Starting phenix.real_space_refine on Sat Aug 23 21:08:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hya_35085/08_2025/8hya_35085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hya_35085/08_2025/8hya_35085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hya_35085/08_2025/8hya_35085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hya_35085/08_2025/8hya_35085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hya_35085/08_2025/8hya_35085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hya_35085/08_2025/8hya_35085.map" } resolution = 3.4 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9536 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14586 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'R16': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'R16': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 3.30, per 1000 atoms: 0.23 Number of scatterers: 14586 At special positions: 0 Unit cell: (115.44, 107.12, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2626 8.00 N 2364 7.00 C 9536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.05 Conformation dependent library (CDL) restraints added in 532.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 69.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.911A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 97 through 114 Proline residue: A 107 - end of helix removed outlier: 4.659A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 125 through 151 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 187 through 213 removed outlier: 3.599A pdb=" N THR A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.086A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 4.014A pdb=" N GLU A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 306 through 339 removed outlier: 4.258A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 349 through 377 removed outlier: 3.669A pdb=" N PHE A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 419 through 450 removed outlier: 4.009A pdb=" N PHE A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 482 removed outlier: 3.678A pdb=" N ILE A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.717A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.883A pdb=" N GLY A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 602 through 638 removed outlier: 5.885A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 699 Processing helix chain 'A' and resid 704 through 723 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.534A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 846 through 866 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.087A pdb=" N LEU A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1042 Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 60 through 77 removed outlier: 3.911A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 97 through 114 Proline residue: B 107 - end of helix removed outlier: 4.659A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 125 through 151 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 187 through 213 removed outlier: 3.599A pdb=" N THR B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 254 removed outlier: 4.086A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 removed outlier: 4.015A pdb=" N GLU B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 306 through 339 removed outlier: 4.258A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 349 through 377 removed outlier: 3.669A pdb=" N PHE B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 419 through 450 removed outlier: 4.009A pdb=" N PHE B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 482 removed outlier: 3.679A pdb=" N ILE B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.717A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 550 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.883A pdb=" N GLY B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 638 removed outlier: 5.886A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 670 through 699 Processing helix chain 'B' and resid 704 through 723 Processing helix chain 'B' and resid 731 through 739 Processing helix chain 'B' and resid 740 through 744 removed outlier: 3.533A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 837 through 844 Processing helix chain 'B' and resid 846 through 866 Processing helix chain 'B' and resid 866 through 871 Processing helix chain 'B' and resid 874 through 884 removed outlier: 4.086A pdb=" N LEU B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 879 " --> pdb=" O MET B 875 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1042 Processing sheet with id=AA1, first strand: chain 'A' and resid 761 through 762 removed outlier: 3.687A pdb=" N ASP A 783 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE A 833 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 781 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 835 " --> pdb=" O TRP A 779 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP A 779 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 807 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 802 through 