Starting phenix.real_space_refine on Fri Jul 3 10:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1m_70012/07_2026/9o1m_70012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1m_70012/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1m_70012/07_2026/9o1m_70012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1m_70012/07_2026/9o1m_70012.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1m_70012/07_2026/9o1m_70012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1m_70012/07_2026/9o1m_70012.cif" } 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-6108/lib/python3.11/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, 183 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'PGW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 3 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: 5.74, per 1000 atoms: 0.43 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: 1.03 Conformation dependent library (CDL) restraints added in 440.0 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: 0.32 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: 2.19 Time building geometry restraints manager: 1.37 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.770 Find NCS groups from input model: 0.070 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:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 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 : 0.378 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: 0.4944 time to fit residues: 125.2205 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 : 0.300 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4486 r_free = 0.4486 target = 0.229447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147904 restraints weight = 12907.192| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.47 r_work: 0.3157 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13672 Z= 0.167 Angle : 0.612 11.615 18486 Z= 0.319 Chirality : 0.042 0.162 1988 Planarity : 0.005 0.048 2288 Dihedral : 15.463 166.939 2062 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.90 % Allowed : 19.01 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1562 helix: 1.35 (0.17), residues: 882 sheet: -0.19 (0.48), residues: 110 loop : -0.76 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 354 TYR 0.013 0.001 TYR B 668 PHE 0.023 0.002 PHE B 215 TRP 0.020 0.001 TRP A 273 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (13662) covalent geometry : angle 0.61052 / 0.32 (18466) SS BOND : bond 0.00163 / 0.10 ( 10) SS BOND : angle 1.56697 / 0.91 ( 20) hydrogen bonds : bond 0.04771 / 3.29 ( 724) hydrogen bonds : angle 4.73803 / 3.29 ( 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 243 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.470 Fit side-chains REVERT: B 101 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: B 183 PHE cc_start: 0.7402 (m-80) cc_final: 0.7127 (m-80) REVERT: B 199 ASP cc_start: 0.6428 (t0) cc_final: 0.6159 (t0) REVERT: B 225 MET cc_start: 0.2312 (ppp) cc_final: 0.1604 (mmm) REVERT: B 255 TYR cc_start: 0.7453 (m-80) cc_final: 0.7191 (m-80) REVERT: B 272 GLU cc_start: 0.7733 (tp30) cc_final: 0.7001 (tm-30) REVERT: B 329 ASP cc_start: 0.8365 (t0) cc_final: 0.7923 (m-30) REVERT: B 366 GLU cc_start: 0.6641 (mp0) cc_final: 0.6265 (mm-30) REVERT: B 465 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6717 (mt) REVERT: B 622 ILE cc_start: 0.7615 (mm) cc_final: 0.7290 (mt) REVERT: B 667 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: B 852 PHE cc_start: 0.7566 (t80) cc_final: 0.6031 (m-80) REVERT: A 199 ASP cc_start: 0.6397 (t0) cc_final: 0.6151 (t0) REVERT: A 255 TYR cc_start: 0.7469 (m-80) cc_final: 0.7235 (m-80) REVERT: A 271 ARG cc_start: 0.7282 (mmm-85) cc_final: 0.7056 (mmm-85) REVERT: A 272 GLU cc_start: 0.7780 (tp30) cc_final: 0.6868 (tm-30) REVERT: A 277 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6640 (ptm160) REVERT: A 465 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6714 (mt) REVERT: A 524 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6475 (mt) REVERT: A 622 ILE cc_start: 0.7467 (mm) cc_final: 0.7156 (mt) REVERT: A 667 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: A 852 PHE cc_start: 0.7619 (t80) cc_final: 0.6052 (m-80) REVERT: A 870 ARG cc_start: 0.6013 (ppp80) cc_final: 0.5586 (ttt180) outliers start: 55 outliers final: 14 residues processed: 222 average time/residue: 0.5000 time to fit residues: 122.5624 Evaluate side-chains 188 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 578 VAL 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 