorted by residual: bond pdb=" C1 PGW A1004 " pdb=" O01 PGW A1004 " ideal model delta sigma weight residual 1.332 1.458 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C1 PGW B1004 " pdb=" O01 PGW B1004 " ideal model delta sigma weight residual 1.332 1.458 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C1 PGW A1006 " pdb=" O01 PGW A1006 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C19 PGW B1006 " pdb=" O03 PGW B1006 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C19 PGW A1007 " pdb=" O03 PGW A1007 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 13657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 17847 2.15 - 4.29: 426 4.29 - 6.44: 129 6.44 - 8.58: 30 8.58 - 10.73: 34 Bond angle restraints: 18466 Sorted by residual: angle pdb=" C ILE B 762 " pdb=" N PRO B 763 " pdb=" CA PRO B 763 " ideal model delta sigma weight residual 120.38 127.01 -6.63 1.03e+00 9.43e-01 4.15e+01 angle pdb=" C ILE A 762 " pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 120.38 127.00 -6.62 1.03e+00 9.43e-01 4.13e+01 angle pdb=" C PHE B 572 " pdb=" N PHE B 573 " pdb=" CA PHE B 573 " ideal model delta sigma weight residual 122.08 115.80 6.28 1.53e+00 4.27e-01 1.69e+01 angle pdb=" C PHE A 572 " pdb=" N PHE A 573 " pdb=" CA PHE A 573 " ideal model delta sigma weight residual 122.08 115.80 6.28 1.53e+00 4.27e-01 1.68e+01 angle pdb=" N LYS B 590 " pdb=" CA LYS B 590 " pdb=" C LYS B 590 " ideal model delta sigma weight residual 112.72 107.52 5.20 1.28e+00 6.10e-01 1.65e+01 ... (remaining 18461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 7856 34.66 - 69.32: 294 69.32 - 103.98: 42 103.98 - 138.63: 4 138.63 - 173.29: 4 Dihedral angle restraints: 8200 sinusoidal: 3526 harmonic: 4674 Sorted by residual: dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 372 " pdb=" CB CYS B 372 " ideal model delta sinusoidal sigma weight residual -86.00 -141.73 55.73 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 372 " pdb=" CB CYS A 372 " ideal model delta sinusoidal sigma weight residual -86.00 -141.70 55.70 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CAD PGW B1008 " pdb=" C04 PGW B1008 " pdb=" C05 PGW B1008 " pdb=" O12 PGW B1008 " ideal model delta sinusoidal sigma weight residual 168.74 -17.97 -173.29 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1375 0.039 - 0.079: 479 0.079 - 0.118: 106 0.118 - 0.158: 16 0.158 - 0.197: 12 Chirality restraints: 1988 Sorted by residual: chirality pdb=" C02 PGW B1007 " pdb=" C01 PGW B1007 " pdb=" C03 PGW B1007 " pdb=" O01 PGW B1007 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" C02 PGW A1007 " pdb=" C01 PGW A1007 " pdb=" C03 PGW A1007 " pdb=" O01 PGW A1007 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" C02 PGW A1006 " pdb=" C01 PGW A1006 " pdb=" C03 PGW A1006 " pdb=" O01 PGW A1006 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1985 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 762 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ILE B 762 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE B 762 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 763 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 762 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ILE A 762 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 762 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 763 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 356 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 357 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 357 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 357 " 0.028 5.00e-02 4.00e+02 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 272 2.68 - 3.23: 13007 3.23 - 3.79: 20557 3.79 - 4.34: 26955 4.34 - 4.90: 44663 Nonbonded interactions: 105454 Sorted by model distance: nonbonded pdb=" OG1 THR B 772 " pdb=" OD1 ASP B 774 " model vdw 2.124 3.040 nonbonded pdb=" OG1 THR A 772 " pdb=" OD1 ASP A 774 " model vdw 2.125 3.040 nonbonded pdb=" N GLN A 68 " pdb=" OE1 GLN A 68 " model vdw 2.250 3.120 nonbonded pdb=" N GLN B 68 " pdb=" OE1 GLN B 68 " model vdw 2.250 3.120 nonbonded pdb=" N GLN B 414 " pdb=" OE1 GLN B 414 " model vdw 2.263 3.120 ... (remaining 105449 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.460 Find NCS groups from input model: 0.100 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 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 : 0.006 0.126 13672 Z= 0.283 Angle : 0.926 10.729 18486 Z= 0.442 Chirality : 0.043 0.197 1988 Planarity : 0.005 0.061 2288 Dihedral : 18.853 173.293 5162 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.21 % Allowed : 22.48 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.21), residues: 