Starting phenix.real_space_refine on Fri Jun 13 05:38:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hya_35085/06_2025/8hya_35085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hya_35085/06_2025/8hya_35085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hya_35085/06_2025/8hya_35085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hya_35085/06_2025/8hya_35085.map" model { file = "/net/cci-nas-00/data/ceres_data/8hya_35085/06_2025/8hya_35085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hya_35085/06_2025/8hya_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.60, per 1000 atoms: 0.59 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 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: 1.81 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: 4.94 Time building geometry restraints manager: 4.39 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: 0.08 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: 1.310 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.810 Find NCS groups from input model: 0.270 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14886 Z= 0.192 Angle : 0.712 10.486 20156 Z= 0.400 Chirality : 0.044 0.322 2372 Planarity : 0.005 0.112 2472 Dihedral : 13.946 88.793 5410 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.13343 ( 949) hydrogen bonds : angle 5.68025 ( 2787) covalent geometry : bond 0.00374 (14886) covalent geometry : angle 0.71181 (20156) *********************** 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 : 1.820 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: 0.2532 time to fit residues: 124.4603 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 : 2.258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.148419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120122 restraints weight = 22996.956| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.97 r_work: 0.3411 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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= 0.136 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 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 949) hydrogen bonds : angle 4.56523 ( 2787) covalent geometry : bond 0.00306 (14886) covalent geometry : angle 0.63117 (20156) *********************** 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 : 1.564 Fit side-chains REVERT: A 94 ASN cc_start: 0.8893 (t0) cc_final: 0.8528 (t0) REVERT: A 252 LYS cc_start: 0.7147 (mmtt) cc_final: 0.6874 (mtpt) REVERT: A 492 ASP cc_start: 0.7692 (t70) cc_final: 0.7207 (t70) REVERT: A 533 MET cc_start: 0.7477 (tmm) cc_final: 0.6894 (tmm) REVERT: A 570 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: A 597 LYS cc_start: 0.2427 (mptt) cc_final: 0.1906 (tptp) REVERT: A 613 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7090 (tt0) REVERT: A 755 HIS cc_start: 0.6322 (m-70) cc_final: 0.5930 (m-70) REVERT: A 761 MET cc_start: 0.7265 (tmm) cc_final: 0.7006 (tmm) REVERT: A 914 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8396 (mmmt) REVERT: A 1011 MET cc_start: 0.7135 (ttm) cc_final: 0.6922 (ttm) REVERT: B 252 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6851 (mtpt) REVERT: B 317 MET cc_start: 0.9002 (tmm) cc_final: 0.8769 (tmm) REVERT: B 533 MET cc_start: 0.7392 (tmm) cc_final: 0.6750 (tmm) REVERT: B 570 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: B 613 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7092 (tt0) REVERT: B 755 HIS cc_start: 0.6256 (m-70) cc_final: 0.5897 (m-70) REVERT: B 761 MET cc_start: 0.7190 (tmm) cc_final: 0.6918 (tmm) outliers start: 18 outliers final: 13 residues processed: 304 average time/residue: 0.2211 time to fit residues: 103.1611 Evaluate side-chains 261 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 246 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 156 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 146 optimal weight: 0.0470 chunk 94 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114803 restraints weight = 23315.974| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.01 r_work: 0.3339 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14886 Z= 0.190 Angle : 0.639 7.206 20156 Z= 0.320 Chirality : 0.042 0.215 2372 Planarity : 0.004 0.060 2472 Dihedral : 5.170 36.360 2028 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.56 % Allowed : 13.12 % Favored : 84.31 % 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: 1.01 (0.20), residues: 1836 helix: 1.50 (0.15), residues: 1216 sheet: 1.44 (0.60), residues: 78 loop : -1.37 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 854 HIS 0.004 0.001 