750 MET 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 524 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 750 MET 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: 0.0870 chunk 127 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.0040 chunk 97 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 overall best weight: 0.2968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 525 ASN B 632 ASN B 652 GLN B 785 ASN A 525 ASN A 632 ASN A 652 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.233770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156890 restraints weight = 13069.459| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.30 r_work: 0.3234 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13672 Z= 0.103 Angle : 0.500 10.094 18486 Z= 0.261 Chirality : 0.039 0.162 1988 Planarity : 0.005 0.051 2288 Dihedral : 13.994 158.220 2060 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.84 % Allowed : 19.29 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1562 helix: 1.68 (0.17), residues: 886 sheet: -0.05 (0.50), residues: 102 loop : -0.77 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.007 0.001 TYR B 299 PHE 0.019 0.001 PHE A 215 TRP 0.017 0.001 TRP B 273 HIS 0.011 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (13662) covalent geometry : angle 0.49889 / 0.26 (18466) SS BOND : bond 0.00120 / 0.07 ( 10) SS BOND : angle 1.28639 / 0.74 ( 20) hydrogen bonds : bond 0.03848 / 2.65 ( 724) hydrogen bonds : angle 4.48813 / 3.10 ( 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 211 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.490 Fit side-chains REVERT: B 183 PHE cc_start: 0.7544 (m-80) cc_final: 0.7193 (m-80) REVERT: B 255 TYR cc_start: 0.7485 (m-80) cc_final: 0.7194 (m-80) REVERT: B 272 GLU cc_start: 0.7660 (tp30) cc_final: 0.7102 (tp30) REVERT: B 329 ASP cc_start: 0.8276 (t0) cc_final: 0.7842 (m-30) REVERT: B 465 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6655 (mt) REVERT: B 524 LEU cc_start: 0.6547 (tp) cc_final: 0.6290 (mt) REVERT: B 553 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7841 (tpt) REVERT: B 631 MET cc_start: 0.6472 (mtp) cc_final: 0.5839 (mtt) REVERT: B 659 MET cc_start: 0.6906 (mtp) cc_final: 0.6678 (mtm) REVERT: B 852 PHE cc_start: 0.7569 (t80) cc_final: 0.6116 (m-10) REVERT: B 870 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5856 (ttt180) REVERT: A 113 GLU cc_start: 0.6857 (pt0) cc_final: 0.6092 (pm20) REVERT: A 183 PHE cc_start: 0.7559 (m-80) cc_final: 0.7104 (m-10) REVERT: A 255 TYR cc_start: 0.7466 (m-80) cc_final: 0.7203 (m-80) REVERT: A 272 GLU cc_start: 0.7682 (tp30) cc_final: 0.7073 (tp30) REVERT: A 277 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6737 (ptm160) REVERT: A 336 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7220 (mt-10) REVERT: A 465 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6633 (mt) REVERT: A 522 MET cc_start: 0.8295 (tpp) cc_final: 0.8091 (tpt) REVERT: A 524 LEU cc_start: 0.6597 (tp) cc_final: 0.6271 (mt) REVERT: A 553 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7809 (tpt) REVERT: A 594 GLU cc_start: 0.6964 (pt0) cc_final: 0.6664 (pt0) REVERT: A 699 GLU cc_start: 0.8266 (tp30) cc_final: 0.7715 (mm-30) REVERT: A 852 PHE cc_start: 0.7652 (t80) cc_final: 0.6179 (m-10) REVERT: A 870 ARG cc_start: 0.6108 (ppp80) cc_final: 0.5622 (ttt180) outliers start: 40 outliers final: 11 residues processed: 194 average time/residue: 0.4581 time to fit residues: 99.4178 Evaluate side-chains 185 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL 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 870 ARG 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 466 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.0060 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 HIS B 652 GLN A 108 HIS A 652 GLN A 726 GLN A 730 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.220902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135006 restraints weight = 12660.230| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.62 r_work: 0.3236 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13672 Z= 0.179 Angle : 0.572 12.502 18486 Z= 0.297 Chirality : 0.042 0.170 1988 Planarity : 0.005 0.057 2288 Dihedral : 14.050 153.152 2060 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.04 % Allowed : 19.15 % Favored : 76.81 % 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 (0.20), residues: 1562 helix: 1.44 (0.17), residues: 882 sheet: -0.19 (0.48), residues: 102 loop : -0.85 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 