Starting phenix.real_space_refine on Sat Feb 17 15:16:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/02_2024/7qd6_13909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/02_2024/7qd6_13909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/02_2024/7qd6_13909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/02_2024/7qd6_13909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/02_2024/7qd6_13909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/02_2024/7qd6_13909.pdb" } resolution = 3.0 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= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 214 5.49 5 S 46 5.16 5 C 11474 2.51 5 N 3400 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19112 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "C" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 838 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "F" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 838 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Time building chain proxies: 10.59, per 1000 atoms: 0.55 Number of scatterers: 19112 At special positions: 0 Unit cell: (167.96, 136.04, 152.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 214 15.00 O 3978 8.00 N 3400 7.00 C 11474 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 - 3.50 Amino acid : False - 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: 8.23 Conformation dependent library (CDL) restraints added in 2.6 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 70.2% alpha, 2.1% beta 98 base pairs and 183 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.623A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 45 through 61 removed outlier: 4.168A pdb=" N ARG A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.628A pdb=" N VAL A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.533A pdb=" N GLU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.093A pdb=" N TRP A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 removed outlier: 4.264A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 159 through 185 removed outlier: 3.877A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.553A pdb=" N PHE A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 318 removed outlier: 4.243A pdb=" N GLN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.638A pdb=" N ALA A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.983A pdb=" N ASN A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.614A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.118A pdb=" N TYR A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 511 through 530 removed outlier: 3.596A pdb=" N ILE A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.439A pdb=" N ALA A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 602 through 619 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 645 removed outlier: 3.557A pdb=" N MET A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.590A pdb=" N GLN A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 4.394A pdb=" N TRP A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 671' Processing helix chain 'A' and resid 728 through 738 removed outlier: 3.545A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.537A pdb=" N PHE A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 810 through 824 Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.599A pdb=" N ILE A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.746A pdb=" N ALA A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 891 Processing helix chain 'A' and resid 892 through 897 removed outlier: 3.849A pdb=" N GLU A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 938 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.582A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 Processing helix chain 'D' and resid 45 through 61 removed outlier: 4.152A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.623A pdb=" N VAL D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.538A pdb=" N GLU D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 4.131A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 removed outlier: 4.368A pdb=" N GLN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 159 through 185 removed outlier: 3.862A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.569A pdb=" N GLY D 204 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 261 through 267 Processing helix chain 'D' and resid 269 through 318 removed outlier: 4.223A pdb=" N GLN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 343 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.877A pdb=" N ALA D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 369 Processing helix chain 'D' and resid 377 through 382 removed outlier: 4.008A pdb=" N ASN D 382 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.543A pdb=" N VAL D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.177A pdb=" N TYR D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 472 Processing helix chain 'D' and resid 484 through 489 removed outlier: 3.530A pdb=" N TYR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 530 Processing helix chain 'D' and resid 557 through 570 removed outlier: 4.445A