Starting phenix.real_space_refine on Sun Nov 17 21:38:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/11_2024/8hya_35085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/11_2024/8hya_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/11_2024/8hya_35085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/11_2024/8hya_35085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/11_2024/8hya_35085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/11_2024/8hya_35085.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 8.95, per 1000 atoms: 0.61 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: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.73 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: 4.47 Time building geometry restraints manager: 4.36 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: 0.00 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.860 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.420 ------------------------------------------------------------------------------- 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= 0.250 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.051 0.002 TRP B 156 HIS 0.003 0.001 HIS B 626 PHE 0.029 0.001 PHE B 425 TYR 0.041 0.002 TYR A 617 ARG 0.008 0.001 ARG B 551 *********************** 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 : 1.966 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: 0.2537 time to fit residues: 125.5935 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 : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.0170 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14886 Z= 0.198 Angle : 0.631 11.818 20156 Z= 0.316 Chirality : 0.041 0.235 2372 Planarity : 0.005 0.072 2472 Dihedral : 5.092 30.124 2028 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.12 % Allowed : 9.69 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1836 helix: 1.51 (0.15), residues: 1214 sheet: 1.51 (0.60), residues: 76 loop : -1.30 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 854 HIS 0.004 0.001 HIS A 120 PHE 0.016 0.001 PHE B 298 TYR 0.027 0.001 TYR A 617 ARG 0.005 0.001 ARG A 601 *********************** 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 314 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 1.761 Fit side-chains REVERT: A 94 ASN cc_start: 0.8867 (t0) cc_final: 0.8563 (t0) REVERT: A 252 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7429 (mtpt) REVERT: A 355 PHE cc_start: 0.8189 (m-10) cc_final: 0.7986 (m-80) REVERT: A 492 ASP cc_start: 0.7526 (t70) cc_final: 0.7206 (t70) REVERT: A 533 MET cc_start: 0.7592 (tmm) cc_final: 0.6976 (tmm) REVERT: A 570 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: A 597 LYS cc_start: 0.2639 (mptt) cc_final: 0.2146 (tptp) REVERT: A 613 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7123 (tt0) REVERT: A 761 MET cc_start: 0.7255 (tmm) cc_final: 0.7010 (tmm) REVERT: A 914 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8285 (mmmt) REVERT: A 1011 MET cc_start: 0.7211 (ttm) cc_final: 0.7000 (ttm) REVERT: B 252 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7421 (mtpt) REVERT: B 533 MET cc_start: 0.7511 (tmm) cc_final: 0.6813 (tmm) REVERT: B 570 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: B 613 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7111 (tt0) REVERT: B 761 MET cc_start: 0.7175 (tmm) cc_final: 0.6914 (tmm) REVERT: B 785 ILE cc_start: 0.8434 (mm) cc_final: 0.8205 (mm) outliers start: 18 outliers final: 13 residues processed: 304 average time/residue: 0.2330 time to fit residues: 109.1000 Evaluate side-chains 260 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 245 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 334 ILE 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 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 256 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 ASN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14886 Z= 0.241 Angle : 0.611 7.560 20156 Z= 0.305 Chirality : 0.041 0.219 2372 Planarity : 0.004 0.060 2472 Dihedral : 5.020 31.072 2028 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.25 % Allowed : 12.88 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1836 helix: 1.58 (0.15), residues: 1214 sheet: 1.37 (0.60), residues: 76 loop : -1.26 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 854 HIS 0.008 0.001 HIS B 755 PHE 0.014 0.001 PHE B 622 TYR 0.016 0.001 TYR B 617 ARG 0.006 0.000 ARG B 601 *********************** 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 298 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8901 (t0) cc_final: 0.8586 (t0) REVERT: A 156 TRP cc_start: 0.7614 (m100) cc_final: 0.7222 (m100) REVERT: A 172 ASP cc_start: 0.8120 (t70) cc_final: 0.7333 (t0) REVERT: A 252 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7446 (mtpt) REVERT: A 492 ASP cc_start: 0.7489 (t70) cc_final: 0.7279 (t0) REVERT: A 570 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: A 597 LYS cc_start: 0.2912 (mptt) cc_final: 0.2651 (tptp) REVERT: A 613 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7440 (tt0) REVERT: A 656 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 693 GLU cc_start: 0.7942 (tp30) cc_final: 0.7721 (tp30) REVERT: A 735 MET cc_start: 0.7780 (mtt) cc_final: 0.7517 (mtt) REVERT: A 891 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8438 (t) REVERT: A 1037 MET cc_start: 0.7076 (ttm) cc_final: 0.6848 (ttm) REVERT: B 94 ASN cc_start: 0.8907 (t0) cc_final: 0.8581 (t0) REVERT: B 172 ASP cc_start: 0.8134 (t70) cc_final: 0.7342 (t0) REVERT: B 252 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7450 (mtpt) REVERT: B 426 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7732 (tp) REVERT: B 492 ASP cc_start: 0.7594 (t70) cc_final: 0.7389 (t0) REVERT: B 570 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: B 613 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7329 (tt0) REVERT: B 656 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 693 GLU cc_start: 0.7954 (tp30) cc_final: 0.7664 (tp30) REVERT: B 735 MET cc_start: 0.7755 (mtt) cc_final: 0.7494 (mtt) REVERT: B 891 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8482 (t) outliers start: 36 outliers final: 26 residues processed: 281 average time/residue: 0.2539 time to fit residues: 108.1486 Evaluate side-chains 286 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 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 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 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 210 LEU 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 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 869 ILE 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 165 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 0.0060 chunk 47 optimal weight: 4.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 308 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14886 Z= 0.233 Angle : 0.604 11.789 20156 Z= 0.297 Chirality : 0.041 0.226 2372 Planarity : 0.004 0.056 2472 Dihedral : 4.968 31.855 2028 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.38 % Allowed : 15.06 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1836 helix: 1.60 (0.15), residues: 1220 sheet: 1.37 (0.59), residues: 78 loop : -1.36 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 854 HIS 0.004 0.001 HIS B 626 PHE 0.012 0.001 PHE A 622 TYR 0.014 0.001 TYR B 617 ARG 0.007 0.001 ARG A 452 *********************** 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 310 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8851 (t0) cc_final: 0.8550 (t0) REVERT: A 151 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 172 ASP cc_start: 0.8229 (t70) cc_final: 0.7496 (t0) REVERT: A 492 ASP cc_start: 0.7577 (t70) cc_final: 0.7338 (t0) REVERT: A 570 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8247 (pt0) REVERT: A 597 LYS cc_start: 0.2988 (mptt) cc_final: 0.2486 (tptp) REVERT: A 693 GLU cc_start: 0.8015 (tp30) cc_final: 0.7709 (tp30) REVERT: A 829 MET cc_start: 0.8499 (ppp) cc_final: 0.8126 (tmm) REVERT: B 94 ASN cc_start: 0.8870 (t0) cc_final: 0.8561 (t0) REVERT: B 151 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8347 (t) REVERT: B 156 TRP cc_start: 0.7593 (m100) cc_final: 0.7253 (m100) REVERT: B 172 ASP cc_start: 0.8214 (t70) cc_final: 0.7496 (t0) REVERT: B 426 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7742 (tp) REVERT: B 492 ASP cc_start: 0.7549 (t70) cc_final: 0.7098 (t70) REVERT: B 570 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: B 693 GLU cc_start: 0.7987 (tp30) cc_final: 0.7676 (tp30) REVERT: B 829 MET cc_start: 0.8516 (ppp) cc_final: 0.8106 (tmm) outliers start: 38 outliers final: 30 residues processed: 293 average time/residue: 0.2394 time to fit residues: 108.8621 Evaluate side-chains 285 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 167 LEU 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 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 869 ILE 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 151 THR Chi-restraints excluded: chain B residue 210 LEU 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 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 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 1010 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 151 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 159 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14886 Z= 0.227 Angle : 0.607 11.397 20156 Z= 0.297 Chirality : 0.041 0.224 2372 Planarity : 0.004 0.052 2472 Dihedral : 4.937 30.728 2028 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.31 % Allowed : 16.00 