HIS B 800 PHE 0.015 0.001 PHE B 152 TYR 0.017 0.001 TYR B 617 ARG 0.005 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 949) hydrogen bonds : angle 4.42168 ( 2787) covalent geometry : bond 0.00456 (14886) covalent geometry : angle 0.63902 (20156) *********************** 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 301 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8930 (t0) cc_final: 0.8554 (t0) REVERT: A 156 TRP cc_start: 0.7936 (m100) cc_final: 0.7086 (m100) REVERT: A 172 ASP cc_start: 0.8158 (t70) cc_final: 0.7318 (t0) REVERT: A 253 PHE cc_start: 0.8639 (m-10) cc_final: 0.8402 (m-10) REVERT: A 492 ASP cc_start: 0.7659 (t70) cc_final: 0.7352 (t0) REVERT: A 570 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: A 597 LYS cc_start: 0.2772 (mptt) cc_final: 0.2265 (tptp) REVERT: A 613 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7302 (tt0) REVERT: A 656 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 693 GLU cc_start: 0.8419 (tp30) cc_final: 0.8151 (tp30) REVERT: A 755 HIS cc_start: 0.6384 (m-70) cc_final: 0.5991 (m-70) REVERT: A 761 MET cc_start: 0.7301 (tmm) cc_final: 0.7073 (tmm) REVERT: A 829 MET cc_start: 0.8942 (ppp) cc_final: 0.8520 (tmm) REVERT: A 891 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8549 (t) REVERT: B 94 ASN cc_start: 0.8917 (t0) cc_final: 0.8524 (t0) REVERT: B 172 ASP cc_start: 0.8171 (t70) cc_final: 0.7323 (t0) REVERT: B 317 MET cc_start: 0.8990 (tmm) cc_final: 0.8736 (tmm) REVERT: B 426 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7741 (tp) REVERT: B 486 GLU cc_start: 0.8500 (pt0) cc_final: 0.8270 (pt0) REVERT: B 492 ASP cc_start: 0.7732 (t70) cc_final: 0.7172 (t70) REVERT: B 570 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: B 613 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7319 (tt0) REVERT: B 656 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 693 GLU cc_start: 0.8470 (tp30) cc_final: 0.8209 (tp30) REVERT: B 755 HIS cc_start: 0.6368 (m-70) cc_final: 0.5992 (m-70) REVERT: B 761 MET cc_start: 0.7074 (tmm) cc_final: 0.6862 (tmm) REVERT: B 829 MET cc_start: 0.8894 (ppp) cc_final: 0.8482 (tmm) REVERT: B 891 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8586 (t) REVERT: B 1011 MET cc_start: 0.7302 (ttm) cc_final: 0.7040 (ttm) outliers start: 41 outliers final: 30 residues processed: 282 average time/residue: 0.2939 time to fit residues: 129.0132 Evaluate side-chains 283 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 330 SER 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 869 ILE 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 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 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 87 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.144743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116165 restraints weight = 22973.503| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.99 r_work: 0.3365 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1844 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= 0.140 Angle : 0.604 11.539 20156 Z= 0.299 Chirality : 0.041 0.232 2372 Planarity : 0.004 0.056 2472 Dihedral : 4.995 31.566 2028 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.56 % Allowed : 16.12 % Favored : 81.31 % 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: 1.15 (0.20), residues: 1836 helix: 1.61 (0.15), residues: 1214 sheet: 1.39 (0.60), residues: 78 loop : -1.30 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 854 HIS 0.015 0.001 HIS A 120 PHE 0.012 0.001 PHE A 622 TYR 0.013 0.001 TYR B 617 ARG 0.007 0.000 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 949) hydrogen bonds : angle 4.29123 ( 2787) covalent geometry : bond 0.00328 (14886) covalent geometry : angle 0.60428 (20156) *********************** 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 319 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8913 (t0) cc_final: 0.8515 (t0) REVERT: A 120 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7513 (p-80) REVERT: A 172 ASP cc_start: 0.8201 (t70) cc_final: 0.7384 (t0) REVERT: A 486 GLU cc_start: 0.8578 (pt0) cc_final: 0.8216 (pt0) REVERT: A 492 ASP cc_start: 0.7660 (t70) cc_final: 0.7304 (t0) REVERT: A 570 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: A 597 LYS cc_start: 0.2715 (mptt) cc_final: 0.2186 (tptp) REVERT: A 693 GLU cc_start: 0.8553 (tp30) cc_final: 0.8232 (tp30) REVERT: A 735 MET cc_start: 0.7721 (mtt) cc_final: 0.7514 (mtt) REVERT: A 755 HIS cc_start: 0.6337 (m-70) cc_final: 0.5968 (m-70) REVERT: A 761 MET cc_start: 0.7244 (tmm) cc_final: 0.7041 (tmm) REVERT: B 94 