271 TYR 0.014 0.001 TYR B 668 PHE 0.019 0.002 PHE B 685 TRP 0.016 0.001 TRP B 273 HIS 0.007 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (13662) covalent geometry : angle 0.57013 / 0.30 (18466) SS BOND : bond 0.00110 / 0.07 ( 10) SS BOND : angle 1.53075 / 0.90 ( 20) hydrogen bonds : bond 0.04542 / 3.12 ( 724) hydrogen bonds : angle 4.61277 / 3.21 ( 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 230 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: B 101 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: B 113 GLU cc_start: 0.6844 (pt0) cc_final: 0.6113 (pm20) REVERT: B 183 PHE cc_start: 0.7539 (m-80) cc_final: 0.7317 (m-10) REVERT: B 255 TYR cc_start: 0.7349 (m-80) cc_final: 0.6971 (m-80) REVERT: B 272 GLU cc_start: 0.7832 (tp30) cc_final: 0.7396 (tt0) REVERT: B 277 ARG cc_start: 0.7322 (ptm160) cc_final: 0.6588 (ptm160) REVERT: B 329 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: B 348 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7572 (mmm) REVERT: B 465 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6701 (mt) REVERT: B 523 ILE cc_start: 0.7729 (tt) cc_final: 0.7348 (pt) REVERT: B 524 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6346 (mt) REVERT: B 659 MET cc_start: 0.7179 (mtp) cc_final: 0.6970 (mtm) REVERT: B 667 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: B 852 PHE cc_start: 0.7602 (t80) cc_final: 0.6078 (m-10) REVERT: B 870 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5638 (ttt180) REVERT: B 874 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4779 (tt) REVERT: A 101 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: A 113 GLU cc_start: 0.6844 (pt0) cc_final: 0.6032 (pm20) REVERT: A 183 PHE cc_start: 0.7583 (m-80) cc_final: 0.7184 (m-10) REVERT: A 255 TYR cc_start: 0.7444 (m-80) cc_final: 0.7106 (m-80) REVERT: A 272 GLU cc_start: 0.7842 (tp30) cc_final: 0.7401 (tt0) REVERT: A 277 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6656 (ptm160) REVERT: A 348 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7656 (mmm) REVERT: A 465 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 523 ILE cc_start: 0.7689 (tt) cc_final: 0.7256 (pt) REVERT: A 667 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8196 (mm-30) REVERT: A 852 PHE cc_start: 0.7600 (t80) cc_final: 0.7349 (t80) REVERT: A 870 ARG cc_start: 0.5935 (ppp80) cc_final: 0.5554 (ttt180) outliers start: 57 outliers final: 15 residues processed: 212 average time/residue: 0.4353 time to fit residues: 102.7913 Evaluate side-chains 190 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 329 ASP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 620 ASN 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 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 348 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 620 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 GLN A 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.222176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139734 restraints weight = 12739.774| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.76 r_work: 0.3261 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13672 Z= 0.136 Angle : 0.524 12.165 18486 Z= 0.271 Chirality : 0.041 0.174 1988 Planarity : 0.005 0.059 2288 Dihedral : 13.205 137.472 2060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.48 % Allowed : 19.65 % Favored : 76.88 % 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: 0.78 (0.21), residues: 1562 helix: 1.46 (0.17), residues: 894 sheet: -0.12 (0.49), residues: 102 loop : -0.86 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 360 TYR 0.009 0.001 TYR A 306 PHE 0.019 0.001 PHE B 215 TRP 0.017 0.001 TRP B 273 HIS 0.013 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (13662) covalent geometry : angle 0.52221 / 0.27 (18466) SS BOND : bond 0.00092 / 0.05 ( 10) SS BOND : angle 1.35427 / 0.79 ( 20) hydrogen bonds : bond 0.04024 / 2.76 ( 724) hydrogen bonds : angle 4.46595 / 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 211 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.494 Fit side-chains REVERT: B 73 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: B 101 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: B 113 GLU cc_start: 0.6677 (pt0) cc_final: 0.6027 (pm20) REVERT: B 183 PHE cc_start: 0.7506 (m-80) cc_final: 0.7274 (m-10) REVERT: B 271 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7417 (mmm160) REVERT: B 272 GLU cc_start: 0.7809 (tp30) cc_final: 0.7333 (tt0) REVERT: B 277 ARG cc_start: 0.7257 (ptm160) cc_final: 0.6617 (ptm160) REVERT: B 289 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7736 (tmt90) REVERT: B 329 ASP cc_start: 0.8491 (t0) cc_final: 0.8030 (m-30) REVERT: B 465 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6696 (mt) REVERT: B 523 ILE cc_start: 0.7690 (tt) cc_final: 0.7298 (pt) REVERT: B 631 MET cc_start: 0.6309 (mtp) cc_final: 0.5761 (mtt) REVERT: B 667 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: B 749 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7940 (t70) REVERT: B 785 ASN cc_start: 0.5420 (t0) cc_final: 0.5005 (t160) REVERT: B 788 ASP cc_start: 0.7400 (m-30) cc_final: 0.6669 (m-30) REVERT: B 852 PHE cc_start: 0.7601 (t80) cc_final: 0.6065 (m-10) REVERT: B 870 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5710 (ttt180) REVERT: B 874 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4759 (tt) REVERT: A 101 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: A 113 GLU cc_start: 0.6680 (pt0) cc_final: 0.5896 (pm20) REVERT: A 255 TYR cc_start: 0.7261 (m-80) cc_final: 0.6932 (m-80) REVERT: A 272 GLU cc_start: 0.7807 (tp30) cc_final: 0.7303 (tt0) REVERT: A 277 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6621 (ptm160) REVERT: A 289 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7741 (tmt90) REVERT: A 465 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6719 (mt) REVERT: A 522 MET cc_start: 0.8081 (tpp) cc_final: 0.7831 (mmm) REVERT: A 667 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8279 (mm-30) REVERT: A 714 MET cc_start: 0.7863 (mtt) cc_final: 0.7588 (mtt) REVERT: A 749 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7915 (t70) REVERT: A 852 PHE cc_start: 0.7595 (t80) cc_final: 0.7319 (t80) REVERT: A 870 ARG cc_start: 0.5909 (ppp80) cc_final: 0.5624 (ttt180) outliers start: 49 outliers final: 12 residues processed: 199 average time/residue: 0.4500 time to fit residues: 100.0167 Evaluate side-chains 186 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain B residue 289 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 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 870 ARG Chi-restraints excluded: chain B residue 874 LEU 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 465 LEU Chi-restraints excluded: chain A residue 529 GLU 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: 10.0000 chunk 106 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.223251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134699 restraints weight = 12631.714| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.68 r_work: 0.3295 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2887 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= 0.115 Angle : 0.504 12.604 18486 Z= 0.260 Chirality : 0.040 0.187 1988 Planarity : 0.005 0.059 2288 Dihedral : 12.435 112.527 2060 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.90 % Allowed : 19.57 % 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: 0.91 (0.21), residues: 1562 helix: 1.56 (0.17), residues: 898 sheet: -0.12 (0.50), residues: 102 loop : -0.79 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.009 0.001 TYR A 306 PHE 0.020 0.001 PHE B 215 TRP 0.018 0.001 TRP B 273 HIS 0.010 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (13662) covalent geometry : angle 0.50235 / 0.26 (18466) SS BOND : bond 0.00087 / 0.05 ( 10) SS BOND : angle 1.28432 / 0.75 ( 20) hydrogen bonds : bond 0.03768 / 2.58 ( 724) hydrogen bonds : angle 4.39447 / 3.05 ( 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 212 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 0.509 Fit side-chains REVERT: B 73 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: B 101 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: B 113 GLU cc_start: 0.6617 (pt0) cc_final: 0.5954 (pm20) REVERT: B 183 PHE cc_start: 0.7535 (m-80) cc_final: 0.7311 (m-10) REVERT: B 198 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7693 (mm) REVERT: B 272 GLU cc_start: 0.7763 (tp30) cc_final: 0.7304 (tt0) REVERT: B 277 ARG cc_start: 0.7279 (ptm160) cc_final: 0.6626 (ptm160) REVERT: B 289 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7747 (tmt90) REVERT: B 329 ASP cc_start: 0.8526 (t0) cc_final: 0.8058 (m-30) REVERT: B 527 ILE cc_start: 0.7703 (mm) cc_final: 0.7476 (mt) REVERT: B 631 MET cc_start: 0.6343 (mtp) cc_final: 0.5825 (mtt) REVERT: B 667 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: B 749 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7850 (t70) REVERT: B 785 ASN cc_start: 0.5447 (t0) cc_final: 0.5062 (t160) REVERT: B 788 ASP cc_start: 0.7324 (m-30) cc_final: 0.6582 (m-30) REVERT: B 852 PHE cc_start: 0.7625 (t80) cc_final: 0.6124 (m-10) REVERT: B 870 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5707 (ttt180) REVERT: B 874 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4740 (tt) REVERT: A 101 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: A 113 GLU cc_start: 0.6640 (pt0) cc_final: 0.5846 (pm20) REVERT: A 198 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 272 GLU cc_start: 0.7720 (tp30) cc_final: 0.7273 (tt0) REVERT: A 289 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7747 (tmt90) REVERT: A 329 ASP cc_start: 0.8336 (m-30) cc_final: 0.8102 (m-30) REVERT: A 522 MET cc_start: 0.8198 (tpp) cc_final: 0.7934 (mmt) REVERT: A 667 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: A 714 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7412 (mtt) REVERT: A 749 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7967 (t70) REVERT: A 852 PHE cc_start: 0.7623 (t80) cc_final: 0.6127 (m-10) REVERT: A 870 ARG cc_start: 0.5872 (ppp80) cc_final: 0.5504 (ttt180) outliers start: 55 outliers final: 16 residues processed: 197 average time/residue: 0.4675 time to fit residues: 103.0678 Evaluate side-chains 181 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 75 LEU 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 289 ARG Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 611 ILE 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 749 ASP Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 874 LEU 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 289 ARG Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 714 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 0.0020 chunk 150 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.224285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133972 restraints weight = 12539.471| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.57 r_work: 0.3281 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3007 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= 0.126 Angle : 0.522 13.359 18486 Z= 0.269 Chirality : 0.040 0.188 1988 Planarity : 0.005 0.059 2288 Dihedral : 11.915 87.109 2060 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.97 % Allowed : 19.79 % Favored : 76.24 % 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: 0.87 (0.21), residues: 1562 helix: 1.56 (0.17), residues: 896 sheet: -0.24 (0.49), residues: 102 loop : -0.85 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.011 0.001 TYR A 528 PHE 0.021 0.001 PHE B 215 TRP 0.018 0.001 TRP A 273 HIS 0.015 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13662) covalent geometry : angle 0.52037 / 0.27 (18466) SS BOND : bond 0.00073 / 0.05 ( 10) SS BOND : angle 1.34804 / 0.79 ( 20) hydrogen bonds : bond 0.03867 / 2.66 ( 724) hydrogen bonds : angle 4.42281 / 3.08 ( 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 211 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: B 101 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: B 113 GLU cc_start: 0.6626 (pt0) cc_final: 0.6254 (pm20) REVERT: B 183 PHE cc_start: 0.7516 (m-80) cc_final: 0.7278 (m-10) REVERT: B 198 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7680 (mm) REVERT: B 272 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: B 277 ARG cc_start: 0.7247 (ptm160) cc_final: 0.6585 (ptm160) REVERT: B 289 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7768 (tmt90) REVERT: B 329 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: B 527 ILE cc_start: 0.7692 (mm) cc_final: 0.7486 (mt) REVERT: B 631 MET cc_start: 0.6336 (mtp) cc_final: 0.5834 (mtt) REVERT: B 667 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: B 749 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7968 (t70) REVERT: B 785 ASN cc_start: 0.5340 (t0) cc_final: 0.4959 (t160) REVERT: B 788 ASP cc_start: 0.7375 (m-30) cc_final: 0.6660 (m-30) REVERT: B 852 PHE cc_start: 0.7587 (t80) cc_final: 0.7332 (t80) REVERT: B 870 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5720 (ttt180) REVERT: B 874 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4713 (tt) REVERT: A 101 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: A 113 GLU cc_start: 0.6650 (pt0) cc_final: 0.5935 (pm20) REVERT: A 183 PHE cc_start: 0.7586 (m-80) cc_final: 0.7336 (m-10) REVERT: A 198 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 272 GLU cc_start: 0.7708 (tp30) cc_final: 0.7270 (tt0) REVERT: A 277 ARG cc_start: 0.7453 (ptm160) cc_final: 0.7194 (ptm160) REVERT: A 289 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7756 (tmt90) REVERT: A 522 MET