803 removed outlier: 3.936A pdb=" N VAL A 786 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 889 through 892 removed outlier: 6.972A pdb=" N ARG A 966 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AA5, first strand: chain 'B' and resid 761 through 762 removed outlier: 3.686A pdb=" N ASP B 783 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE B 833 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE B 781 " --> pdb=" O PHE B 833 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 835 " --> pdb=" O TRP B 779 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP B 779 " --> pdb=" O ILE B 835 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 807 " --> pdb=" O ILE B 781 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 802 through 803 removed outlier: 3.936A pdb=" N VAL B 786 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 889 through 892 removed outlier: 6.972A pdb=" N ARG B 966 " --> pdb=" O LEU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 914 949 hydrogen bonds defined for protein. 2787 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: 2.22 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2314 1.32 - 1.44: 3852 1.44 - 1.56: 8616 1.56 - 1.69: 2 1.69 - 1.81: 102 Bond restraints: 14886 Sorted by residual: bond pdb=" C THR B 423 " pdb=" O THR B 423 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" C THR A 423 " pdb=" O THR A 423 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N SER A 418 " pdb=" CA SER A 418 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N SER B 418 " pdb=" CA SER B 418 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" CA SER A 418 " pdb=" CB SER A 418 " ideal model delta sigma weight residual 1.530 1.477 0.054 1.69e-02 3.50e+03 1.01e+01 ... (remaining 14881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19702 2.10 - 4.19: 382 4.19 - 6.29: 50 6.29 - 8.39: 16 8.39 - 10.49: 6 Bond angle restraints: 20156 Sorted by residual: angle pdb=" N LEU B 424 " pdb=" CA LEU B 424 " pdb=" C LEU B 424 " ideal model delta sigma weight residual 111.33 104.16 7.17 1.21e+00 6.83e-01 3.51e+01 angle pdb=" N LEU A 424 " pdb=" CA LEU A 424 " pdb=" C LEU A 424 " ideal model delta sigma weight residual 111.33 104.17 7.16 1.21e+00 6.83e-01 3.50e+01 angle pdb=" C LEU B 424 " pdb=" N PHE B 425 " pdb=" CA PHE B 425 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C LEU A 424 " pdb=" N PHE A 425 " pdb=" CA PHE A 425 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" N GLU A 420 " pdb=" CA GLU A 420 " pdb=" C GLU A 420 " ideal model delta sigma weight residual 111.07 105.65 5.42 1.07e+00 8.73e-01 2.57e+01 ... (remaining 20151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7965 17.76 - 35.52: 765 35.52 - 53.28: 110 53.28 - 71.03: 12 71.03 - 88.79: 14 Dihedral angle restraints: 8866 sinusoidal: 3506 harmonic: 5360 Sorted by residual: dihedral pdb=" CA PHE A 152 " pdb=" C PHE A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE B 152 " pdb=" C PHE B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual 180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU B 168 " pdb=" C LEU B 168 " pdb=" N SER B 169 " pdb=" CA SER B 169 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2089 0.064 - 0.129: 263 0.129 - 0.193: 14 0.193 - 0.258: 2 0.258 - 0.322: 4 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CB THR B 421 " pdb=" CA THR B 421 " pdb=" OG1 THR B 421 " pdb=" CG2 THR B 421 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB THR A 421 " pdb=" CA THR A 421 " pdb=" OG1 THR A 421 " pdb=" CG2 THR A 421 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU B 420 " pdb=" N GLU B 420 " pdb=" C GLU B 420 " pdb=" CB GLU B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 489 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 490 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 489 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 490 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 156 " 0.020 2.00e-02 2.50e+03 1.90e-02 9.03e+00 pdb=" CG TRP B 156 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 156 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 156 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 156 " 0.002 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2821 2.77 - 3.31: 15207 3.31 - 3.84: 24700 3.84 - 4.37: 27883 4.37 - 4.90: 48491 Nonbonded interactions: 119102 Sorted by model distance: nonbonded pdb=" OG SER A 897 " pdb=" O GLN A 958 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 897 " pdb=" O GLN B 958 " model vdw 2.243 3.040 nonbonded pdb=" NE2 GLN A 128 " pdb=" O TYR A 381 " model vdw 2.252 3.120 nonbonded pdb=" NE2 GLN B 128 " pdb=" O TYR B 381 " model vdw 2.252 3.120 nonbonded pdb=" NZ LYS A 386 " pdb=" O LEU A 451 " model vdw 2.276 3.120 ... (remaining 119097 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.004 0.080 14886 Z= 0.192 Angle : 0.712 10.486 20156 Z= 0.400 Chirality : 0.044 0.322 2372 Planarity : 0.005 0.112 2472 Dihedral : 13.946 88.793 5410 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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 aren not related