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1836 helix: 1.67 (0.15), residues: 1214 sheet: 1.38 (0.60), residues: 78 loop : -1.30 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 854 HIS 0.014 0.001 HIS A 120 PHE 0.012 0.001 PHE B 622 TYR 0.012 0.001 TYR B 617 ARG 0.006 0.000 ARG A 601 *********************** 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 327 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8840 (t0) cc_final: 0.8529 (t0) REVERT: A 120 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7516 (p-80) REVERT: A 151 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8372 (t) REVERT: A 172 ASP cc_start: 0.8218 (t70) cc_final: 0.7510 (t0) REVERT: A 214 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.4556 (ppp) REVERT: A 492 ASP cc_start: 0.7561 (t70) cc_final: 0.7305 (t0) REVERT: A 570 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: A 597 LYS cc_start: 0.2998 (mptt) cc_final: 0.2481 (tptp) REVERT: A 693 GLU cc_start: 0.8045 (tp30) cc_final: 0.7733 (tp30) REVERT: A 868 GLN cc_start: 0.8029 (pm20) cc_final: 0.7760 (pp30) REVERT: A 891 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8600 (t) REVERT: B 94 ASN cc_start: 0.8844 (t0) cc_final: 0.8495 (t0) REVERT: B 151 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8344 (t) REVERT: B 172 ASP cc_start: 0.8209 (t70) cc_final: 0.7515 (t0) REVERT: B 214 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.4712 (ppp) REVERT: B 426 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7792 (tp) REVERT: B 492 ASP cc_start: 0.7541 (t70) cc_final: 0.7065 (t70) REVERT: B 656 GLU cc_start: 0.7805 (tp30) cc_final: 0.7553 (tm-30) REVERT: B 693 GLU cc_start: 0.7989 (tp30) cc_final: 0.7693 (tp30) REVERT: B 868 GLN cc_start: 0.7975 (pm20) cc_final: 0.7748 (pp30) REVERT: B 891 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8600 (t) outliers start: 53 outliers final: 32 residues processed: 304 average time/residue: 0.2304 time to fit residues: 108.7603 Evaluate side-chains 297 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 151 THR 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 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 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 122 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 210 LEU 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 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 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 59 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14886 Z= 0.241 Angle : 0.623 11.312 20156 Z= 0.302 Chirality : 0.041 0.221 2372 Planarity : 0.004 0.049 2472 Dihedral : 4.941 30.701 2028 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.38 % Allowed : 17.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1836 helix: 1.65 (0.15), residues: 1216 sheet: 1.41 (0.61), residues: 78 loop : -1.34 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 854 HIS 0.013 0.001 HIS A 120 PHE 0.025 0.001 PHE B 970 TYR 0.011 0.001 TYR B 270 ARG 0.007 0.000 ARG A 452 *********************** 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 323 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8847 (t0) cc_final: 0.8447 (t0) REVERT: A 118 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: A 120 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7440 (p-80) REVERT: A 151 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8372 (t) REVERT: A 172 ASP cc_start: 0.8225 (t70) cc_final: 0.7527 (t0) REVERT: A 214 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.4584 (ppp) REVERT: A 492 ASP cc_start: 0.7580 (t70) cc_final: 0.7100 (t70) REVERT: A 570 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8293 (pt0) REVERT: A 597 LYS cc_start: 0.3021 (mptt) cc_final: 0.2510 (tptp) REVERT: A 693 GLU cc_start: 0.8050 (tp30) cc_final: 0.7768 (tp30) REVERT: A 868 GLN cc_start: 0.8105 (pm20) cc_final: 0.7692 (pp30) REVERT: A 891 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 1037 MET cc_start: 0.7271 (ttm) cc_final: 0.6919 (ttm) REVERT: B 94 ASN cc_start: 0.8853 (t0) cc_final: 0.8438 (t0) REVERT: B 118 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6641 (pt0) REVERT: B 151 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8361 (t) REVERT: B 172 ASP cc_start: 0.8219 (t70) cc_final: 0.7580 (t0) REVERT: B 214 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.4646 (ppp) REVERT: B 426 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7813 (tp) REVERT: B 492 ASP cc_start: 0.7554 (t70) cc_final: 0.7082 (t70) REVERT: B 693 GLU cc_start: 0.8015 (tp30) cc_final: 0.7743 (tp30) REVERT: B 735 MET cc_start: 0.7733 (mtt) cc_final: 0.7530 (mtt) REVERT: B 829 MET cc_start: 0.8483 (ppp) cc_final: 0.8060 (tmm) REVERT: B 868 GLN cc_start: 0.8090 (pm20) cc_final: 0.7721 (pp30) REVERT: B 891 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8675 (t) outliers start: 54 outliers final: 34 residues processed: 303 average time/residue: 0.2282 time to fit residues: 108.2946 Evaluate side-chains 308 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 151 THR 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 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 672 LEU Chi-restraints excluded: chain A residue 711 ASP 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 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 210 LEU 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 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 616 CYS Chi-restraints excluded: chain B residue 711 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 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 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2262 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= 0.193 Angle : 0.617 11.944 20156 Z= 0.298 Chirality : 0.040 0.142 2372 Planarity : 0.004 0.045 2472 Dihedral : 4.864 27.677 2028 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.12 % Allowed : 18.56 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1836 helix: 1.73 (0.15), residues: 1216 sheet: 1.64 (0.62), residues: 78 loop : -1.30 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 854 HIS 0.011 0.001 HIS A 120 PHE 0.030 0.001 PHE A 970 TYR 0.012 0.001 TYR A 270 ARG 0.007 0.000 ARG A 452 *********************** 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 337 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8784 (t0) cc_final: 0.8374 (t0) REVERT: A 118 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6609 (pt0) REVERT: A 120 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7509 (p-80) REVERT: A 151 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8274 (t) REVERT: A 172 ASP cc_start: 0.8212 (t70) cc_final: 0.7558 (t0) REVERT: A 214 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.4514 (ppp) REVERT: A 492 ASP cc_start: 0.7548 (t70) cc_final: 0.7058 (t70) REVERT: A 559 ILE cc_start: 0.8165 (mt) cc_final: 0.7900 (mp) REVERT: A 597 LYS cc_start: 0.3119 (mptt) cc_final: 0.2695 (tptp) REVERT: A 693 GLU cc_start: 0.8054 (tp30) cc_final: 0.7784 (tp30) REVERT: A 829 MET cc_start: 0.8479 (ppp) cc_final: 0.8039 (tmm) REVERT: A 891 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8729 (t) REVERT: A 1037 MET cc_start: 0.7229 (ttm) cc_final: 0.6913 (ttm) REVERT: B 94 ASN cc_start: 0.8827 (t0) cc_final: 0.8411 (t0) REVERT: B 118 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6522 (pt0) REVERT: B 120 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7087 (p90) REVERT: B 172 ASP cc_start: 0.8134 (t70) cc_final: 0.7515 (t0) REVERT: B 214 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.4346 (ppp) REVERT: B 241 LEU cc_start: 0.8703 (mt) cc_final: 0.8494 (mt) REVERT: B 492 ASP cc_start: 0.7519 (t70) cc_final: 0.7272 (t0) REVERT: B 693 GLU cc_start: 0.8006 (tp30) cc_final: 0.7737 (tp30) REVERT: B 755 HIS cc_start: 0.6999 (m90) cc_final: 0.6632 (m90) REVERT: B 891 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8722 (t) REVERT: B 1042 PHE cc_start: 0.7891 (m-10) cc_final: 0.7620 (m-10) outliers start: 50 outliers final: 30 residues processed: 318 average time/residue: 0.2479 time to fit residues: 123.7939 Evaluate side-chains 304 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 151 THR 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 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 672 LEU Chi-restraints excluded: chain A residue 862 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 210 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 616 CYS Chi-restraints excluded: chain B residue 711 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN A 800 HIS ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14886 Z= 0.193 Angle : 0.631 11.903 20156 Z= 0.301 Chirality : 0.040 0.228 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.818 27.307 2028 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.00 % Allowed : 18.62 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1836 helix: 1.72 (0.15), residues: 1218 sheet: 1.75 (0.61), residues: 78 loop : -1.26 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 854 HIS 0.011 0.001 HIS A 120 PHE 0.021 0.001 PHE A 970 TYR 0.012 0.001 TYR B 769 ARG 0.006 0.000 ARG B 601 *********************** 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 332 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8761 (t0) cc_final: 0.8355 (t0) REVERT: A 118 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5692 (pt0) REVERT: A 120 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7475 (p-80) REVERT: A 121 GLN cc_start: 0.7814 (mp10) cc_final: 0.6726 (mp10) REVERT: A 151 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 172 ASP cc_start: 0.8171 (t70) cc_final: 0.7525 (t0) REVERT: A 214 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.4438 (ppp) REVERT: A 241 LEU cc_start: 0.8732 (mt) cc_final: 0.8516 (mt) REVERT: A 425 PHE cc_start: 0.7181 (m-10) cc_final: 0.6635 (m-10) REVERT: A 492 ASP cc_start: 0.7545 (t70) cc_final: 0.7057 (t70) REVERT: A 559 ILE cc_start: 0.8148 (mt) cc_final: 0.7878 (mp) REVERT: A 693 GLU cc_start: 0.8069 (tp30) cc_final: 0.7792 (tp30) REVERT: A 891 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8702 (t) REVERT: B 94 ASN cc_start: 0.8810 (t0) cc_final: 0.8382 (t0) REVERT: B 118 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6158 (pt0) REVERT: B 120 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.6992 (p90) REVERT: B 121 GLN cc_start: 0.7559 (mp10) cc_final: 0.6513 (mp10) REVERT: B 172 ASP cc_start: 0.8119 (t70) cc_final: 0.7508 (t0) REVERT: B 214 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.4316 (ppp) REVERT: B 241 LEU cc_start: 0.8702 (mt) cc_final: 0.8477 (mt) REVERT: B 492 ASP cc_start: 0.7515 (t70) cc_final: 0.7258 (t0) REVERT: B 693 GLU cc_start: 0.8044 (tp30) cc_final: 0.7772 (tp30) REVERT: B 815 LEU cc_start: 0.8422 (mm) cc_final: 0.8216 (mm) REVERT: B 891 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8699 (t) outliers start: 48 outliers final: 35 residues processed: 315 average time/residue: 0.2365 time to fit residues: 118.5506 Evaluate side-chains 317 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 151 THR 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 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 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 210 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 616 CYS Chi-restraints excluded: chain B residue 711 ASP 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 169 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2498 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= 0.188 Angle : 0.630 11.882 20156 Z= 0.302 Chirality : 0.041 0.300 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.741 26.870 2028 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.06 % Allowed : 19.25 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1836 helix: 1.75 (0.15), residues: 1220 sheet: 1.34 (0.69), residues: 62 loop : -1.21 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 854 HIS 0.010 0.001 HIS A 120 PHE 0.019 0.001 PHE A 970 TYR 0.013 0.001 TYR B 617 ARG 0.007 0.000 ARG B 601 *********************** 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 341 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8746 (t0) cc_final: 0.8331 (t0) REVERT: A 118 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6489 (pt0) REVERT: A 120 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7616 (p-80) REVERT: A 151 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 172 ASP cc_start: 0.8125 (t70) cc_final: 0.7503 (t0) REVERT: A 214 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.4447 (ppp) REVERT: A 225 ILE cc_start: 0.8472 (tt) cc_final: 0.8202 (tt) REVERT: A 228 PHE cc_start: 0.8627 (t80) cc_final: 0.8366 (t80) REVERT: A 241 LEU cc_start: 0.8715 (mt) cc_final: 0.8487 (mt) REVERT: A 252 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7365 (mtpt) REVERT: A 492 ASP cc_start: 0.7534 (t70) cc_final: 0.7042 (t70) REVERT: A 559 ILE cc_start: 0.8136 (mt) cc_final: 0.7876 (mp) REVERT: A 597 LYS cc_start: 0.3005 (mptt) cc_final: 0.2696 (tptp) REVERT: A 693 GLU cc_start: 0.8076 (tp30) cc_final: 0.7800 (tp30) REVERT: A 735 MET cc_start: 0.7744 (mtt) cc_final: 0.7534 (mtt) REVERT: A 891 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8677 (t) REVERT: B 94 ASN cc_start: 0.8796 (t0) cc_final: 0.8367 (t0) REVERT: B 118 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.5909 (pt0) REVERT: B 120 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7070 (p90) REVERT: B 121 GLN cc_start: 0.7620 (mp10) cc_final: 0.6329 (mp10) REVERT: B 172 ASP cc_start: 0.8090 (t70) cc_final: 0.7481 (t0) REVERT: B 214 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.4260 (ppp) REVERT: B 241 LEU cc_start: 0.8713 (mt) cc_final: 0.8503 (mt) REVERT: B 492 ASP cc_start: 0.7484 (t70) cc_final: 0.6976 (t70) REVERT: B 693 GLU cc_start: 0.8061 (tp30) cc_final: 0.7784 (tp30) REVERT: B 697 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8773 (ttpp) REVERT: B 805 HIS cc_start: 0.7634 (p90) cc_final: 0.7385 (p90) REVERT: B 829 MET cc_start: 0.8468 (ppp) cc_final: 0.7991 (tmm) REVERT: B 891 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8705 (t) REVERT: B 1042 PHE cc_start: 0.7839 (m-10) cc_final: 0.7586 (m-10) outliers start: 49 outliers final: 34 residues processed: 320 average time/residue: 0.2339 time to fit residues: 117.3745 Evaluate side-chains 323 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 151 THR 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 