cc_start: 0.8174 (tpp) cc_final: 0.7937 (mmt) REVERT: A 631 MET cc_start: 0.6515 (mtp) cc_final: 0.5963 (mtt) REVERT: A 667 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: A 749 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.7967 (t70) REVERT: A 852 PHE cc_start: 0.7608 (t80) cc_final: 0.7348 (t80) REVERT: A 870 ARG cc_start: 0.5914 (ppp80) cc_final: 0.5523 (ttt180) outliers start: 56 outliers final: 22 residues processed: 198 average time/residue: 0.4304 time to fit residues: 95.9593 Evaluate side-chains 189 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 289 ARG Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 611 ILE 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 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 289 ARG Chi-restraints excluded: chain A residue 376 SER 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 Chi-restraints excluded: chain A residue 874 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 13 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.219377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128903 restraints weight = 12556.977| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.23 r_work: 0.3259 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13672 Z= 0.195 Angle : 0.594 14.736 18486 Z= 0.304 Chirality : 0.043 0.199 1988 Planarity : 0.005 0.058 2288 Dihedral : 11.974 82.855 2060 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.90 % Allowed : 19.79 % 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: 0.59 (0.21), residues: 1562 helix: 1.32 (0.17), residues: 898 sheet: -0.36 (0.48), residues: 102 loop : -0.94 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 360 TYR 0.025 0.002 TYR A 528 PHE 0.023 0.002 PHE A 215 TRP 0.014 0.002 TRP A 273 HIS 0.012 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (13662) covalent geometry : angle 0.59165 / 0.30 (18466) SS BOND : bond 0.00086 / 0.06 ( 10) SS BOND : angle 1.55667 / 0.92 ( 20) hydrogen bonds : bond 0.04512 / 3.10 ( 724) hydrogen bonds : angle 4.59701 / 3.22 ( 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 216 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: B 101 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: B 113 GLU cc_start: 0.6821 (pt0) cc_final: 0.6235 (pm20) REVERT: B 198 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7697 (mm) REVERT: B 277 ARG cc_start: 0.7225 (ptm160) cc_final: 0.6589 (ptm160) REVERT: B 289 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (tmt90) REVERT: B 329 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: B 465 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6760 (mt) REVERT: B 534 MET cc_start: 0.6601 (mtt) cc_final: 0.6351 (mtm) REVERT: B 631 MET cc_start: 0.6506 (mtp) cc_final: 0.5996 (mtt) REVERT: B 667 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8541 (mm-30) REVERT: B 749 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8034 (t70) REVERT: B 785 ASN cc_start: 0.5616 (t0) cc_final: 0.5254 (t160) REVERT: B 788 ASP cc_start: 0.7412 (m-30) cc_final: 0.6663 (m-30) REVERT: B 852 PHE cc_start: 0.7602 (t80) cc_final: 0.7323 (t80) REVERT: B 870 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5847 (ttt180) REVERT: B 874 LEU cc_start: 0.5111 (OUTLIER) cc_final: 0.4895 (tt) REVERT: A 101 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 113 GLU cc_start: 0.6814 (pt0) cc_final: 0.6039 (pm20) REVERT: A 183 PHE cc_start: 0.7569 (m-80) cc_final: 0.7334 (m-10) REVERT: A 198 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7781 (mm) REVERT: A 277 ARG cc_start: 0.7609 (ptm160) cc_final: 0.7304 (ptm160) REVERT: A 289 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7904 (tmt90) REVERT: A 329 ASP cc_start: 0.8410 (m-30) cc_final: 0.8146 (m-30) REVERT: A 465 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6792 (mt) REVERT: A 522 MET cc_start: 0.8190 (tpp) cc_final: 0.7974 (mmt) REVERT: A 534 MET cc_start: 0.6544 (mtt) cc_final: 0.6247 (mtp) REVERT: A 555 MET cc_start: 0.8552 (mmt) cc_final: 0.8340 (mmt) REVERT: A 631 MET cc_start: 0.6659 (mtp) cc_final: 0.6103 (mtt) REVERT: A 667 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8317 (mm-30) REVERT: A 749 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8042 (t70) REVERT: A 852 PHE cc_start: 0.7583 (t80) cc_final: 0.7297 (t80) outliers start: 55 outliers final: 21 residues processed: 203 average time/residue: 0.4431 time to fit residues: 101.2424 Evaluate side-chains 196 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain B residue 99 GLN 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 