1562 helix: 1.35 (0.18), residues: 866 sheet: -0.06 (0.48), residues: 102 loop : -0.46 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 354 TYR 0.023 0.001 TYR B 580 PHE 0.013 0.001 PHE B 852 TRP 0.016 0.001 TRP A 273 HIS 0.001 0.000 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (13662) covalent geometry : angle 0.92506 / 0.44 (18466) SS BOND : bond 0.00262 / 0.15 ( 10) SS BOND : angle 1.48922 / 0.86 ( 20) hydrogen bonds : bond 0.15768 / 10.45 ( 724) hydrogen bonds : angle 6.21732 / 4.32 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 0.526 Fit side-chains REVERT: B 73 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.4551 (m-80) REVERT: B 192 MET cc_start: 0.6372 (mmp) cc_final: 0.5854 (mpt) REVERT: B 199 ASP cc_start: 0.5079 (t0) cc_final: 0.4813 (t0) REVERT: B 200 ARG cc_start: 0.7406 (mtt180) cc_final: 0.7058 (ttm170) REVERT: B 255 TYR cc_start: 0.6064 (m-80) cc_final: 0.5754 (m-80) REVERT: B 271 ARG cc_start: 0.6119 (mmm-85) cc_final: 0.5544 (mmm-85) REVERT: B 272 GLU cc_start: 0.6895 (tp30) cc_final: 0.6136 (tm-30) REVERT: B 277 ARG cc_start: 0.6087 (ttm-80) cc_final: 0.5252 (ptm160) REVERT: B 329 ASP cc_start: 0.8288 (t0) cc_final: 0.7746 (m-30) REVERT: B 347 LEU cc_start: 0.6705 (tt) cc_final: 0.6440 (tm) REVERT: B 555 MET cc_start: 0.6700 (mmm) cc_final: 0.6447 (mmt) REVERT: B 594 GLU cc_start: 0.6133 (pt0) cc_final: 0.5919 (pt0) REVERT: B 611 ILE cc_start: 0.6334 (mm) cc_final: 0.6060 (mp) REVERT: B 631 MET cc_start: 0.5734 (mmt) cc_final: 0.5515 (mmt) REVERT: B 661 LYS cc_start: 0.6853 (tppp) cc_final: 0.6615 (pttm) REVERT: B 810 ARG cc_start: 0.6607 (ttt-90) cc_final: 0.6338 (ttt-90) REVERT: B 852 PHE cc_start: 0.5174 (t80) cc_final: 0.3789 (m-10) REVERT: A 199 ASP cc_start: 0.5086 (t0) cc_final: 0.4822 (t0) REVERT: A 200 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7069 (ttm170) REVERT: A 255 TYR cc_start: 0.6137 (m-80) cc_final: 0.5822 (m-80) REVERT: A 271 ARG cc_start: 0.6113 (mmm-85) cc_final: 0.5532 (mmm-85) REVERT: A 272 GLU cc_start: 0.6868 (tp30) cc_final: 0.6095 (tm-30) REVERT: A 277 ARG cc_start: 0.6106 (ttm-80) cc_final: 0.5356 (ptm160) REVERT: A 555 MET cc_start: 0.6766 (mmm) cc_final: 0.6548 (mmt) REVERT: A 586 TYR cc_start: 0.7066 (m-80) cc_final: 0.6819 (m-80) REVERT: A 611 ILE cc_start: 0.6309 (mm) cc_final: 0.6053 (mp) REVERT: A 631 MET cc_start: 0.5739 (mmt) cc_final: 0.5299 (mtt) REVERT: A 661 LYS cc_start: 0.6935 (tppp) cc_final: 0.6641 (pttm) REVERT: A 810 ARG cc_start: 0.6523 (ttt-90) cc_final: 0.6276 (ttt-90) REVERT: A 852 PHE cc_start: 0.5344 (t80) cc_final: 0.3948 (m-10) REVERT: A 870 ARG cc_start: 0.5061 (ppp80) cc_final: 0.4676 (ttt180) outliers start: 3 outliers final: 0 residues processed: 229 average time/residue: 0.5605 time to fit residues: 141.1516 Evaluate side-chains 185 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS B 401 GLN B 437 GLN B 525 ASN B 549 ASN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 844 HIS A 143 HIS A 401 GLN A 437 GLN A 525 ASN A 549 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 785 ASN A 844 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.227254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150303 restraints weight = 12867.251| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.43 r_work: 0.3303 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13672 Z= 0.182 Angle : 0.634 11.868 18486 Z= 0.329 Chirality : 0.043 0.158 1988 Planarity : 0.005 0.047 2288 Dihedral : 15.611 168.106 2062 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.40 % Allowed : 18.23 % Favored : 77.38 % 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 (0.20), residues: 1562 helix: 1.25 (0.17), residues: 884 sheet: -0.25 (0.47), residues: 110 loop : -0.76 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 354 TYR 0.013 0.001 TYR B 668 PHE 0.022 0.002 PHE B 215 TRP 0.019 0.002 TRP A 273 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (13662) covalent geometry : angle 0.63216 / 0.33 (18466) SS BOND : bond 0.00154 / 0.10 ( 10) SS BOND : angle 1.67917 / 0.98 ( 20) hydrogen bonds : bond 0.05024 / 3.46 ( 724) hydrogen bonds : angle 4.80058 / 3.34 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 0.484 Fit side-chains REVERT: B 101 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.5684 (m-80) REVERT: B 183 PHE cc_start: 0.7406 (m-80) cc_final: 0.7091 (m-80) REVERT: B 199 ASP cc_start: 0.6417 (t0) cc_final: 0.6167 (t0) REVERT: B 225 MET cc_start: 0.2368 (ppp) cc_final: 0.1692 (mmm) REVERT: B 255 TYR cc_start: 0.7488 (m-80) cc_final: 0.7191 (m-80) REVERT: B 272 GLU cc_start: 0.7861 (tp30) cc_final: 0.7047 (tm-30) REVERT: B 277 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6688 (ptm160) REVERT: B 329 ASP cc_start: 0.8427 (t0) cc_final: 0.7959 (m-30) REVERT: B 366 GLU cc_start: 0.6695 (mp0) cc_final: 0.6340 (mm-30) REVERT: B 465 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6686 (mt) REVERT: B 667 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: B 852 PHE cc_start: 0.7685 (t80) cc_final: 0.6063 (m-80) REVERT: B 864 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7629 (m) REVERT: A 113 GLU cc_start: 0.7172 (tt0) cc_final: 0.6826 (pt0) REVERT: A 199 ASP cc_start: 0.6443 (t0) cc_final: 0.6206 (t0) REVERT: A 255 TYR cc_start: 0.7543 (m-80) cc_final: 0.7243 (m-80) REVERT: A 272 GLU cc_start: 0.7895 (tp30) cc_final: 0.7026 (tm-30) REVERT: A 277 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6668 (ptm160) REVERT: A 329 ASP cc_start: 0.8357 (t0) cc_final: 0.8143 (m-30) REVERT: A 465 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6775 (mt) REVERT: A 622 ILE cc_start: 0.7543 (mm) cc_final: 0.7217 (mt) REVERT: A 631 MET cc_start: 0.6547 (mmt) cc_final: 0.6336 (mtp) REVERT: A 667 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: A 852 PHE cc_start: 0.7728 (t80) cc_final: 0.6089 (m-80) REVERT: A 870 ARG cc_start: 0.6054 (ppp80) cc_final: 0.5576 (ttt180) outliers start: 62 outliers final: 12 residues processed: 227 average time/residue: 0.5293 time to fit residues: 132.1583 Evaluate side-chains 186 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 862 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 632 ASN B 652 GLN B 785 ASN A 525 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 726 GLN A 730 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.229356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149560 restraints weight = 12974.546| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.35 r_work: 0.3342 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13672 Z= 0.119 Angle : 0.522 10.821 18486 Z= 0.273 Chirality : 0.040 0.166 1988 Planarity : 0.005 0.048 2288 Dihedral : 14.559 162.694 2060 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.40 % Allowed : 19.22 % Favored : 77.38 % 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: 0.84 (0.20), residues: 1562 helix: 1.53 (0.17), residues: 882 sheet: -0.20 (0.48), residues: 102 loop : -0.80 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.008 0.001 TYR A 306 PHE 0.019 0.001 PHE A 215 TRP 0.017 0.001 TRP A 273 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13662) covalent geometry : angle 0.52080 / 0.27 (18466) SS BOND : bond 0.00103 / 0.06 ( 10) SS BOND : angle 1.33953 / 0.77 ( 20) hydrogen bonds : bond 0.04188 / 2.89 ( 724) hydrogen bonds : angle 4.58200 / 3.18 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.501 Fit side-chains REVERT: B 73 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: B 183 PHE cc_start: 0.7568 (m-80) cc_final: 0.7219 (m-80) REVERT: B 255 TYR cc_start: 0.7478 (m-80) cc_final: 0.7183 (m-80) REVERT: B 272 GLU cc_start: 0.7730 (tp30) cc_final: 0.7152 (tp30) REVERT: B 277 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6741 (ptm160) REVERT: B 329 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: B 465 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6765 (mt) REVERT: B 523 ILE cc_start: 0.7795 (tt) cc_final: 0.7516 (pt) REVERT: B 553 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7867 (tpt) REVERT: B 631 MET cc_start: 0.6522 (mtp) cc_final: 0.5827 (mtt) REVERT: B 659 MET cc_start: 0.6982 (mtp) cc_final: 0.6742 (mtm) REVERT: B 667 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: B 852 PHE cc_start: 0.7655 (t80) cc_final: 0.6241 (m-10) REVERT: B 864 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7601 (m) REVERT: B 870 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5899 (ttt180) REVERT: A 255 TYR cc_start: 0.7506 (m-80) cc_final: 0.7241 (m-80) REVERT: A 272 GLU cc_start: 0.7760 (tp30) cc_final: 0.7157 (tp30) REVERT: A 277 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6736 (ptm160) REVERT: A 465 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6753 (mt) REVERT: A 522 MET cc_start: 0.8364 (tpp) cc_final: 0.8148 (tpt) REVERT: A 523 ILE cc_start: 0.7762 (tt) cc_final: 0.7411 (pt) REVERT: A 553 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7857 (tpt) REVERT: A 659 MET cc_start: 0.6973 (mtp) cc_final: 0.6703 (mtm) REVERT: A 667 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8314 (mm-30) REVERT: A 852 PHE cc_start: 0.7674 (t80) cc_final: 0.6212 (m-10) REVERT: A 870 ARG cc_start: 0.6145 (ppp80) cc_final: 0.5730 (ttt180) outliers start: 48 outliers final: 10 residues processed: 201 