ASN cc_start: 0.8934 (t0) cc_final: 0.8517 (t0) REVERT: B 120 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7601 (p-80) REVERT: B 172 ASP cc_start: 0.8209 (t70) cc_final: 0.7390 (t0) REVERT: B 426 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7735 (tp) REVERT: B 486 GLU cc_start: 0.8578 (pt0) cc_final: 0.8349 (pt0) REVERT: B 492 ASP cc_start: 0.7649 (t70) cc_final: 0.7050 (t70) REVERT: B 570 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: B 693 GLU cc_start: 0.8474 (tp30) cc_final: 0.8167 (tp30) REVERT: B 755 HIS cc_start: 0.6335 (m-70) cc_final: 0.5994 (m-70) REVERT: B 761 MET cc_start: 0.7057 (tmm) cc_final: 0.6778 (tmm) REVERT: B 829 MET cc_start: 0.8811 (ppp) cc_final: 0.8425 (tmm) REVERT: B 966 ARG cc_start: 0.6771 (ttm-80) cc_final: 0.6323 (ttm110) outliers start: 41 outliers final: 28 residues processed: 298 average time/residue: 0.2372 time to fit residues: 109.1657 Evaluate side-chains 290 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 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 873 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 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 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 121 optimal weight: 0.6980 chunk 128 optimal weight: 0.0870 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 161 optimal weight: 0.1980 chunk 155 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.147204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118656 restraints weight = 23079.877| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.00 r_work: 0.3393 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14886 Z= 0.118 Angle : 0.599 11.525 20156 Z= 0.290 Chirality : 0.040 0.236 2372 Planarity : 0.004 0.052 2472 Dihedral : 4.821 27.609 2028 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.56 % Allowed : 16.62 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.20), residues: 1836 helix: 1.71 (0.15), residues: 1220 sheet: 1.37 (0.60), residues: 78 loop : -1.38 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 854 HIS 0.011 0.001 HIS A 120 PHE 0.012 0.001 PHE A 622 TYR 0.013 0.001 TYR B 617 ARG 0.005 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 949) hydrogen bonds : angle 4.17470 ( 2787) covalent geometry : bond 0.00270 (14886) covalent geometry : angle 0.59872 (20156) *********************** 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 330 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8855 (t0) cc_final: 0.8440 (t0) REVERT: A 118 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: A 120 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7533 (p-80) REVERT: A 172 ASP cc_start: 0.8183 (t70) cc_final: 0.7423 (t0) REVERT: A 214 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.4632 (ppp) REVERT: A 252 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6848 (mtpt) REVERT: A 486 GLU cc_start: 0.8556 (pt0) cc_final: 0.8224 (pt0) REVERT: A 492 ASP cc_start: 0.7593 (t70) cc_final: 0.7230 (t0) REVERT: A 559 ILE cc_start: 0.7917 (mt) cc_final: 0.7643 (mp) REVERT: A 597 LYS cc_start: 0.2639 (mptt) cc_final: 0.2318 (tptp) REVERT: A 656 GLU cc_start: 0.8037 (tp30) cc_final: 0.7614 (tm-30) REVERT: A 693 GLU cc_start: 0.8569 (tp30) cc_final: 0.8247 (tp30) REVERT: A 755 HIS cc_start: 0.6284 (m-70) cc_final: 0.5914 (m-70) REVERT: A 829 MET cc_start: 0.8793 (ppp) cc_final: 0.8302 (tmm) REVERT: A 891 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8645 (t) REVERT: B 94 ASN cc_start: 0.8873 (t0) cc_final: 0.8455 (t0) REVERT: B 118 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: B 120 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7439 (p-80) REVERT: B 172 ASP cc_start: 0.8178 (t70) cc_final: 0.7421 (t0) REVERT: B 214 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.4683 (ppp) REVERT: B 252 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6840 (mtpt) REVERT: B 426 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 486 GLU cc_start: 0.8581 (pt0) cc_final: 0.8338 (pt0) REVERT: B 656 GLU cc_start: 0.8159 (tp30) cc_final: 0.7913 (tm-30) REVERT: B 693 GLU cc_start: 0.8493 (tp30) cc_final: 0.8183 (tp30) REVERT: B 755 HIS cc_start: 0.6256 (m-70) cc_final: 0.5887 (m-70) REVERT: B 761 MET cc_start: 0.7220 (tmm) cc_final: 0.6946 (tmm) REVERT: B 891 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8650 (t) REVERT: B 966 ARG cc_start: 0.6710 (ttm-80) cc_final: 0.6424 (ttm110) outliers start: 41 outliers final: 24 residues processed: 312 average time/residue: 0.2258 time to fit residues: 109.3917 Evaluate side-chains 297 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR 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 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 426 LEU 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 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 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 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 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 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.144652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115934 restraints weight = 23178.741| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.03 r_work: 0.3360 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2182 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= 0.144 Angle : 0.611 11.411 20156 Z= 0.296 Chirality : 0.040 0.215 2372 Planarity : 0.004 0.047 2472 Dihedral : 4.838 28.885 2028 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.56 % Allowed : 17.44 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1220 sheet: 1.51 (0.61), residues: 78 loop : -1.33 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 854 HIS 0.010 0.001 HIS B 120 PHE 0.028 0.001 PHE B 970 TYR 0.012 0.001 TYR A 270 ARG 0.007 0.001 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 949) hydrogen bonds : angle 4.14745 ( 2787) covalent geometry : bond 0.00342 (14886) covalent geometry : angle 0.61073 (20156) *********************** 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 329 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8870 (t0) cc_final: 0.8415 (t0) REVERT: A 118 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: A 120 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7379 (p-80) REVERT: A 172 ASP cc_start: 0.8232 (t70) cc_final: 0.7475 (t0) REVERT: A 214 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.4749 (ppp) REVERT: A 486 GLU cc_start: 0.8610 (pt0) cc_final: 0.8271 (pt0) REVERT: A 492 ASP cc_start: 0.7663 (t70) cc_final: 0.7029 (t70) REVERT: A 597 LYS cc_start: 0.2901 (mptt) cc_final: 0.2579 (tptp) REVERT: A 693 GLU cc_start: 0.8603 (tp30) cc_final: 0.8292 (tp30) REVERT: A 755 HIS cc_start: 0.6336 (m-70) cc_final: 0.5670 (m-70) REVERT: A 761 MET cc_start: 0.7189 (tmm) cc_final: 0.6908 (tmm) REVERT: A 891 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8677 (t) REVERT: B 94 ASN cc_start: 0.8872 (t0) cc_final: 0.8384 (t0) REVERT: B 118 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6653 (pt0) REVERT: B 120 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7382 (p-80) REVERT: B 172 ASP cc_start: 0.8246 (t70) cc_final: 0.7535 (t0) REVERT: B 214 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.4530 (ppp) REVERT: B 317 MET cc_start: 0.8997 (tmm) cc_final: 0.8733 (tmm) REVERT: B 426 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7909 (tp) REVERT: B 486 GLU cc_start: 0.8602 (pt0) cc_final: 0.8353 (pt0) REVERT: B 492 ASP cc_start: 0.7614 (t70) cc_final: 0.7255 (t0) REVERT: B 693 GLU cc_start: 0.8544 (tp30) cc_final: 0.8244 (tp30) REVERT: B 755 HIS cc_start: 0.6340 (m-70) cc_final: 0.5677 (m-70) REVERT: B 761 MET cc_start: 0.7221 (tmm) cc_final: 0.6936 (tmm) REVERT: B 829 MET cc_start: 0.8770 (ppp) cc_final: 0.8248 (tmm) REVERT: B 966 ARG cc_start: 0.6765 (ttm-80) cc_final: 0.6426 (ttm110) outliers start: 57 outliers final: 37 residues processed: 308 average time/residue: 0.2130 time to fit residues: 102.9331 Evaluate side-chains 305 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 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 555 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114924 restraints weight = 23215.295| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.03 r_work: 0.3347 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14886 Z= 0.155 Angle : 0.635 11.383 20156 Z= 0.305 Chirality : 0.041 0.159 2372 Planarity : 0.004 0.044 2472 Dihedral : 4.875 28.972 2028 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.19 % Allowed : 18.19 % Favored : 78.62 % 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: 1.28 (0.20), residues: 1836 helix: 1.71 (0.15), residues: 1220 sheet: 1.47 (0.61), residues: 78 loop : -1.31 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 854 HIS 0.010 0.001 HIS B 120 PHE 0.021 0.001 PHE B 970 TYR 0.011 0.001 TYR A 270 ARG 0.006 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 949) hydrogen bonds : angle 4.17772 ( 2787) covalent geometry : bond 0.00371 (14886) covalent geometry : angle 0.63536 (20156) *********************** 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 325 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8893 (t0) cc_final: 