289 ARG Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 507 MET 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 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 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 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 Chi-restraints excluded: chain A residue 874 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 147 optimal weight: 0.9980 chunk 119 optimal weight: 0.1980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.222398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133498 restraints weight = 12677.043| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.63 r_work: 0.3278 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3291 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= 0.119 Angle : 0.533 14.147 18486 Z= 0.273 Chirality : 0.040 0.209 1988 Planarity : 0.005 0.057 2288 Dihedral : 11.268 80.470 2060 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.19 % Allowed : 20.57 % Favored : 76.24 % 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: 0.81 (0.21), residues: 1562 helix: 1.55 (0.17), residues: 896 sheet: -0.30 (0.48), residues: 102 loop : -0.93 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.027 0.001 TYR A 580 PHE 0.025 0.001 PHE B 215 TRP 0.017 0.001 TRP B 650 HIS 0.011 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13662) covalent geometry : angle 0.53120 / 0.27 (18466) SS BOND : bond 0.00074 / 0.05 ( 10) SS BOND : angle 1.31433 / 0.77 ( 20) hydrogen bonds : bond 0.03835 / 2.63 ( 724) hydrogen bonds : angle 4.44713 / 3.11 ( 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 202 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: B 101 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: B 113 GLU cc_start: 0.6653 (pt0) cc_final: 0.5991 (pm20) REVERT: B 198 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7692 (mm) REVERT: B 277 ARG cc_start: 0.7163 (ptm160) cc_final: 0.6537 (ptm160) REVERT: B 289 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7746 (tmt90) REVERT: B 329 ASP cc_start: 0.8604 (t0) cc_final: 0.8122 (m-30) REVERT: B 534 MET cc_start: 0.6373 (mtt) cc_final: 0.6125 (mtm) REVERT: B 631 MET cc_start: 0.6426 (mtp) cc_final: 0.5934 (mtt) REVERT: B 667 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: B 749 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8057 (t70) REVERT: B 785 ASN cc_start: 0.5434 (t0) cc_final: 0.5048 (t160) REVERT: B 788 ASP cc_start: 0.7383 (m-30) cc_final: 0.6636 (m-30) REVERT: B 852 PHE cc_start: 0.7591 (t80) cc_final: 0.7311 (t80) REVERT: B 870 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5786 (ttt180) REVERT: A 101 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: A 113 GLU cc_start: 0.6683 (pt0) cc_final: 0.5941 (pm20) REVERT: A 183 PHE cc_start: 0.7528 (m-80) cc_final: 0.7264 (m-10) REVERT: A 198 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 225 MET cc_start: 0.4339 (pmt) cc_final: 0.3527 (mtp) REVERT: A 277 ARG cc_start: 0.7541 (ptm160) cc_final: 0.7269 (ptm160) REVERT: A 289 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7756 (tmt90) REVERT: A 329 ASP cc_start: 0.8389 (m-30) cc_final: 0.8111 (m-30) REVERT: A 466 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6802 (mp) REVERT: A 534 MET cc_start: 0.6386 (mtt) cc_final: 0.6115 (mtp) REVERT: A 631 MET cc_start: 0.6619 (mtp) cc_final: 0.6080 (mtt) REVERT: A 667 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: A 749 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8033 (t70) REVERT: A 852 PHE cc_start: 0.7570 (t80) cc_final: 0.7286 (t80) outliers start: 45 outliers final: 21 residues processed: 192 average time/residue: 0.4590 time to fit residues: 98.5726 Evaluate side-chains 188 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 75 LEU 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 278 SER Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 507 MET 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 870 ARG 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 289 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 466 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 Chi-restraints excluded: chain A residue 874 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 0.0070 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.227305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146995 restraints weight = 12677.849| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.85 r_work: 0.3316 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13672 Z= 0.095 Angle : 0.502 13.852 