average time/residue: 0.4980 time to fit residues: 111.3050 Evaluate side-chains 184 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 862 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 17 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS A 108 HIS ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.218014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126969 restraints weight = 12620.384| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.22 r_work: 0.3235 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13672 Z= 0.228 Angle : 0.629 12.633 18486 Z= 0.327 Chirality : 0.044 0.165 1988 Planarity : 0.005 0.053 2288 Dihedral : 14.491 162.725 2060 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.75 % Allowed : 18.58 % Favored : 76.67 % 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: 0.35 (0.20), residues: 1562 helix: 1.06 (0.17), residues: 896 sheet: -0.41 (0.47), residues: 102 loop : -0.93 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 200 TYR 0.016 0.002 TYR A 668 PHE 0.022 0.002 PHE A 685 TRP 0.017 0.002 TRP A 273 HIS 0.006 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (13662) covalent geometry : angle 0.62640 / 0.33 (18466) SS BOND : bond 0.00140 / 0.08 ( 10) SS BOND : angle 1.73522 / 1.02 ( 20) hydrogen bonds : bond 0.05071 / 3.48 ( 724) hydrogen bonds : angle 4.77326 / 3.33 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: B 101 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: B 183 PHE cc_start: 0.7525 (m-80) cc_final: 0.7256 (m-10) REVERT: B 277 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6495 (ptm160) REVERT: B 289 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7966 (tmt90) REVERT: B 329 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: B 348 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7806 (mmm) REVERT: B 465 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6802 (mt) REVERT: B 603 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7815 (tp) REVERT: B 631 MET cc_start: 0.6406 (mtp) cc_final: 0.5872 (mtt) REVERT: B 659 MET cc_start: 0.7230 (mtp) cc_final: 0.7010 (mtm) REVERT: B 667 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: B 714 MET cc_start: 0.7870 (mtt) cc_final: 0.7654 (mtt) REVERT: B 852 PHE cc_start: 0.7712 (t80) cc_final: 0.7452 (t80) REVERT: B 870 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5843 (ttt180) REVERT: B 874 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.5093 (tt) REVERT: A 101 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: A 183 PHE cc_start: 0.7558 (m-80) cc_final: 0.7305 (m-10) REVERT: A 255 TYR cc_start: 0.7369 (m-80) cc_final: 0.6993 (m-80) REVERT: A 277 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6472 (ptm160) REVERT: A 289 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7993 (tmt90) REVERT: A 329 ASP cc_start: 0.8462 (m-30) cc_final: 0.8211 (m-30) REVERT: A 348 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7836 (mmm) REVERT: A 465 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6775 (mt) REVERT: A 603 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 667 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: A 852 PHE cc_start: 0.7718 (t80) cc_final: 0.7451 (t80) REVERT: A 870 ARG cc_start: 0.5987 (ppp80) cc_final: 0.5621 (ttt180) outliers start: 67 outliers final: 22 residues processed: 214 average time/residue: 0.5166 time to fit residues: 122.6621 Evaluate side-chains 195 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 874 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.224392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140849 restraints weight = 12718.984| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.98 r_work: 0.3248 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13672 Z= 0.109 Angle : 0.501 10.554 18486 Z= 0.263 Chirality : 0.040 0.182 1988 Planarity : 0.005 0.057 2288 Dihedral : 13.429 152.406 2060 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.19 % Allowed : 20.28 % Favored : 76.52 % 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: 0.75 (0.21), residues: 1562 helix: 1.47 (0.17), residues: 894 sheet: -0.33 (0.48), residues: 102 loop : -0.89 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.021 0.001 TYR A 580 PHE 0.018 0.001 PHE A 215 TRP 0.020 0.001 TRP B 273 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13662) covalent geometry : angle 0.49958 / 0.26 (18466) SS BOND : bond 0.00090 / 0.05 ( 10) SS BOND : angle 1.28102 / 0.75 ( 20) hydrogen bonds : bond 0.03828 / 2.63 ( 724) hydrogen bonds : angle 4.46748 / 3.11 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.536 Fit side-chains REVERT: B 73 