pdb=" N ALA D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 586 Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 602 through 619 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 633 through 645 removed outlier: 3.521A pdb=" N MET D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 664 removed outlier: 3.654A pdb=" N GLN D 664 " --> pdb=" O PHE D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 4.475A pdb=" N TRP D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 671 " --> pdb=" O SER D 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 666 through 671' Processing helix chain 'D' and resid 728 through 738 removed outlier: 3.590A pdb=" N VAL D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 766 removed outlier: 3.989A pdb=" N ALA D 761 " --> pdb=" O ASP D 757 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 762 " --> pdb=" O GLN D 758 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 764 " --> pdb=" O PHE D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 824 removed outlier: 5.179A pdb=" N GLU D 812 " --> pdb=" O LYS D 808 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP D 813 " --> pdb=" O GLU D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 834 removed outlier: 3.587A pdb=" N ILE D 831 " --> pdb=" O SER D 827 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 866 removed outlier: 3.639A pdb=" N ALA D 845 " --> pdb=" O GLN D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 891 Processing helix chain 'D' and resid 902 through 938 Processing helix chain 'D' and resid 945 through 949 Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.333A pdb=" N ILE A 573 " --> pdb=" O ASN A 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 679 through 683 removed outlier: 3.580A pdb=" N THR A 705 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 722 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 750 Processing sheet with id=AA5, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 574 removed outlier: 7.372A pdb=" N ILE D 573 " --> pdb=" O ASN D 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 679 through 683 removed outlier: 3.559A pdb=" N THR D 705 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 722 " --> pdb=" O THR D 705 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 748 through 750 883 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 244 hydrogen bonds 488 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 183 stacking parallelities Total time for adding SS restraints: 11.57 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4221 1.33 - 1.46: 5924 1.46 - 1.58: 9279 1.58 - 1.71: 424 1.71 - 1.83: 90 Bond restraints: 19938 Sorted by residual: bond pdb=" C GLU A 408 " pdb=" N PRO A 409 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.85e+00 bond pdb=" CG LEU D 256 " pdb=" CD1 LEU D 256 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" N HIS D 969 " pdb=" CA HIS D 969 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.42e-02 4.96e+03 2.64e+00 bond pdb=" SD MET A 276 " pdb=" CE MET A 276 " ideal model delta sigma weight residual 1.791 1.751 0.040 2.50e-02 1.60e+03 2.62e+00 bond pdb=" N HIS A 969 " pdb=" CA HIS A 969 " ideal model delta sigma weight residual 1.460 1.483 -0.024 1.54e-02 4.22e+03 2.36e+00 ... (remaining 19933 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.15: 423 103.15 - 110.89: 7783 110.89 - 118.64: 8504 118.64 - 126.38: 10291 126.38 - 134.13: 871 Bond angle restraints: 27872 Sorted by residual: angle pdb=" C LYS D 425 " pdb=" N ARG D 426 " pdb=" CA ARG D 426 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" N GLU D 144 " pdb=" CA GLU D 144 " pdb=" CB GLU D 144 " ideal model delta sigma weight residual 110.28 117.54 -7.26 1.55e+00 4.16e-01 2.20e+01 angle pdb=" C LYS A 425 " pdb=" N ARG A 426 " pdb=" CA ARG A 426 " ideal model delta sigma weight residual 123.91 131.14 -7.23 1.66e+00 3.63e-01 1.89e+01 angle pdb=" C GLU D 23 " pdb=" N TRP D 24 " pdb=" CA TRP D 24 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C GLU A 23 " pdb=" N TRP A 24 " pdb=" CA TRP A 24 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 ... (remaining 27867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8833 17.88 - 35.76: 1430 35.76 - 53.63: 870 53.63 - 71.51: 202 71.51 - 89.39: 41 Dihedral angle restraints: 11376 sinusoidal: 6062 harmonic: 5314 Sorted by residual: dihedral pdb=" CA ARG D 45 " pdb=" C ARG D 45 " pdb=" N GLY D 46 " pdb=" CA GLY D 46 " ideal model delta harmonic sigma weight residual 180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA MET D 645 " pdb=" C MET D 645 " pdb=" N TYR D 646 " pdb=" CA TYR D 646 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ARG A 45 " pdb=" C ARG A 45 " pdb=" N GLY A 46 " pdb=" CA GLY A 46 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 11373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2737 0.072 - 0.145: 325 0.145 - 0.217: 31 0.217 - 0.290: 2 0.290 - 0.362: 1 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB ILE D 452 " pdb=" CA ILE D 452 " pdb=" CG1 ILE D 452 " pdb=" CG2 ILE D 452 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA GLN A 172 " pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CB