in a simple way. whole: 0.88 (0.20), residues: 1836 helix: 1.41 (0.15), residues: 1212 sheet: 1.66 (0.57), residues: 80 loop : -1.47 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 551 TYR 0.041 0.002 TYR A 617 PHE 0.029 0.001 PHE B 425 TRP 0.051 0.002 TRP B 156 HIS 0.003 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00374 (14886) covalent geometry : angle 0.71181 (20156) hydrogen bonds : bond 0.13343 ( 949) hydrogen bonds : angle 5.68025 ( 2787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.409 Fit side-chains REVERT: A 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8613 (t0) REVERT: A 172 ASP cc_start: 0.8508 (t0) cc_final: 0.8222 (t70) REVERT: A 355 PHE cc_start: 0.8176 (m-10) cc_final: 0.7946 (m-80) REVERT: A 492 ASP cc_start: 0.7556 (t70) cc_final: 0.7344 (t70) REVERT: A 533 MET cc_start: 0.7611 (tmm) cc_final: 0.6994 (tmm) REVERT: A 613 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 755 HIS cc_start: 0.6008 (m-70) cc_final: 0.5565 (m-70) REVERT: A 914 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8413 (mmmt) REVERT: B 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8608 (t0) REVERT: B 172 ASP cc_start: 0.8472 (t0) cc_final: 0.8222 (t0) REVERT: B 533 MET cc_start: 0.7573 (tmm) cc_final: 0.6928 (tmm) REVERT: B 613 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 755 HIS cc_start: 0.5964 (m-70) cc_final: 0.5569 (m-70) REVERT: B 865 LEU cc_start: 0.8822 (mm) cc_final: 0.8477 (mt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.0950 time to fit residues: 47.2146 Evaluate side-chains 247 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118338 restraints weight = 23147.413| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.97 r_work: 0.3385 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14886 Z= 0.156 Angle : 0.638 11.621 20156 Z= 0.321 Chirality : 0.042 0.227 2372 Planarity : 0.005 0.073 2472 Dihedral : 5.141 31.168 2028 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.25 % Allowed : 9.75 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1836 helix: 1.48 (0.15), residues: 1214 sheet: 1.51 (0.60), residues: 76 loop : -1.33 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 601 TYR 0.027 0.002 TYR A 617 PHE 0.016 0.001 PHE B 298 TRP 0.011 0.001 TRP B 854 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00363 (14886) covalent geometry : angle 0.63768 (20156) hydrogen bonds : bond 0.04242 ( 949) hydrogen bonds : angle 4.59739 ( 2787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 0.551 Fit side-chains REVERT: A 172 ASP cc_start: 0.7992 (t0) cc_final: 0.7283 (t0) REVERT: A 252 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6902 (mtpt) REVERT: A 298 PHE cc_start: 0.8668 (m-10) cc_final: 0.8451 (m-10) REVERT: A 492 ASP cc_start: 0.7698 (t70) cc_final: 0.7222 (t70) REVERT: A 570 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: A 597 LYS cc_start: 0.2393 (mptt) cc_final: 0.2064 (tptp) REVERT: A 613 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7083 (tt0) REVERT: A 755 HIS cc_start: 0.6326 (m-70) cc_final: 0.5928 (m-70) REVERT: A 761 MET cc_start: 0.7280 (tmm) cc_final: 0.7036 (tmm) REVERT: B 172 ASP cc_start: 0.8009 (t0) cc_final: 0.7322 (t0) REVERT: B 252 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6883 (mtpt) REVERT: B 298 PHE cc_start: 0.8690 (m-10) cc_final: 0.8471 (m-10) REVERT: B 317 MET cc_start: 0.8988 (tmm) cc_final: 0.8751 (tmm) REVERT: B 492 ASP cc_start: 0.7735 (t70) cc_final: 0.7236 (t70) REVERT: B 533 MET cc_start: 0.7420 (tmm) cc_final: 0.6780 (tmm) REVERT: B 570 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: B 613 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7150 (tt0) REVERT: B 755 HIS cc_start: 0.6321 (m-70) cc_final: 0.5946 (m-70) REVERT: B 761 MET cc_start: 0.7142 (tmm) cc_final: 0.6906 (tmm) outliers start: 20 outliers final: 13 residues processed: 296 average time/residue: 0.0854 time to fit residues: 39.9100 Evaluate side-chains 269 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 862 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 94 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 256 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 256 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 ASN B 592 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117443 restraints weight = 23284.430| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.09 r_work: 0.3390 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14886 Z= 0.131 Angle : 0.594 11.553 20156 Z= 0.295 Chirality : 0.041 0.230 2372 Planarity : 0.004 0.060 2472 Dihedral : 4.963 29.090 2028 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.19 % Allowed : 12.88 % Favored : 84.94 % 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 aren not related in a simple way. whole: 1.14 (0.20), residues: 1836 helix: 1.59 (0.15), residues: 1214 sheet: 1.38 (0.61), residues: 76 loop : -1.26 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 601 TYR 0.018 0.001 TYR B 617 PHE 0.013 0.001 PHE B 622 TRP 0.015 0.001 TRP B 854 HIS 0.004 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00303 (14886) covalent geometry : angle 0.59392 (20156) hydrogen bonds : bond 0.03740 ( 949) hydrogen bonds : angle 4.33254 ( 2787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8855 (t0) cc_final: 0.8493 (t0) REVERT: A 252 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6782 (mtpt) REVERT: A 298 PHE cc_start: 0.8622 (m-10) cc_final: 0.8412 (m-10) REVERT: A 317 MET cc_start: 0.8978 (tmm) cc_final: 0.8710 (tmm) REVERT: A 486 GLU cc_start: 0.8649 (pt0) cc_final: 0.8446 (pt0) REVERT: A 492 ASP cc_start: 0.7524 (t70) cc_final: 0.7200 (t0) REVERT: A 533 MET cc_start: 0.7899 (tmm) cc_final: 0.7584 (tmm) REVERT: A 570 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: A 597 LYS cc_start: 0.2684 (mptt) cc_final: 0.2398 (tptp) REVERT: A 613 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7198 (tt0) REVERT: A 656 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 693 GLU cc_start: 0.8460 (tp30) cc_final: 0.8213 (tp30) REVERT: A 755 HIS cc_start: 0.6384 (m-70) cc_final: 0.5989 (m-70) REVERT: A 761 MET cc_start: 0.7228 (tmm) cc_final: 0.7008 (tmm) REVERT: A 829 MET cc_start: 0.8755 (ppp) cc_final: 0.8327 (tmm) REVERT: A 891 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8524 (t) REVERT: B 94 ASN cc_start: 0.8863 (t0) cc_final: 0.8464 (t0) REVERT: B 252 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6756 (mtpt) REVERT: B 298 PHE cc_start: 0.8623 (m-10) cc_final: 0.8406 (m-10) REVERT: B 317 MET cc_start: 0.8941 (tmm) cc_final: 0.8718 (tmm) REVERT: B 426 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 486 GLU cc_start: 0.8561 (pt0) cc_final: 0.8305 (pt0) REVERT: B 570 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: B 613 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7210 (tt0) REVERT: B 656 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 693 GLU cc_start: 0.8420 (tp30) cc_final: 0.8137 (tp30) REVERT: B 755 HIS cc_start: 0.6345 (m-70) cc_final: 0.5975 (m-70) REVERT: B 829 MET cc_start: 0.8755 (ppp) cc_final: 0.8362 (tmm) REVERT: B 891 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8596 (t) outliers start: 35 outliers final: 25 residues processed: 304 average time/residue: 0.0859 time to fit residues: 40.4148 Evaluate side-chains 282 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 7 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117431 restraints weight = 23114.486| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.01 r_work: 0.3377 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14886 Z= 0.141 Angle : 0.609 11.927 20156 Z= 0.296 Chirality : 0.041 0.226 2372 Planarity : 0.004 0.055 2472 Dihedral : 4.905 29.577 2028 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.44 % Allowed : 15.25 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.16 (0.20), residues: 1836 helix: 1.61 (0.15), residues: 1214 sheet: 1.46 (0.59), residues: 78 loop : -1.27 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 452 TYR 0.015 0.001 TYR A 617 PHE 0.013 0.001 PHE A 622 TRP 0.015 0.001 TRP B 854 HIS 0.013 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00333 (14886) covalent geometry : angle 0.60852 (20156) hydrogen bonds : bond 0.03686 ( 949) hydrogen bonds : angle 4.24789 ( 2787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.566 Fit side-chains REVERT: A 94 ASN cc_start: 0.8881 (t0) cc_final: 0.8476 (t0) REVERT: A 156 TRP cc_start: 0.7732 (m100) cc_final: 0.6961 (m100) REVERT: A 492 ASP cc_start: 0.7708 (t70) cc_final: 0.7353 (t0) REVERT: A 533 MET cc_start: 0.7977 (tmm) cc_final: 0.7592 (tmm) REVERT: A 570 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: A 597 LYS cc_start: 0.2747 (mptt) cc_final: 0.2406 (tptp) REVERT: A 693 GLU cc_start: 0.8542 (tp30) cc_final: 0.8208 (tp30) REVERT: A 755 HIS cc_start: 0.6292 (m-70) cc_final: 0.5920 (m-70) REVERT: B 94 ASN cc_start: 0.8909 (t0) cc_final: 0.8507 (t0) REVERT: B 120 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7528 (p-80) REVERT: B 156 TRP cc_start: 0.7731 (m100) cc_final: 0.6954 (m100) REVERT: B 252 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6867 (mtpt) REVERT: B 426 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7746 (tp) REVERT: B 486 GLU cc_start: 0.8549 (pt0) cc_final: 0.8334 (pt0) REVERT: B 492 ASP cc_start: 0.7651 (t70) cc_final: 0.7311 (t0) REVERT: B 570 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: B 693 GLU cc_start: 0.8457 (tp30) cc_final: 0.8141 (tp30) REVERT: B 755 HIS cc_start: 0.6299 (m-70) cc_final: 0.5964 (m-70) REVERT: B 966 ARG cc_start: 0.6657 (ttm-80) cc_final: 0.6333 (ttm110) REVERT: B 1037 MET cc_start: 0.6526 (ttm) cc_final: 0.6308 (ttm) outliers start: 39 outliers final: 26 residues processed: 294 average time/residue: 0.0887 time to fit residues: 40.7833 Evaluate side-chains 289 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 0.0050 chunk 182 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.146824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118559 restraints weight = 22990.679| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.98 r_work: 0.3391 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14886 Z= 0.124 Angle : 0.600 11.677 