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: B 101 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: B 183 PHE cc_start: 0.7539 (m-80) cc_final: 0.7229 (m-10) REVERT: B 191 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7105 (mtp180) REVERT: B 272 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7049 (tp30) REVERT: B 277 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6557 (ptm160) REVERT: B 329 ASP cc_start: 0.8506 (t0) cc_final: 0.8046 (m-30) REVERT: B 465 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6664 (mt) REVERT: B 529 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: B 553 MET cc_start: 0.8214 (tpp) cc_final: 0.7890 (tpt) REVERT: B 555 MET cc_start: 0.8558 (mmt) cc_final: 0.8291 (mmt) REVERT: B 631 MET cc_start: 0.6475 (mtp) cc_final: 0.5936 (mtt) REVERT: B 667 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: B 852 PHE cc_start: 0.7623 (t80) cc_final: 0.6086 (m-10) REVERT: B 864 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7338 (m) REVERT: B 870 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5683 (ttt180) REVERT: A 101 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 277 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6549 (ptm160) REVERT: A 329 ASP cc_start: 0.8350 (m-30) cc_final: 0.8108 (m-30) REVERT: A 465 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6670 (mt) REVERT: A 522 MET cc_start: 0.8098 (tpp) cc_final: 0.7827 (mmm) REVERT: A 553 MET cc_start: 0.8198 (tpp) cc_final: 0.7881 (tpt) REVERT: A 631 MET cc_start: 0.6524 (mtp) cc_final: 0.5981 (mtt) REVERT: A 667 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: A 749 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8053 (t70) REVERT: A 852 PHE cc_start: 0.7609 (t80) cc_final: 0.7342 (t80) REVERT: A 870 ARG cc_start: 0.5866 (ppp80) cc_final: 0.5554 (ttt180) outliers start: 45 outliers final: 9 residues processed: 187 average time/residue: 0.4940 time to fit residues: 102.8267 Evaluate side-chains 178 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 874 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 141 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.223817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135040 restraints weight = 12638.994| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.68 r_work: 0.3280 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 13672 Z= 0.114 Angle : 0.505 12.228 18486 Z= 0.262 Chirality : 0.040 0.190 1988 Planarity : 0.005 0.059 2288 Dihedral : 12.870 137.581 2060 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.40 % Allowed : 19.57 % Favored : 76.03 % 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: 0.85 (0.21), residues: 1562 helix: 1.57 (0.17), residues: 896 sheet: -0.25 (0.49), residues: 102 loop : -0.89 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.021 0.001 TYR A 580 PHE 0.018 0.001 PHE A 215 TRP 0.018 0.001 TRP A 273 HIS 0.014 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (13662) covalent geometry : angle 0.50333 / 0.26 (18466) SS BOND : bond 0.00082 / 0.04 ( 10) SS BOND : angle 1.28271 / 0.75 ( 20) hydrogen bonds : bond 0.03821 / 2.62 ( 724) hydrogen bonds : angle 4.41925 / 3.08 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: B 101 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: B 183 PHE cc_start: 0.7535 (m-80) cc_final: 0.7273 (m-10) REVERT: B 198 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7717 (mm) REVERT: B 272 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: B 277 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6613 (ptm160) REVERT: B 329 ASP cc_start: 0.8555 (t0) cc_final: 0.8074 (m-30) REVERT: B 465 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6711 (mt) REVERT: B 631 MET cc_start: 0.6542 (mtp) cc_final: 0.6037 (mtt) REVERT: B 667 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: B 749 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7996 (t70) REVERT: B 852 PHE cc_start: 0.7612 (t80) cc_final: 0.6103 (m-10) REVERT: B 864 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7386 (m) REVERT: B 870 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5707 (ttt180) REVERT: A 101 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: A 198 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7719 (mm) REVERT: A 277 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6561 (ptm160) REVERT: A 522 MET cc_start: 0.8172 (tpp) cc_final: 0.7884 (mmt) REVERT: A 631 MET cc_start: 0.6503 (mtp) cc_final: 0.5975 (mtt) REVERT: A 667 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8301 (mm-30) REVERT: A 749 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8051 (t70) REVERT: A 852 PHE cc_start: 