GLN A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 759 " pdb=" CA VAL A 759 " pdb=" CG1 VAL A 759 " pdb=" CG2 VAL A 759 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3093 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 485 " 0.017 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE A 485 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 485 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 485 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 485 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 485 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 485 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 485 " -0.015 2.00e-02 2.50e+03 2.26e-02 8.97e+00 pdb=" CG PHE D 485 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE D 485 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE D 485 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE D 485 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 485 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 485 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 371 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO A 372 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " 0.038 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4201 2.80 - 3.32: 16701 3.32 - 3.85: 35673 3.85 - 4.37: 40616 4.37 - 4.90: 62985 Nonbonded interactions: 160176 Sorted by model distance: nonbonded pdb=" O MET A 614 " pdb=" OG1 THR A 618 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASP A 734 " pdb=" OG SER A 828 " model vdw 2.296 2.440 nonbonded pdb=" OE2 GLU D 581 " pdb=" OH TYR D 927 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR A 749 " pdb=" NE ARG A 872 " model vdw 2.317 2.520 nonbonded pdb=" OD1 ASP D 734 " pdb=" OG SER D 828 " model vdw 2.322 2.440 ... (remaining 160171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.500 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 60.840 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 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 : 0.005 0.054 19938 Z= 0.288 Angle : 0.887 12.820 27872 Z= 0.481 Chirality : 0.048 0.362 3096 Planarity : 0.007 0.069 2804 Dihedral : 22.481 89.389 7940 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.81 (0.18), residues: 1780 helix: -0.40 (0.13), residues: 1154 sheet: 0.12 (0.99), residues: 36 loop : -0.53 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 64 HIS 0.017 0.002 HIS D 525 PHE 0.060 0.003 PHE A 485 TYR 0.036 0.002 TYR D 141 ARG 0.015 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 872 ARG cc_start: 0.5346 (ttp-170) cc_final: 0.4482 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 1.1309 time to fit residues: 231.8022 Evaluate side-chains 122 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN A 400 HIS ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 131 GLN D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19938 Z= 0.317 Angle : 0.662 9.680 27872 Z= 0.369 Chirality : 0.041 0.186 3096 Planarity : 0.005 0.056 2804 Dihedral : 25.019 95.868 4350 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.87 % Allowed : 9.16 % Favored : 88.97 % 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: 0.27 (0.19), residues: 1780 helix: 0.61 (0.14), residues: 1180 sheet: 0.31 (0.98), residues: 36 loop : -0.57 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 102 HIS 0.010 0.002 HIS D 748 PHE 0.024 0.002 PHE D 592 TYR 0.019 0.002 TYR D 291 ARG 0.012 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.5123 (ptm) cc_final: 0.4546 (ttp) REVERT: A 614 MET cc_start: 0.7569 (ttp) cc_final: 0.7182 (ttp) REVERT: A 760 PHE cc_start: 0.4275 (OUTLIER) cc_final: 0.3158 (t80) REVERT: A 859 PHE cc_start: 0.5074 (t80) cc_final: 0.4803 (t80) REVERT: D 230 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6657 (mt) REVERT: D 614 MET cc_start: 0.7681 (ttp) cc_final: 0.7413 (ttp) REVERT: D 647 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: D 872 ARG cc_start: 0.5537 (ttp-170) cc_final: 0.4585 (ttt-90) outliers start: 29 outliers final: 13 residues processed: 151 average time/residue: 1.2977 time to fit residues: 222.9722 Evaluate side-chains 136 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 647 ASP Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 928 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 181 optimal weight: 0.8980 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 183 HIS A 400 HIS A 481 HIS ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19938 Z= 0.190 Angle : 0.558 8.173 27872 Z= 0.317 Chirality : 0.037 0.139 3096 Planarity : 0.004 0.048 2804 Dihedral : 24.884 99.014 4350 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.61 % Allowed : 12.39 % Favored : 86.00 % 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: 1.02 (0.20), residues: 1780 helix: 1.27 (0.15), residues: 1186 sheet: 0.36 (0.92), residues: 36 loop : -0.48 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 102 HIS 0.010 0.001 HIS D 104 PHE 0.020 0.002 PHE D 128 TYR 0.032 0.001 TYR D 141 ARG 0.004 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5109 (ptm) cc_final: 0.4480 (ttp) REVERT: A 760 PHE cc_start: 