18486 Z= 0.256 Chirality : 0.039 0.207 1988 Planarity : 0.005 0.058 2288 Dihedral : 10.294 76.806 2060 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.91 % Allowed : 20.78 % 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: 1.01 (0.21), residues: 1562 helix: 1.73 (0.17), residues: 902 sheet: -0.37 (0.48), residues: 102 loop : -0.88 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 360 TYR 0.025 0.001 TYR A 528 PHE 0.025 0.001 PHE B 556 TRP 0.019 0.001 TRP B 273 HIS 0.015 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (13662) covalent geometry : angle 0.50024 / 0.26 (18466) SS BOND : bond 0.00095 / 0.06 ( 10) SS BOND : angle 1.19661 / 0.70 ( 20) hydrogen bonds : bond 0.03389 / 2.32 ( 724) hydrogen bonds : angle 4.32833 / 3.01 ( 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 195 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: B 73 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: B 113 GLU cc_start: 0.6529 (pt0) cc_final: 0.5924 (pm20) REVERT: B 198 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7623 (mm) REVERT: B 272 GLU cc_start: 0.7730 (tp30) cc_final: 0.7272 (tt0) REVERT: B 277 ARG cc_start: 0.7084 (ptm160) cc_final: 0.6472 (ptm160) REVERT: B 329 ASP cc_start: 0.8599 (t0) cc_final: 0.8104 (m-30) REVERT: B 534 MET cc_start: 0.6294 (mtt) cc_final: 0.6059 (mtp) REVERT: B 631 MET cc_start: 0.6420 (mtp) cc_final: 0.5928 (mtt) REVERT: B 667 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: B 699 GLU cc_start: 0.8296 (tp30) cc_final: 0.7754 (mm-30) REVERT: B 749 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.7987 (t70) REVERT: B 785 ASN cc_start: 0.5400 (t0) cc_final: 0.5026 (t160) REVERT: B 788 ASP cc_start: 0.7365 (m-30) cc_final: 0.6600 (m-30) REVERT: B 870 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5578 (ptm160) REVERT: A 113 GLU cc_start: 0.6534 (pt0) cc_final: 0.5830 (pm20) REVERT: A 183 PHE cc_start: 0.7505 (m-80) cc_final: 0.7262 (m-10) REVERT: A 198 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7694 (mm) REVERT: A 272 GLU cc_start: 0.7717 (tp30) cc_final: 0.7309 (tt0) REVERT: A 277 ARG cc_start: 0.7518 (ptm160) cc_final: 0.7250 (ptm160) REVERT: A 289 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7721 (tmt90) REVERT: A 534 MET cc_start: 0.6279 (mtt) cc_final: 0.6035 (mtp) REVERT: A 631 MET cc_start: 0.6481 (mtp) cc_final: 0.5968 (mtt) REVERT: A 667 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: A 699 GLU cc_start: 0.8277 (tp30) cc_final: 0.7766 (mm-30) REVERT: A 749 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8022 (t70) outliers start: 41 outliers final: 18 residues processed: 187 average time/residue: 0.5052 time to fit residues: 105.0865 Evaluate side-chains 173 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 507 MET 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 870 ARG Chi-restraints excluded: chain A residue 70 ARG 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 289 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 578 VAL 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 874 LEU 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: 0.6980 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 147 optimal weight: 0.0370 chunk 132 optimal weight: 0.0010 chunk 113 optimal weight: 0.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 401 GLN B 559 GLN A 401 GLN A 559 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.229311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141819 restraints weight = 12705.228| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.66 r_work: 0.3342 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13672 Z= 0.093 Angle : 0.506 14.480 18486 Z= 0.256 Chirality : 0.039 0.198 1988 Planarity : 0.005 0.059 2288 Dihedral : 9.805 75.819 2060 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.34 % Allowed : 21.35 % 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: 1.09 (0.21), residues: 1562 helix: 1.82 (0.17), residues: 902 sheet: -0.39 (0.48), residues: 102 loop : -0.90 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 400 TYR 0.025 0.001 TYR B 528 PHE 0.021 0.001 PHE B 215 TRP 0.017 0.001 TRP A 273 HIS 0.014 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (13662) covalent geometry : angle 0.50494 / 0.26 (18466) SS BOND : bond 0.00083 / 0.05 ( 10) SS BOND : angle 1.18411 / 0.70 ( 20) hydrogen bonds : bond 0.03309 / 2.26 ( 724) hydrogen bonds : angle 4.28770 / 2.98 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4396.63 seconds wall clock time: 75 minutes 46.13 seconds (4546.13 seconds total)