0.8441 (t0) REVERT: A 118 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6472 (pt0) REVERT: A 120 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7318 (p-80) REVERT: A 172 ASP cc_start: 0.8245 (t70) cc_final: 0.7516 (t0) REVERT: A 214 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.4590 (ppp) REVERT: A 228 PHE cc_start: 0.8341 (t80) cc_final: 0.8061 (t80) REVERT: A 486 GLU cc_start: 0.8628 (pt0) cc_final: 0.8246 (pt0) REVERT: A 492 ASP cc_start: 0.7708 (t70) cc_final: 0.7066 (t70) REVERT: A 693 GLU cc_start: 0.8614 (tp30) cc_final: 0.8308 (tp30) REVERT: A 755 HIS cc_start: 0.6490 (m-70) cc_final: 0.5899 (m-70) REVERT: A 761 MET cc_start: 0.7170 (tmm) cc_final: 0.6856 (tmm) REVERT: A 829 MET cc_start: 0.8764 (ppp) cc_final: 0.8252 (tmm) REVERT: A 891 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 94 ASN cc_start: 0.8909 (t0) cc_final: 0.8397 (t0) REVERT: B 118 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6517 (pt0) REVERT: B 120 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7474 (p-80) REVERT: B 172 ASP cc_start: 0.8247 (t70) cc_final: 0.7522 (t0) REVERT: B 214 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.4384 (ppp) REVERT: B 317 MET cc_start: 0.9003 (tmm) cc_final: 0.8736 (tmm) REVERT: B 426 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 486 GLU cc_start: 0.8626 (pt0) cc_final: 0.8352 (pt0) REVERT: B 492 ASP cc_start: 0.7635 (t70) cc_final: 0.7254 (t0) REVERT: B 693 GLU cc_start: 0.8567 (tp30) cc_final: 0.8273 (tp30) REVERT: B 755 HIS cc_start: 0.6491 (m-70) cc_final: 0.5939 (m-70) REVERT: B 761 MET cc_start: 0.7175 (tmm) cc_final: 0.6871 (tmm) outliers start: 51 outliers final: 37 residues processed: 305 average time/residue: 0.2508 time to fit residues: 121.5214 Evaluate side-chains 310 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 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 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 802 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 162 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 592 ASN ** 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 570 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 = 0.3839 r_free = 0.3839 target = 0.144176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115515 restraints weight = 23019.056| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.02 r_work: 0.3358 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14886 Z= 0.137 Angle : 0.623 11.905 20156 Z= 0.298 Chirality : 0.040 0.157 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.823 27.485 2028 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.44 % Allowed : 18.00 % Favored : 78.56 % 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: 1.33 (0.20), residues: 1836 helix: 1.75 (0.15), residues: 1220 sheet: 1.43 (0.61), residues: 78 loop : -1.27 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.009 0.001 HIS A 120 PHE 0.017 0.001 PHE B 970 TYR 0.012 0.001 TYR B 270 ARG 0.006 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 949) hydrogen bonds : angle 4.15112 ( 2787) covalent geometry : bond 0.00327 (14886) covalent geometry : angle 0.62349 (20156) *********************** 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 340 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8438 (t0) REVERT: A 118 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6489 (pt0) REVERT: A 120 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7491 (p-80) REVERT: A 172 ASP cc_start: 0.8228 (t70) cc_final: 0.7507 (t0) REVERT: A 214 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.4511 (ppp) REVERT: A 228 PHE cc_start: 0.8356 (t80) cc_final: 0.8151 (t80) REVERT: A 486 GLU cc_start: 0.8612 (pt0) cc_final: 0.8284 (pt0) REVERT: A 492 ASP cc_start: 0.7697 (t70) cc_final: 0.7047 (t70) REVERT: A 559 ILE cc_start: 0.7939 (mt) cc_final: 0.7672 (mp) REVERT: A 597 LYS cc_start: 0.2919 (mptt) cc_final: 0.2386 (tptp) REVERT: A 693 GLU cc_start: 0.8618 (tp30) cc_final: 0.8312 (tp30) REVERT: A 755 HIS cc_start: 0.6380 (m-70) cc_final: 0.5865 (m-70) REVERT: A 761 MET cc_start: 0.7234 (tmm) cc_final: 0.6912 (tmm) REVERT: A 829 MET cc_start: 0.8751 (ppp) cc_final: 0.8210 (tmm) REVERT: A 891 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8777 (t) REVERT: B 94 ASN cc_start: 0.8898 (t0) cc_final: 0.8382 (t0) REVERT: B 118 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6484 (pt0) REVERT: B 120 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7523 (p-80) REVERT: B 172 ASP cc_start: 0.8163 (t70) cc_final: 0.7460 (t0) REVERT: B 214 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.4429 (ppp) REVERT: B 426 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 486 GLU cc_start: 0.8648 (pt0) cc_final: 0.8387 (pt0) REVERT: B 492 ASP cc_start: 0.7631 (t70) cc_final: 0.7250 (t0) REVERT: B 570 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: B 693 GLU cc_start: 0.8565 (tp30) cc_final: 0.8273 (tp30) REVERT: B 755 HIS cc_start: 0.6338 (m-70) cc_final: 0.5844 (m-70) REVERT: B 761 MET cc_start: 0.7217 (tmm) cc_final: 0.6942 (tmm) REVERT: B 815 LEU cc_start: 0.8497 (mm) cc_final: 0.8297 (mm) REVERT: B 829 MET cc_start: 0.8752 (ppp) cc_final: 0.8321 (tmm) REVERT: B 1013 TRP cc_start: 0.7725 (t60) cc_final: 0.7521 (t60) outliers start: 55 outliers final: 42 residues processed: 321 average time/residue: 0.2310 time to fit residues: 117.0804 Evaluate side-chains 324 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 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 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 830 VAL 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 119 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 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 = 0.3852 r_free = 0.3852 target = 0.145376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116762 restraints weight = 23027.375| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.14 r_work: 0.3355 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14886 Z= 0.134 Angle : 0.636 11.788 20156 Z= 0.303 Chirality : 0.040 0.156 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.808 27.266 2028 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.38 % Allowed : 18.50 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.20), residues: 1836 helix: 1.72 (0.15), residues: 1218 sheet: 1.36 (0.60), residues: 78 loop : -1.27 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 854 HIS 0.008 0.001 HIS A 120 PHE 0.015 0.001 PHE B 970 TYR 0.013 0.001 TYR B 812 ARG 0.006 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 949) hydrogen bonds : angle 4.13333 ( 2787) covalent geometry : bond 0.00317 (14886) covalent geometry : angle 0.63611 (20156) *********************** 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 332 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8823 (t0) cc_final: 0.8388 (t0) REVERT: A 118 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6569 (pt0) REVERT: A 120 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7542 (p-80) REVERT: A 172 ASP cc_start: 0.8148 (t70) cc_final: 0.7432 (t0) REVERT: A 214 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.4434 (ppp) REVERT: A 228 PHE cc_start: 0.8174 (t80) cc_final: 0.7925 (t80) REVERT: A 486 GLU cc_start: 0.8600 (pt0) cc_final: 0.8282 (pt0) REVERT: A 492 ASP cc_start: 0.7662 (t70) cc_final: 0.7004 (t70) REVERT: A 559 ILE cc_start: 0.7879 (mt) cc_final: 0.7615 (mp) REVERT: A 570 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: A 693 GLU cc_start: 0.8622 (tp30) cc_final: 0.8322 (tp30) REVERT: A 755 HIS cc_start: 0.6405 (m-70) cc_final: 0.5864 (m-70) REVERT: A 761 MET cc_start: 0.7231 (tmm) cc_final: 0.6944 (tmm) REVERT: A 770 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8074 (mptt) REVERT: B 94 ASN cc_start: 0.8877 (t0) cc_final: 0.8364 (t0) REVERT: B 118 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6429 (pt0) REVERT: B 120 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7583 (p-80) REVERT: B 172 ASP cc_start: 0.8103 (t70) cc_final: 0.7408 (t0) REVERT: B 214 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.4330 (ppp) REVERT: B 426 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7825 (tp) REVERT: B 486 GLU cc_start: 0.8671 (pt0) cc_final: 0.8403 (pt0) REVERT: B 492 ASP cc_start: 0.7594 (t70) cc_final: 0.7207 (t0) REVERT: B 570 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: B 693 GLU cc_start: 0.8560 (tp30) cc_final: 0.8288 (tp30) REVERT: B 755 HIS cc_start: 0.6267 (m-70) cc_final: 0.5813 (m-70) REVERT: B 761 MET cc_start: 0.7226 (tmm) cc_final: 0.6939 (tmm) REVERT: B 770 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8025 (mptt) REVERT: B 1011 MET cc_start: 0.7639 (ttm) cc_final: 0.7126 (tpp) outliers start: 54 outliers final: 42 residues processed: 312 average time/residue: 0.2132 time to fit residues: 104.8783 Evaluate side-chains 324 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 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 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 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 134 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115983 restraints weight = 22995.726| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.10 