20156 Z= 0.291 Chirality : 0.040 0.224 2372 Planarity : 0.004 0.052 2472 Dihedral : 4.789 27.093 2028 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.62 % Allowed : 16.44 % Favored : 80.94 % 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 aren not related in a simple way. whole: 1.31 (0.20), residues: 1836 helix: 1.72 (0.15), residues: 1218 sheet: 1.46 (0.60), residues: 78 loop : -1.23 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 601 TYR 0.012 0.001 TYR B 617 PHE 0.012 0.001 PHE A 622 TRP 0.014 0.001 TRP A 854 HIS 0.011 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00288 (14886) covalent geometry : angle 0.59981 (20156) hydrogen bonds : bond 0.03502 ( 949) hydrogen bonds : angle 4.15339 ( 2787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8850 (t0) cc_final: 0.8401 (t0) REVERT: A 118 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6775 (pt0) REVERT: A 214 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.4671 (ppp) REVERT: A 252 LYS cc_start: 0.7238 (mmtt) cc_final: 0.6885 (mtpt) REVERT: A 316 GLU cc_start: 0.8901 (tp30) cc_final: 0.8599 (tp30) REVERT: A 486 GLU cc_start: 0.8588 (pt0) cc_final: 0.8213 (pt0) REVERT: A 492 ASP cc_start: 0.7656 (t70) cc_final: 0.7025 (t70) REVERT: A 533 MET cc_start: 0.7924 (tmm) cc_final: 0.7513 (tmm) REVERT: A 570 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: A 597 LYS cc_start: 0.2789 (mptt) cc_final: 0.2452 (tptp) REVERT: A 656 GLU cc_start: 0.8054 (tp30) cc_final: 0.7615 (tm-30) REVERT: A 693 GLU cc_start: 0.8566 (tp30) cc_final: 0.8237 (tp30) REVERT: A 735 MET cc_start: 0.7581 (mtt) cc_final: 0.7351 (mtt) REVERT: A 755 HIS cc_start: 0.6283 (m-70) cc_final: 0.5869 (m-70) REVERT: A 891 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8626 (t) REVERT: A 1037 MET cc_start: 0.6583 (tpp) cc_final: 0.6370 (ttm) REVERT: B 94 ASN cc_start: 0.8869 (t0) cc_final: 0.8449 (t0) REVERT: B 118 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6725 (pt0) REVERT: B 120 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7447 (p-80) REVERT: B 214 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.4722 (ppp) REVERT: B 252 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6878 (mtpt) REVERT: B 426 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 486 GLU cc_start: 0.8529 (pt0) cc_final: 0.8306 (pt0) REVERT: B 570 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: B 656 GLU cc_start: 0.8213 (tp30) cc_final: 0.7964 (tm-30) REVERT: B 693 GLU cc_start: 0.8504 (tp30) cc_final: 0.8192 (tp30) REVERT: B 755 HIS cc_start: 0.6228 (m-70) cc_final: 0.5900 (m-70) REVERT: B 891 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8616 (t) REVERT: B 966 ARG cc_start: 0.6626 (ttm-80) cc_final: 0.6320 (ttm110) outliers start: 42 outliers final: 24 residues processed: 297 average time/residue: 0.0869 time to fit residues: 40.9826 Evaluate side-chains 302 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115704 restraints weight = 23060.170| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.00 r_work: 0.3364 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14886 Z= 0.146 Angle : 0.610 11.502 20156 Z= 0.297 Chirality : 0.041 0.210 2372 Planarity : 0.004 0.048 2472 Dihedral : 4.799 28.806 2028 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.38 % Allowed : 16.75 % Favored : 79.88 % 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 aren not related in a simple way. whole: 1.33 (0.20), residues: 1836 helix: 1.72 (0.15), residues: 1218 sheet: 1.48 (0.61), residues: 78 loop : -1.19 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 452 TYR 0.012 0.001 TYR A 617 PHE 0.031 0.001 PHE B 970 TRP 0.017 0.001 TRP A 854 HIS 0.010 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00348 (14886) covalent geometry : angle 0.60987 (20156) hydrogen bonds : bond 0.03570 ( 949) hydrogen bonds : angle 4.10812 ( 2787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8844 (t0) cc_final: 0.8390 (t0) REVERT: A 118 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6197 (pt0) REVERT: A 120 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7414 (p-80) REVERT: A 121 GLN cc_start: 0.7766 (mp10) cc_final: 0.6895 (mp10) REVERT: A 214 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.4716 (ppp) REVERT: A 228 PHE cc_start: 0.8331 (t80) cc_final: 0.8103 (t80) REVERT: A 486 GLU cc_start: 0.8628 (pt0) cc_final: 0.8241 (pt0) REVERT: A 492 ASP cc_start: 0.7632 (t70) cc_final: 0.6979 (t70) REVERT: A 533 MET cc_start: 0.7862 (tmm) cc_final: 0.7410 (tmm) REVERT: A 570 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: A 597 LYS cc_start: 0.2868 (mptt) cc_final: 0.2401 (tptp) REVERT: A 693 GLU cc_start: 0.8580 (tp30) cc_final: 0.8259 (tp30) REVERT: A 755 HIS cc_start: 0.6351 (m-70) cc_final: 0.5664 (m-70) REVERT: A 829 MET cc_start: 0.8738 (ppp) cc_final: 0.8226 (tmm) REVERT: A 891 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8650 (t) REVERT: B 94 ASN cc_start: 0.8844 (t0) cc_final: 0.8365 (t0) REVERT: B 118 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6577 (pt0) REVERT: B 120 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7361 (p-80) REVERT: B 214 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.4640 (ppp) REVERT: B 228 PHE cc_start: 0.8236 (t80) cc_final: 0.7999 (t80) REVERT: B 317 MET cc_start: 0.8951 (tmm) cc_final: 0.8671 (tmm) REVERT: B 426 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7845 (tp) REVERT: B 486 GLU cc_start: 0.8609 (pt0) cc_final: 0.8346 (pt0) REVERT: B 492 ASP cc_start: 0.7607 (t70) cc_final: 0.7238 (t0) REVERT: B 570 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: B 693 GLU cc_start: 0.8499 (tp30) cc_final: 0.8196 (tp30) REVERT: B 755 HIS cc_start: 0.6345 (m-70) cc_final: 0.5661 (m-70) REVERT: B 829 MET cc_start: 0.8752 (ppp) cc_final: 0.8232 (tmm) REVERT: B 966 ARG cc_start: 0.6607 (ttm-80) cc_final: 0.6376 (ttm110) outliers start: 54 outliers final: 35 residues processed: 315 average time/residue: 0.0890 time to fit residues: 44.9433 Evaluate side-chains 310 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 7 optimal weight: 0.0980 chunk 171 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117958 restraints weight = 23008.966| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.07 r_work: 0.3386 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14886 Z= 0.121 Angle : 0.618 12.192 20156 Z= 0.296 Chirality : 0.040 0.199 2372 Planarity : 0.004 0.045 2472 Dihedral : 4.704 26.804 2028 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.00 % Allowed : 17.81 % Favored : 79.19 % 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 aren not related in a simple way. whole: 1.41 (0.21), residues: 1836 helix: 1.77 (0.15), residues: 1216 sheet: 1.54 (0.62), residues: 78 loop : -1.11 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 601 TYR 0.013 0.001 TYR A 812 PHE 0.027 0.001 PHE A 970 TRP 0.012 0.001 TRP A 854 HIS 0.009 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00276 (14886) covalent geometry : angle 0.61782 (20156) hydrogen bonds : bond 0.03459 ( 949) hydrogen bonds : angle 4.11285 ( 2787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8801 (t0) cc_final: 0.8345 (t0) REVERT: A 118 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6623 (pt0) REVERT: A 120 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7341 (p90) REVERT: A 214 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.4508 (ppp) REVERT: A 228 PHE cc_start: 0.8244 (t80) cc_final: 0.8036 (t80) REVERT: A 252 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6781 (mtpt) REVERT: A 486 GLU cc_start: 0.8616 (pt0) cc_final: 0.8224 (pt0) REVERT: A 492 ASP cc_start: 0.7588 (t70) cc_final: 0.6934 (t70) REVERT: A 533 MET cc_start: 0.7871 (tmm) cc_final: 0.7609 (tmm) REVERT: A 559 ILE cc_start: 0.7813 (mt) cc_final: 0.7565 (mp) REVERT: A 597 LYS cc_start: 0.2874 (mptt) cc_final: 0.2492 (tptp) REVERT: A 693 GLU cc_start: 0.8582 (tp30) cc_final: 0.8264 (tp30) REVERT: A 755 HIS cc_start: 0.6448 (m-70) cc_final: 0.5970 (m-70) REVERT: A 891 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8608 (t) REVERT: B 94 ASN cc_start: 0.8809 (t0) cc_final: 0.8333 (t0) REVERT: B 118 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6497 (pt0) REVERT: B 120 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7433 (p-80) REVERT: B 214 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.4470 (ppp) REVERT: B 228 PHE cc_start: 0.8221 (t80) cc_final: 0.7994 (t80) REVERT: B 252 LYS cc_start: 0.7128 (mmtt) cc_final: 0.6729 (mtpt) REVERT: B 426 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 486 GLU cc_start: 0.8615 (pt0) cc_final: 0.8329 (pt0) REVERT: B 492 ASP cc_start: 0.7566 (t70) cc_final: 0.7195 (t0) REVERT: B 559 ILE cc_start: 0.7852 (mt) cc_final: 0.7594 (mp) REVERT: B 570 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: B 693 GLU cc_start: 0.8503 (tp30) cc_final: 0.8228 (tp30) REVERT: B 755 HIS cc_start: 0.6403 (m-70) cc_final: 0.5979 (m-70) REVERT: B 966 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.6329 (ttm110) REVERT: B 1037 MET cc_start: 0.6430 (ttm) cc_final: 0.6195 (ttm) REVERT: B 1042 PHE cc_start: 0.7290 (m-10) cc_final: 0.7024 (m-10) outliers start: 48 outliers final: 33 residues processed: 319 average time/residue: 0.0890 time to fit residues: 44.8584 Evaluate side-chains 313 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 130 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117936 restraints weight = 22921.637| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.07 r_work: 0.3378 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14886 Z= 0.127 Angle : 0.620 11.999 20156 Z= 0.296 Chirality : 0.040 0.187 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.679 26.748 2028 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.00 % Allowed : 18.25 % Favored : 78.75 % 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 aren not related in a simple way. whole: 1.46 (0.21), residues: 1836 helix: 1.81 (0.15), residues: 1212 sheet: 1.62 (0.62), residues: 78 loop : -1.10 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 601 TYR 0.012 0.001 TYR A 812 PHE 0.024 0.001 PHE A 970 TRP 0.021 0.001 TRP A 854 HIS 0.008 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00299 (14886) covalent geometry : angle 0.61998 (20156) hydrogen bonds : bond 0.03447 ( 949) hydrogen bonds : angle 4.09545 ( 2787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8808 (t0) cc_final: 0.8335 (t0) REVERT: A 118 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6576 (pt0) REVERT: A 120 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7369 (p90) REVERT: A 214 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.4511 (ppp) REVERT: A 228 PHE cc_start: 0.8211 (t80) cc_final: 0.7992 (t80) REVERT: A 252 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6741 (mtpt) REVERT: A 486 GLU cc_start: 0.8624 (pt0) cc_final: 0.8220 (pt0) REVERT: A 492 ASP cc_start: 0.7611 (t70) cc_final: 0.6959 (t70) REVERT: A 533 MET cc_start: 0.7862 (tmm) cc_final: 0.7413 (tmm) REVERT: A 559 ILE cc_start: 0.7799 (mt) cc_final: 0.7542 (mp) REVERT: A 597 LYS cc_start: 0.2846 (mptt) cc_final: 0.2501 (tptp) REVERT: A 693 GLU cc_start: 0.8598 (tp30) cc_final: 0.8286 (tp30) REVERT: A 755 HIS cc_start: 0.6327 (m-70) cc_final: 0.5927 (m-70) REVERT: A 770 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7978 (mptt) REVERT: A 891 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8596 (t) REVERT: B 94 ASN cc_start: 0.8808 (t0) cc_final: 0.8327 (t0) REVERT: B 118 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6442 (pt0) REVERT: B 120 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7462 (p-80) REVERT: B 214 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.4512 (ppp) REVERT: B 228 PHE cc_start: 0.8176 (t80) cc_final: 0.7965 (t80) REVERT: B 252 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6760 (mtpt) REVERT: B 426 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (tp) REVERT: B 486 GLU cc_start: 0.8620 (pt0) cc_final: 0.8332 (pt0) REVERT: B 492 ASP cc_start: 0.7581 (t70) cc_final: 0.7207 (t0) REVERT: B 570 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: B 693 GLU cc_start: 0.8597 (tp30) cc_final: 0.8321 (tp30) REVERT: B 755 HIS cc_start: 0.6311 (m-70) cc_final: 0.5703 (m-70) REVERT: B 966 ARG cc_start: 0.6772 (ttm-80) cc_final: 0.6269 (ttm110) REVERT: B 1013 TRP cc_start: 0.7715 (t60) cc_final: 0.7508 (t60) REVERT: B 1037 MET cc_start: 0.6320 (ttm) cc_final: 0.6115 (ttm) REVERT: B 1042 PHE cc_start: 0.7191 (m-10) cc_final: 0.6917 (m-10) outliers start: 48 outliers final: 37 residues processed: 304 average time/residue: 0.1056 time to fit residues: 50.7380 Evaluate side-chains 314 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116559 restraints weight = 23155.116| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.83 r_work: 0.3380 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14886 Z= 0.139 Angle : 0.632 11.980 20156 Z= 0.302 Chirality : 0.040 0.187 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.700 26.383 2028 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.56 % Allowed : 18.25 % Favored : 78.19 % 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 aren not related in a simple way. whole: 1.36 (0.21), residues: 1836 helix: 1.75 (0.15), residues: 1216 sheet: 1.47 (0.61), residues: 78 loop : -1.16 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 601 TYR 0.019 0.001 TYR A 812 PHE 0.020 0.001 PHE A 970 TRP 0.019 0.001 TRP A 854 HIS 0.008 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00332 (14886) covalent geometry : angle 0.63180 (20156) hydrogen bonds : bond 0.03492 ( 949) hydrogen bonds : angle 4.12494 ( 2787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8835 (t0) cc_final: 0.8350 (t0) REVERT: A 118 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6618 (pt0) REVERT: A 120 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7315 (p90) REVERT: A 214 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.4479 (ppp) REVERT: A 228 PHE cc_start: 0.8223 (t80) cc_final: 0.7993 (t80) REVERT: A 486 GLU cc_start: 0.8588 (pt0) cc_final: 0.8194 (pt0) REVERT: A 492 ASP cc_start: 0.7617 (t70) cc_final: 0.6956 (t70) REVERT: A 533 MET cc_start: 0.7883 (tmm) cc_final: 0.7397 (tmm) REVERT: A 559 ILE cc_start: 0.7863 (mt) cc_final: 0.7605 (mp) REVERT: A 597 LYS cc_start: 0.2855 (mptt) cc_final: 0.2503 (tptp) REVERT: A 693 GLU cc_start: 0.8602 (tp30) cc_final: 0.8289 (tp30) REVERT: A 755 HIS cc_start: 0.6300 (m-70) cc_final: 0.5815 (m-70) REVERT: A 770 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8103 (mptt) REVERT: A 891 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8627 (t) REVERT: B 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8339 (t0) REVERT: B 118 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6466 (pt0) REVERT: B 120 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7586 (p-80) REVERT: B 214 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.4478 (ppp) REVERT: B 252 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6791 (mtpt) REVERT: B 426 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 486 GLU cc_start: 0.8612 (pt0) cc_final: 0.8332 (pt0) REVERT: B 492 ASP cc_start: 0.7638 (t70) cc_final: 0.7258 (t0) REVERT: B 570 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: B 693 GLU cc_start: 0.8600 (tp30) cc_final: 0.8328 (tp30) REVERT: B 755 HIS cc_start: 0.6486 (m-70) cc_final: 0.5932 (m-70) REVERT: B 770 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8052 (mptt) REVERT: B 966 ARG cc_start: 0.6862 (ttm-80) cc_final: 0.6333 (ttm110) REVERT: B 1011 MET cc_start: 0.7579 (ttm) cc_final: 0.7283 (tpp) REVERT: B 1037 MET cc_start: 0.6423 (ttm) cc_final: 0.6208 (ttm) REVERT: B 1042 PHE cc_start: 0.7301 (m-10) cc_final: 0.7036 (m-10) outliers start: 57 outliers final: 38 residues processed: 306 average time/residue: 0.1059 time to fit residues: 51.2684 Evaluate side-chains 319 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117913 restraints weight = 23006.101| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.96 r_work: 0.3387 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14886 Z= 0.129 Angle : 0.644 12.095 20156 Z= 0.305 Chirality : 0.040 0.191 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.683 26.356 2028 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.94 % Allowed : 18.94 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.20), residues: 1836 helix: 1.74 (0.15), residues: 1216 sheet: 1.45 (0.61), residues: 78 loop : -1.22 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 601 TYR 0.017 0.001 TYR A 812 PHE 0.018 0.001 PHE A 970 TRP 0.021 0.001 TRP B1013 HIS 0.008 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00305 (14886) covalent geometry : angle 0.64434 (20156) hydrogen bonds : bond 0.03440 ( 949) hydrogen bonds : angle 4.11173 ( 2787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8836 (t0) cc_final: 0.8353 (t0) REVERT: A 118 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6592 (pt0) REVERT: A 120 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7305 (p90) REVERT: A 214 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.4450 (ppp) REVERT: A 228 PHE cc_start: 0.8211 (t80) cc_final: 0.7979 (t80) REVERT: A 252 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6813 (mtpt) REVERT: A 486 GLU cc_start: 0.8558 (pt0) cc_final: 0.8044 (pt0) REVERT: A 492 ASP cc_start: 0.7629 (t70) cc_final: 0.6967 (t70) REVERT: A 533 MET cc_start: 0.7887 (tmm) cc_final: 0.7409 (tmm) REVERT: A 559 ILE cc_start: 0.7879 (mt) cc_final: 0.7617 (mp) REVERT: A 597 LYS cc_start: 0.2837 (mptt) cc_final: 0.2333 (tptp) REVERT: A 693 GLU cc_start: 0.8610 (tp30) cc_final: 0.8324 (tp30) REVERT: A 697 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8605 (ttpp) REVERT: A 755 HIS cc_start: 0.6207 (m-70) cc_final: 0.5848 (m-70) REVERT: A 770 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8077 (mptt) REVERT: A 829 MET cc_start: 0.8738 (ppp) cc_final: 0.8231 (tmm) REVERT: B 94 ASN cc_start: 0.8856 (t0) cc_final: 0.8342 (t0) REVERT: B 118 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6173 (pt0) REVERT: B 120 HIS cc_start: 0.8062 (OUTLIER) cc_final: 0.7602 (p-80) REVERT: B 121 GLN cc_start: 0.7777 (mp10) cc_final: 0.7397 (mp10) REVERT: B 214 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.4478 (ppp) REVERT: B 252 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6835 (mtpt) REVERT: B 426 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7881 (tp) REVERT: B 486 GLU cc_start: 0.8600 (pt0) cc_final: 0.8201 (pt0) REVERT: B 492 ASP cc_start: 0.7644 (t70) cc_final: 0.7262 (t0) REVERT: B 559 ILE cc_start: 0.7903 (mt) cc_final: 0.7652 (mp) REVERT: B 570 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: B 693 GLU cc_start: 0.8627 (tp30) cc_final: 0.8349 (tp30) REVERT: B 735 MET cc_start: 0.7587 (mtt) cc_final: 0.7333 (mtt) REVERT: B 755 HIS cc_start: 0.6383 (m-70) cc_final: 0.5923 (m-70) REVERT: B 770 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8128 (mmtm) REVERT: B 829 MET cc_start: 0.8732 (ppp) cc_final: 0.8219 (tmm) REVERT: B 966 ARG cc_start: 0.6915 (ttm-80) cc_final: 0.6360 (ttm110) REVERT: B 1011 MET cc_start: 0.7604 (ttm) cc_final: 0.6342 (tpp) outliers start: 47 outliers final: 36 residues processed: 303 average time/residue: 0.1048 time to fit residues: 50.7159 Evaluate side-chains 313 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114548 restraints weight = 23110.716| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.03 r_work: 0.3324 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14886 Z= 0.197 Angle : 0.683 11.556 20156 Z= 0.327 Chirality : 0.042 0.178 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.874 27.735 2028 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.06 % Allowed : 19.00 % Favored : 77.94 % 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 aren not related in a simple way. whole: 1.19 (0.20), residues: 1836 helix: 1.65 (0.15), residues: 1212 sheet: 1.39 (0.61), residues: 78 loop : -1.28 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 601 TYR 0.017 0.001 TYR A 812 PHE 0.033 0.002 PHE B 228 TRP 0.022 0.002 TRP A 854 HIS 0.009 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00473 (14886) covalent geometry : angle 0.68256 (20156) hydrogen bonds : bond 0.03703 ( 949) hydrogen bonds : angle 4.19530 ( 2787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.58 seconds wall clock time: 51 minutes 4.52 seconds (3064.52 seconds total)