0.7609 (t80) cc_final: 0.7340 (t80) REVERT: A 870 ARG cc_start: 0.5961 (ppp80) cc_final: 0.5664 (ttt180) outliers start: 62 outliers final: 17 residues processed: 204 average time/residue: 0.4828 time to fit residues: 110.1088 Evaluate side-chains 185 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 749 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 0.0010 chunk 150 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.223787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135276 restraints weight = 12581.320| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.52 r_work: 0.3284 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13672 Z= 0.121 Angle : 0.513 13.138 18486 Z= 0.266 Chirality : 0.040 0.192 1988 Planarity : 0.005 0.059 2288 Dihedral : 12.259 115.021 2060 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.18 % Allowed : 20.00 % Favored : 75.82 % 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: 0.84 (0.21), residues: 1562 helix: 1.56 (0.17), residues: 898 sheet: -0.23 (0.49), residues: 102 loop : -0.91 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 360 TYR 0.022 0.001 TYR A 580 PHE 0.018 0.001 PHE B 215 TRP 0.017 0.001 TRP A 273 HIS 0.011 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (13662) covalent geometry : angle 0.51117 / 0.27 (18466) SS BOND : bond 0.00074 / 0.05 ( 10) SS BOND : angle 1.33925 / 0.79 ( 20) hydrogen bonds : bond 0.03854 / 2.64 ( 724) hydrogen bonds : angle 4.43726 / 3.09 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: B 101 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: B 183 PHE cc_start: 0.7513 (m-80) cc_final: 0.7280 (m-10) REVERT: B 198 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7686 (mm) REVERT: B 272 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: B 277 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6567 (ptm160) REVERT: B 329 ASP cc_start: 0.8584 (t0) cc_final: 0.8074 (m-30) REVERT: B 534 MET cc_start: 0.6447 (mtt) cc_final: 0.6149 (mtp) REVERT: B 631 MET cc_start: 0.6490 (mtp) cc_final: 0.6005 (mtt) REVERT: B 667 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: B 749 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7978 (t70) REVERT: B 852 PHE cc_start: 0.7568 (t80) cc_final: 0.6077 (m-10) REVERT: B 864 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7362 (m) REVERT: B 870 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5697 (ttt180) REVERT: A 101 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: A 198 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7687 (mm) REVERT: A 277 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6552 (ptm160) REVERT: A 522 MET cc_start: 0.8128 (tpp) cc_final: 0.7896 (mmt) REVERT: A 534 MET cc_start: 0.6465 (mtt) cc_final: 0.6167 (mtp) REVERT: A 631 MET cc_start: 0.6526 (mtp) cc_final: 0.6013 (mtt) REVERT: A 667 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: A 749 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8025 (t70) REVERT: A 852 PHE cc_start: 0.7583 (t80) cc_final: 0.7316 (t80) REVERT: A 870 ARG cc_start: 0.5978 (ppp80) cc_final: 0.5502 (ptm160) outliers start: 59 outliers final: 24 residues processed: 203 average time/residue: 0.4816 time to fit residues: 109.4557 Evaluate side-chains 192 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 862 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.222876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133298 restraints weight = 12566.760| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.21 r_work: 0.3278 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13672 Z= 0.135 Angle : 0.535 14.057 18486 Z= 0.275 Chirality : 0.040 0.191 1988 Planarity : 0.005 0.057 2288 Dihedral : 11.729 85.895 2060 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.97 % Allowed : 20.07 % Favored : 75.96 % 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: 0.76 (0.21), residues: 1562 helix: 1.50 (0.17), residues: 898 sheet: -0.30 (0.48), residues: 102 loop : -0.96 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 360 TYR 0.025 0.001 TYR A 580 PHE 0.021 0.001 PHE A 215 TRP 0.016 0.001 TRP B 273 HIS 0.015 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (13662) covalent geometry : angle 0.53321 / 0.27 (18466) SS BOND : bond 0.00079 / 0.05 ( 10) SS BOND : angle 1.37712 / 0.81 ( 20) hydrogen bonds : bond 0.03997 / 2.74 ( 724) hydrogen bonds : angle 4.47704 / 3.13 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5796 (ttp-170) REVERT: B 73 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: B 101 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: B 183 PHE cc_start: 0.7596 (m-80) cc_final: 0.7354 (m-10) REVERT: B 198 