r_work: 0.3352 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14886 Z= 0.143 Angle : 0.658 11.863 20156 Z= 0.311 Chirality : 0.041 0.181 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.808 27.009 2028 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.44 % Allowed : 18.75 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.15), residues: 1218 sheet: 1.36 (0.60), residues: 78 loop : -1.29 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 854 HIS 0.008 0.001 HIS A 120 PHE 0.013 0.001 PHE B 970 TYR 0.015 0.001 TYR B 812 ARG 0.007 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 949) hydrogen bonds : angle 4.14958 ( 2787) covalent geometry : bond 0.00341 (14886) covalent geometry : angle 0.65775 (20156) ********************** 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 327 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8846 (t0) cc_final: 0.8432 (t0) REVERT: A 118 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: A 120 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7579 (p-80) REVERT: A 172 ASP cc_start: 0.8154 (t70) cc_final: 0.7433 (t0) REVERT: A 214 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.4503 (ppp) REVERT: A 228 PHE cc_start: 0.8200 (t80) cc_final: 0.7951 (t80) REVERT: A 486 GLU cc_start: 0.8597 (pt0) cc_final: 0.8290 (pt0) REVERT: A 492 ASP cc_start: 0.7689 (t70) cc_final: 0.7035 (t70) REVERT: A 559 ILE cc_start: 0.7910 (mt) cc_final: 0.7646 (mp) REVERT: A 693 GLU cc_start: 0.8618 (tp30) cc_final: 0.8341 (tp30) REVERT: A 755 HIS cc_start: 0.6336 (m-70) cc_final: 0.5828 (m-70) REVERT: A 761 MET cc_start: 0.7221 (tmm) cc_final: 0.6911 (tmm) REVERT: A 770 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8124 (mptt) REVERT: A 829 MET cc_start: 0.8737 (ppp) cc_final: 0.8277 (tmm) REVERT: B 94 ASN cc_start: 0.8905 (t0) cc_final: 0.8456 (t0) REVERT: B 118 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6444 (pt0) REVERT: B 120 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7625 (p-80) REVERT: B 172 ASP cc_start: 0.8115 (t70) cc_final: 0.7417 (t0) REVERT: B 214 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.4413 (ppp) REVERT: B 426 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7839 (tp) REVERT: B 486 GLU cc_start: 0.8647 (pt0) cc_final: 0.8227 (pt0) REVERT: B 492 ASP cc_start: 0.7608 (t70) cc_final: 0.7220 (t0) REVERT: B 570 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: B 693 GLU cc_start: 0.8569 (tp30) cc_final: 0.8296 (tp30) REVERT: B 735 MET cc_start: 0.7576 (mtt) cc_final: 0.7323 (mtt) REVERT: B 755 HIS cc_start: 0.6266 (m-70) cc_final: 0.5820 (m-70) REVERT: B 770 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8136 (mmtm) REVERT: B 829 MET cc_start: 0.8753 (ppp) cc_final: 0.8327 (tmm) REVERT: B 1011 MET cc_start: 0.7687 (ttm) cc_final: 0.7187 (tpp) outliers start: 55 outliers final: 42 residues processed: 306 average time/residue: 0.2246 time to fit residues: 108.9846 Evaluate side-chains 321 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 830 VAL 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 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 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 111 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 67 optimal weight: 0.0010 chunk 64 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 overall best weight: 0.2944 ------------------------------------------------------------------------------- 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 570 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.146875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118151 restraints weight = 23190.203| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.17 r_work: 0.3392 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14886 Z= 0.118 Angle : 0.645 12.126 20156 Z= 0.304 Chirality : 0.040 0.220 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.707 26.893 2028 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.31 % Allowed : 19.19 % Favored : 77.50 % 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: 1222 sheet: 1.39 (0.59), residues: 78 loop : -1.28 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 854 HIS 0.007 0.001 HIS A 120 PHE 0.013 0.001 PHE B 970 TYR 0.015 0.001 TYR B 769 ARG 0.007 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 949) hydrogen bonds : angle 4.11509 ( 2787) covalent geometry : bond 0.00270 (14886) covalent geometry : angle 0.64500 (20156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6635.74 seconds wall clock time: 116 minutes 52.13 seconds (7012.13 seconds total)