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 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 363 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 711 ASP 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 Chi-restraints excluded: chain B residue 1045 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2567 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= 0.213 Angle : 0.658 12.003 20156 Z= 0.314 Chirality : 0.041 0.298 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.747 26.554 2028 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.75 % Allowed : 20.00 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1836 helix: 1.72 (0.15), residues: 1222 sheet: 1.23 (0.68), residues: 62 loop : -1.23 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 854 HIS 0.010 0.001 HIS A 120 PHE 0.027 0.001 PHE A1042 TYR 0.040 0.002 TYR B 892 ARG 0.007 0.000 ARG B 601 ********************** 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 333 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8751 (t0) cc_final: 0.8336 (t0) REVERT: A 118 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5879 (pt0) REVERT: A 120 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7548 (p-80) REVERT: A 121 GLN cc_start: 0.7836 (mp10) cc_final: 0.7055 (mp10) REVERT: A 151 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8250 (t) REVERT: A 172 ASP cc_start: 0.8132 (t70) cc_final: 0.7501 (t0) REVERT: A 214 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.4362 (ppp) REVERT: A 225 ILE cc_start: 0.8472 (tt) cc_final: 0.8255 (tt) REVERT: A 228 PHE cc_start: 0.8594 (t80) cc_final: 0.8336 (t80) REVERT: A 241 LEU cc_start: 0.8721 (mt) cc_final: 0.8494 (mt) REVERT: A 492 ASP cc_start: 0.7545 (t70) cc_final: 0.7048 (t70) REVERT: A 559 ILE cc_start: 0.8132 (mt) cc_final: 0.7865 (mp) REVERT: A 597 LYS cc_start: 0.3167 (mptt) cc_final: 0.2782 (tptp) REVERT: A 693 GLU cc_start: 0.8079 (tp30) cc_final: 0.7817 (tp30) REVERT: A 697 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8495 (ttmm) REVERT: A 735 MET cc_start: 0.7754 (mtt) cc_final: 0.7531 (mtt) REVERT: A 755 HIS cc_start: 0.7025 (m90) cc_final: 0.6716 (m90) REVERT: A 770 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8345 (mptt) REVERT: A 889 LEU cc_start: 0.7740 (tt) cc_final: 0.7437 (tp) REVERT: B 94 ASN cc_start: 0.8805 (t0) cc_final: 0.8368 (t0) REVERT: B 118 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6022 (pt0) REVERT: B 120 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7080 (p90) REVERT: B 121 GLN cc_start: 0.7643 (mp10) cc_final: 0.6535 (mp10) REVERT: B 172 ASP cc_start: 0.8092 (t70) cc_final: 0.7482 (t0) REVERT: B 214 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.4206 (ppp) REVERT: B 241 LEU cc_start: 0.8718 (mt) cc_final: 0.8503 (mt) REVERT: B 492 ASP cc_start: 0.7492 (t70) cc_final: 0.6984 (t70) REVERT: B 693 GLU cc_start: 0.8069 (tp30) cc_final: 0.7791 (tp30) REVERT: B 697 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8636 (ttpp) REVERT: B 770 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8335 (mptt) REVERT: B 805 HIS cc_start: 0.7665 (p90) cc_final: 0.7424 (p90) REVERT: B 889 LEU cc_start: 0.7799 (tt) cc_final: 0.7482 (tp) outliers start: 44 outliers final: 33 residues processed: 313 average time/residue: 0.2324 time to fit residues: 114.4691 Evaluate side-chains 322 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 1.799 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 160 THR 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 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 573 THR 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 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 364 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1045 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.0000 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** 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 = 0.3863 r_free = 0.3863 target = 0.145992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117181 restraints weight = 22902.651| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.07 r_work: 0.3386 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14886 Z= 0.199 Angle : 0.654 11.897 20156 Z= 0.312 Chirality : 0.042 0.297 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.705 26.343 2028 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.12 % Allowed : 19.81 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1836 helix: 1.77 (0.15), residues: 1218 sheet: 1.12 (0.66), residues: 62 loop : -1.26 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 854 HIS 0.010 0.001 HIS A 120 PHE 0.015 0.001 PHE A 970 TYR 0.029 0.001 TYR B 892 ARG 0.007 0.000 ARG B 601 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.10 seconds wall clock time: 79 minutes 21.12 seconds (4761.12 seconds total)