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7656 (mm) REVERT: B 272 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: B 277 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6704 (ptm160) REVERT: B 289 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7811 (tmt90) REVERT: B 329 ASP cc_start: 0.8558 (t0) cc_final: 0.8057 (m-30) REVERT: B 534 MET cc_start: 0.6573 (mtt) cc_final: 0.6236 (mtp) REVERT: B 631 MET cc_start: 0.6531 (mtp) cc_final: 0.6058 (mtt) REVERT: B 667 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8422 (mm-30) REVERT: B 749 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8029 (t70) REVERT: B 852 PHE cc_start: 0.7635 (t80) cc_final: 0.7394 (t80) REVERT: B 864 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7432 (m) REVERT: B 870 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.5839 (ttt180) REVERT: A 101 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: A 198 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7691 (mm) REVERT: A 277 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6639 (ptm160) REVERT: A 289 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7816 (tmt90) REVERT: A 534 MET cc_start: 0.6584 (mtt) cc_final: 0.6299 (mtm) REVERT: A 631 MET cc_start: 0.6634 (mtp) cc_final: 0.6124 (mtt) REVERT: A 667 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: A 749 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8114 (t70) REVERT: A 852 PHE cc_start: 0.7670 (t80) cc_final: 0.7418 (t80) REVERT: A 870 ARG cc_start: 0.6034 (ppp80) cc_final: 0.5560 (ptm160) outliers start: 56 outliers final: 23 residues processed: 204 average time/residue: 0.4950 time to fit residues: 112.5265 Evaluate side-chains 195 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 862 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 147 optimal weight: 0.0010 chunk 119 optimal weight: 4.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 GLN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.217788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127871 restraints weight = 12745.418| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.20 r_work: 0.3230 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13672 Z= 0.226 Angle : 0.623 15.366 18486 Z= 0.321 Chirality : 0.044 0.191 1988 Planarity : 0.005 0.058 2288 Dihedral : 12.114 85.580 2060 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.40 % Allowed : 19.15 % Favored : 76.45 % 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: 0.38 (0.20), residues: 1562 helix: 1.17 (0.17), residues: 898 sheet: -0.41 (0.48), residues: 102 loop : -1.09 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.032 0.002 TYR B 580 PHE 0.026 0.002 PHE A 215 TRP 0.013 0.002 TRP A 273 HIS 0.014 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 (13662) covalent geometry : angle 0.62125 / 0.32 (18466) SS BOND : bond 0.00099 / 0.06 ( 10) SS BOND : angle 1.68622 / 1.00 ( 20) hydrogen bonds : bond 0.04820 / 3.30 ( 724) hydrogen bonds : angle 4.69175 / 3.29 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: B 101 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: B 183 PHE cc_start: 0.7633 (m-80) cc_final: 0.7416 (m-10) REVERT: B 198 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7663 (mm) REVERT: B 272 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: B 277 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6763 (ptm160) REVERT: B 289 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7883 (tmt90) REVERT: B 329 ASP cc_start: 0.8543 (t0) cc_final: 0.8122 (m-30) REVERT: B 465 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6765 (mt) REVERT: B 534 MET cc_start: 0.6521 (mtt) cc_final: 0.6214 (mtp) REVERT: B 631 MET cc_start: 0.6638 (mtp) cc_final: 0.6152 (mtt) REVERT: B 667 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8536 (mm-30) REVERT: B 852 PHE cc_start: 0.7633 (t80) cc_final: 0.7353 (t80) REVERT: B 870 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5848 (ttt180) REVERT: A 101 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6589 (m-80) REVERT: A 198 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 277 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6828 (ptm160) REVERT: A 289 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7902 (tmt90) REVERT: A 329 ASP cc_start: 0.8460 (m-30) cc_final: 0.8203 (m-30) REVERT: A 465 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6878 (mt) REVERT: A 534 MET cc_start: 0.6532 (mtt) cc_final: 0.6232 (mtp) REVERT: A 622 ILE cc_start: 0.7633 (mm) cc_final: 0.7337 (OUTLIER) REVERT: A 631 MET cc_start: 0.6637 (mtp) cc_final: 0.6127 (mtt) REVERT: A 667 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: A 749 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8130 (t70) REVERT: A 852 PHE cc_start: 0.7627 (t80) cc_final: 0.7339 (t80) REVERT: A 870 ARG cc_start: 0.6124 (ppp80) cc_final: 0.5597 (ptm160) outliers start: 62 outliers final: 24 residues processed: 200 average time/residue: 0.4788 time to fit residues: 106.9683 Evaluate side-chains 191 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 862 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 89 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.224347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136472 restraints weight = 12711.914| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.19 r_work: 0.3302 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13672 Z= 0.111 Angle : 0.532 14.437 18486 Z= 0.272 Chirality : 0.040 0.209 1988 Planarity : 0.005 0.057 2288 Dihedral : 11.007 77.958 2060 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.55 % Allowed : 21.28 % Favored : 76.17 % 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: 0.73 (0.21), residues: 1562 helix: 1.51 (0.17), residues: 898 sheet: -0.37 (0.49), residues: 102 loop : -1.02 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 360 TYR 0.027 0.001 TYR A 580 PHE 0.026 0.001 PHE A 215 TRP 0.019 0.001 TRP B 273 HIS 0.014 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13662) covalent geometry : angle 0.53027 / 0.27 (18466) SS BOND : bond 0.00090 / 0.06 ( 10) SS BOND : angle 1.30462 / 0.77 ( 20) hydrogen bonds : bond 0.03773 / 2.59 ( 724) hydrogen bonds : angle 4.44954 / 3.11 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: B 101 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: B 183 PHE cc_start: 0.7532 (m-80) cc_final: 0.7317 (m-10) REVERT: B 198 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 277 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6772 (ptm160) REVERT: B 329 ASP cc_start: 0.8463 (t0) cc_final: 0.8049 (m-30) REVERT: B 534 MET cc_start: 0.6393 (mtt) cc_final: 0.6103 (mtp) REVERT: B 553 MET cc_start: 0.8130 (tpp) cc_final: 0.7841 (tpt) REVERT: B 631 MET cc_start: 0.6617 (mtp) cc_final: 0.6144 (mtt) REVERT: B 667 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: B 864 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7355 (m) REVERT: B 870 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.5749 (ttt180) REVERT: A 198 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7683 (mm) REVERT: A 225 MET cc_start: 0.4227 (pmt) cc_final: 0.3284 (ttm) REVERT: A 277 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6749 (ptm160) REVERT: A 329 ASP cc_start: 0.8352 (m-30) cc_final: 0.8117 (m-30) REVERT: A 534 MET cc_start: 0.6391 (mtt) cc_final: 0.6118 (mtp) REVERT: A 553 MET cc_start: 0.8114 (tpp) cc_final: 0.7839 (tpt) REVERT: A 631 MET cc_start: 0.6635 (mtp) cc_final: 0.6146 (mtt) REVERT: A 667 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: A 749 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8099 (t70) REVERT: A 870 ARG cc_start: 0.6055 (ppp80) cc_final: 0.5551 (ptm160) outliers start: 36 outliers final: 14 residues processed: 181 average time/residue: 0.5082 time to fit residues: 103.0409 Evaluate side-chains 175 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 862 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 0.0470 chunk 113 optimal weight: 9.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** 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 = 0.4453 r_free = 0.4453 target = 0.222787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140099 restraints weight = 12692.221| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.84 r_work: 0.3236 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13672 Z= 0.140 Angle : 0.559 15.098 18486 Z= 0.284 Chirality : 0.041 0.198 1988 Planarity : 0.005 0.058 2288 Dihedral : 10.962 87.964 2060 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.77 % Allowed : 20.92 % Favored : 76.31 % 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: 0.67 (0.21), residues: 1562 helix: 1.49 (0.17), residues: 896 sheet: -0.48 (0.48), residues: 102 loop : -1.08 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 360 TYR 0.026 0.001 TYR A 580 PHE 0.025 0.002 PHE A 215 TRP 0.016 0.001 TRP B 273 HIS 0.016 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13662) covalent geometry : angle 0.55686 / 0.28 (18466) SS BOND : bond 0.00077 / 0.05 ( 10) SS BOND : angle 1.43294 / 0.84 ( 20) hydrogen bonds : bond 0.04057 / 2.78 ( 724) hydrogen bonds : angle 4.49995 / 3.15 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5064.60 seconds wall clock time: 86 minutes 59.67 seconds (5219.67 seconds total)