0.4118 (OUTLIER) cc_final: 0.3154 (t80) REVERT: D 354 MET cc_start: 0.4180 (ppp) cc_final: 0.3243 (ptt) REVERT: D 388 VAL cc_start: 0.7569 (OUTLIER) cc_final: 0.7202 (m) REVERT: D 872 ARG cc_start: 0.5378 (ttp-170) cc_final: 0.4572 (mtp85) outliers start: 25 outliers final: 9 residues processed: 152 average time/residue: 1.1305 time to fit residues: 197.6790 Evaluate side-chains 131 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 131 GLN A 203 ASN A 400 HIS A 481 HIS ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19938 Z= 0.219 Angle : 0.570 10.816 27872 Z= 0.321 Chirality : 0.038 0.218 3096 Planarity : 0.004 0.046 2804 Dihedral : 24.822 104.267 4350 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.39 % Allowed : 14.19 % Favored : 83.42 % 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: 1.26 (0.20), residues: 1780 helix: 1.48 (0.15), residues: 1186 sheet: 0.49 (0.91), residues: 36 loop : -0.45 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 102 HIS 0.009 0.001 HIS A 748 PHE 0.028 0.002 PHE A 128 TYR 0.023 0.002 TYR A 79 ARG 0.007 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5082 (ptm) cc_final: 0.4488 (ttp) REVERT: A 760 PHE cc_start: 0.4158 (OUTLIER) cc_final: 0.3174 (t80) REVERT: D 297 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (t70) REVERT: D 635 ARG cc_start: 0.6767 (tpt90) cc_final: 0.6268 (tmt170) REVERT: D 647 ASP cc_start: 0.6765 (m-30) cc_final: 0.6483 (m-30) REVERT: D 872 ARG cc_start: 0.5262 (ttp-170) cc_final: 0.4483 (mtp85) outliers start: 37 outliers final: 16 residues processed: 162 average time/residue: 1.2010 time to fit residues: 222.4449 Evaluate side-chains 147 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.5980 chunk 109 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19938 Z= 0.228 Angle : 0.572 7.678 27872 Z= 0.323 Chirality : 0.038 0.186 3096 Planarity : 0.004 0.045 2804 Dihedral : 24.815 108.661 4350 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.74 % 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: 1.35 (0.20), residues: 1780 helix: 1.53 (0.15), residues: 1186 sheet: 0.58 (0.91), residues: 36 loop : -0.38 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 102 HIS 0.012 0.001 HIS D 748 PHE 0.014 0.002 PHE D 592 TYR 0.032 0.002 TYR A 141 ARG 0.005 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5059 (ptm) cc_final: 0.4477 (ttp) REVERT: A 359 MET cc_start: 0.4602 (tpt) cc_final: 0.4378 (tpp) REVERT: A 635 ARG cc_start: 0.6708 (tpt90) cc_final: 0.6401 (tpt170) REVERT: D 354 MET cc_start: 0.3526 (ppp) cc_final: 0.2657 (ptt) REVERT: D 647 ASP cc_start: 0.6828 (m-30) cc_final: 0.6522 (m-30) REVERT: D 872 ARG cc_start: 0.5255 (ttp-170) cc_final: 0.4498 (mtp85) outliers start: 41 outliers final: 19 residues processed: 162 average time/residue: 1.1885 time to fit residues: 221.0703 Evaluate side-chains 148 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19938 Z= 0.223 Angle : 0.576 9.505 27872 Z= 0.324 Chirality : 0.038 0.177 3096 Planarity : 0.004 0.044 2804 Dihedral : 24.818 112.286 4350 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.65 % Allowed : 16.97 % Favored : 80.39 % 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: 1.42 (0.20), residues: 1780 helix: 1.61 (0.15), residues: 1186 sheet: 0.41 (0.85), residues: 36 loop : -0.39 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 102 HIS 0.013 0.001 HIS D 748 PHE 0.029 0.002 PHE A 128 TYR 0.028 0.002 TYR A 79 ARG 0.007 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 138 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4989 (ptm) cc_final: 0.4472 (ttp) REVERT: D 297 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7369 (t70) REVERT: D 635 ARG cc_start: 0.6652 (tpt90) cc_final: 0.6441 (tpt90) REVERT: D 647 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: D 872 ARG cc_start: 0.5249 (ttp-170) cc_final: 0.4510 (mtp85) outliers start: 41 outliers final: 19 residues processed: 161 average time/residue: 1.2426 time to fit residues: 227.5220 Evaluate side-chains 147 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 647 ASP Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 110 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 162 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 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 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19938 Z= 0.195 Angle : 0.576 12.784 27872 Z= 0.320 Chirality : 0.037 0.154 3096 Planarity : 0.004 0.043 2804 Dihedral : 24.808 117.347 4350 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 18.19 % Favored : 79.35 % 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: 1.67 (0.20), residues: 1780 helix: 1.82 (0.15), residues: 1166 sheet: 0.54 (0.85), residues: 36 loop : -0.27 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 102 HIS 0.015 0.001 HIS A 748 PHE 0.012 0.002 PHE A 892 TYR 0.034 0.001 TYR A 141 ARG 0.003 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.735 Fit side-chains REVERT: A 153 MET cc_start: 0.4984 (ptm) cc_final: 0.4494 (ttp) REVERT: D 297 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7315 (t70) REVERT: D 354 MET cc_start: 0.3880 (ppp) cc_final: 0.2898 (ptp) REVERT: D 647 ASP cc_start: 0.6703 (m-30) cc_final: 0.6374 (m-30) REVERT: D 872 ARG cc_start: 0.5324 (ttp-170) cc_final: 0.4622 (mtp85) outliers start: 38 outliers final: 18 residues processed: 161 average time/residue: 1.1511 time to fit residues: 211.9922 Evaluate side-chains 147 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.0070 chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19938 Z= 0.183 Angle : 0.555 11.153 27872 Z= 0.313 Chirality : 0.037 0.152 3096 Planarity : 0.004 0.041 2804 Dihedral : 24.787 122.820 4350 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.26 % Allowed : 18.90 % Favored : 78.84 % 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: 1.69 (0.20), residues: 1780 helix: 1.84 (0.15), residues: 1176 sheet: 0.56 (0.85), residues: 36 loop : -0.30 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 102 HIS 0.016 0.001 HIS A 748 PHE 0.021 0.002 PHE A 128 TYR 0.032 0.002 TYR A 79 ARG 0.003 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 2.373 Fit side-chains REVERT: A 153 MET cc_start: 0.4986 (ptm) cc_final: 0.4515 (ttp) REVERT: D 354 MET cc_start: 0.3654 (ppp) cc_final: 0.3005 (ptp) REVERT: D 647 ASP cc_start: 0.6709 (m-30) cc_final: 0.6405 (m-30) REVERT: D 872 ARG cc_start: 0.5256 (ttp-170) cc_final: 0.4644 (mtp85) outliers start: 35 outliers final: 21 residues processed: 149 average time/residue: 1.2531 time to fit residues: 213.0319 Evaluate side-chains 140 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 108 optimal weight: 0.0770 chunk 78 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 48 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19938 Z= 0.215 Angle : 0.593 12.552 27872 Z= 0.327 Chirality : 0.038 0.156 3096 Planarity : 0.004 0.044 2804 Dihedral : 24.775 125.136 4350 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.32 % Allowed : 19.23 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.20), residues: 1780 helix: 1.79 (0.15), residues: 1178 sheet: 0.38 (0.82), residues: 36 loop : -0.28 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 102 HIS 0.018 0.001 HIS A 748 PHE 0.015 0.001 PHE A 760 TYR 0.036 0.002 TYR A 141 ARG 0.006 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.800 Fit side-chains REVERT: A 153 MET cc_start: 0.4978 (ptm) cc_final: 0.4516 (ttp) REVERT: D 354 MET cc_start: 0.3703 (ppp) cc_final: 0.2845 (ptp) REVERT: D 647 ASP cc_start: 0.6731 (m-30) cc_final: 0.6416 (m-30) REVERT: D 663 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.4488 (pp20) REVERT: D 872 ARG cc_start: 0.5394 (ttp-170) cc_final: 0.4814 (mtp85) outliers start: 36 outliers final: 21 residues processed: 150 average time/residue: 1.2338 time to fit residues: 213.6813 Evaluate side-chains 146 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19938 Z= 0.184 Angle : 0.568 11.430 27872 Z= 0.319 Chirality : 0.037 0.185 3096 Planarity : 0.004 0.041 2804 Dihedral : 24.755 129.238 4350 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.55 % Allowed : 20.13 % Favored : 78.32 % 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: 1.71 (0.20), residues: 1780 helix: 1.83 (0.15), residues: 1176 sheet: 0.45 (0.83), residues: 36 loop : -0.24 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 102 HIS 0.018 0.001 HIS A 748 PHE 0.026 0.002 PHE A 128 TYR 0.025 0.001 TYR A 79 ARG 0.003 0.000 ARG D 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.911 Fit side-chains REVERT: A 153 MET cc_start: 0.4956 (ptm) cc_final: 0.4539 (ttp) REVERT: D 297 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7288 (t70) REVERT: D 354 MET cc_start: 0.3679 (ppp) cc_final: 0.2908 (ptp) REVERT: D 647 ASP cc_start: 0.6706 (m-30) cc_final: 0.6399 (m-30) REVERT: D 872 ARG cc_start: 0.5375 (ttp-170) cc_final: 0.4788 (mtp85) outliers start: 24 outliers final: 18 residues processed: 138 average time/residue: 1.2256 time to fit residues: 193.0267 Evaluate side-chains 137 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 163 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 HIS ** 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 = 0.5398 r_free = 0.5398 target = 0.260418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.246858 restraints weight = 20650.295| |-----------------------------------------------------------------------------| r_work (start): 0.5312 rms_B_bonded: 0.34 r_work: 0.5204 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.5185 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.5185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19938 Z= 0.159 Angle : 0.567 13.055 27872 Z= 0.313 Chirality : 0.036 0.174 3096 Planarity : 0.003 0.040 2804 Dihedral : 24.717 133.209 4350 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.23 % Allowed : 20.26 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.20), residues: 1780 helix: 2.10 (0.15), residues: 1154 sheet: 0.48 (0.84), residues: 36 loop : 0.07 (0.28), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 102 HIS 0.018 0.001 HIS A 748 PHE 0.012 0.001 PHE A 760 TYR 0.037 0.001 TYR A 141 ARG 0.003 0.000 ARG D 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5145.25 seconds wall clock time: 93 minutes 15.15 seconds (5595.15 seconds total)