Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 15 20:25:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/08_2023/7qd6_13909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/08_2023/7qd6_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_13909/08_2023/7qd6_13909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/08_2023/7qd6_13909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/08_2023/7qd6_13909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd6_13909/08_2023/7qd6_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-1.21rc1-5044/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: 9.96, per 1000 atoms: 0.52 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: 8.67 Conformation dependent library (CDL) restraints added in 2.1 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: 7.36 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: 9.76 Time building geometry restraints manager: 9.14 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: 8771 17.88 - 35.76: 1318 35.76 - 53.63: 834 53.63 - 71.51: 196 71.51 - 89.39: 41 Dihedral angle restraints: 11160 sinusoidal: 5846 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 11157 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: 3.270 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: 17.890 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 58.520 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.120 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.020 ------------------------------------------------------------------------------- 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 : 22.281 89.389 7724 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 % 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 *********************** 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 : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 1.2075 time to fit residues: 247.6202 Evaluate side-chains 122 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.944 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5441 ------------------------------------------------------------------------------- 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: 9.9990 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 131 GLN A 400 HIS A 481 HIS ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 131 GLN D 311 GLN D 525 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 19938 Z= 0.320 Angle : 0.667 8.760 27872 Z= 0.371 Chirality : 0.041 0.186 3096 Planarity : 0.005 0.056 2804 Dihedral : 25.024 95.874 4134 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.19), residues: 1780 helix: 0.61 (0.14), residues: 1182 sheet: 0.23 (0.96), residues: 36 loop : -0.64 (0.26), residues: 562 *********************** 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 169 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 154 average time/residue: 1.2188 time to fit residues: 214.9211 Evaluate side-chains 135 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.7380 time to fit residues: 7.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 145 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 127 GLN A 183 HIS 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19938 Z= 0.195 Angle : 0.563 8.404 27872 Z= 0.319 Chirality : 0.037 0.139 3096 Planarity : 0.004 0.047 2804 Dihedral : 24.956 96.778 4134 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.00 % 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: 0.99 (0.20), residues: 1780 helix: 1.24 (0.15), residues: 1188 sheet: 0.32 (0.93), residues: 36 loop : -0.49 (0.27), residues: 556 *********************** 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 168 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 158 average time/residue: 1.2591 time to fit residues: 227.6370 Evaluate side-chains 137 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.9327 time to fit residues: 9.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 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: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS ** 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 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19938 Z= 0.254 Angle : 0.596 8.389 27872 Z= 0.334 Chirality : 0.039 0.229 3096 Planarity : 0.005 0.061 2804 Dihedral : 24.942 99.926 4134 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 2.13 % 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: 1.07 (0.20), residues: 1780 helix: 1.33 (0.15), residues: 1184 sheet: 0.27 (0.93), residues: 36 loop : -0.49 (0.27), residues: 560 *********************** 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 167 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 156 average time/residue: 1.1884 time to fit residues: 212.8418 Evaluate side-chains 144 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.8724 time to fit residues: 8.7322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 143 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 127 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN D 48 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 203 ASN D 311 GLN ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS D 914 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 19938 Z= 0.342 Angle : 0.668 10.276 27872 Z= 0.370 Chirality : 0.042 0.242 3096 Planarity : 0.005 0.048 2804 Dihedral : 25.045 102.356 4134 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 3.03 % 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: 0.67 (0.20), residues: 1780 helix: 1.02 (0.15), residues: 1184 sheet: -0.50 (0.86), residues: 36 loop : -0.60 (0.27), residues: 560 *********************** 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 183 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 1.795 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 17 residues processed: 168 average time/residue: 1.1700 time to fit residues: 226.4250 Evaluate side-chains 144 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 0.7040 time to fit residues: 5.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.0020 chunk 101 optimal weight: 0.4980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 104 HIS ** 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** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19938 Z= 0.175 Angle : 0.565 9.541 27872 Z= 0.316 Chirality : 0.037 0.168 3096 Planarity : 0.004 0.043 2804 Dihedral : 25.022 105.721 4134 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.26 % 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: 1.58 (0.15), residues: 1184 sheet: -0.29 (0.87), residues: 36 loop : -0.45 (0.27), residues: 560 *********************** 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 172 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 1.857 Fit side-chains outliers start: 35 outliers final: 18 residues processed: 163 average time/residue: 1.2069 time to fit residues: 226.1871 Evaluate side-chains 145 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 1.2868 time to fit residues: 6.8370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 110 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS D 810 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 19938 Z= 0.229 Angle : 0.586 10.587 27872 Z= 0.329 Chirality : 0.038 0.171 3096 Planarity : 0.004 0.044 2804 Dihedral : 24.995 107.698 4134 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1780 helix: 1.56 (0.15), residues: 1174 sheet: -0.19 (0.87), residues: 36 loop : -0.44 (0.27), residues: 570 *********************** 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: 41 poor density : 131 time to evaluate : 1.832 Fit side-chains outliers start: 41 outliers final: 23 residues processed: 159 average time/residue: 1.2358 time to fit residues: 225.1026 Evaluate side-chains 148 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 7 average time/residue: 0.8494 time to fit residues: 9.6191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 496 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 311 GLN ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS D 810 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 19938 Z= 0.281 Angle : 0.636 10.185 27872 Z= 0.350 Chirality : 0.039 0.180 3096 Planarity : 0.004 0.044 2804 Dihedral : 25.012 109.164 4134 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 2.58 % 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: 1.10 (0.20), residues: 1780 helix: 1.38 (0.15), residues: 1186 sheet: -0.27 (0.85), residues: 36 loop : -0.51 (0.27), residues: 558 *********************** 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 168 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.936 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 158 average time/residue: 1.1820 time to fit residues: 216.7651 Evaluate side-chains 149 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 6 average time/residue: 0.8771 time to fit residues: 8.6214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19938 Z= 0.228 Angle : 0.595 10.975 27872 Z= 0.333 Chirality : 0.038 0.173 3096 Planarity : 0.004 0.043 2804 Dihedral : 25.026 112.273 4134 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 2.19 % 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: 1.26 (0.20), residues: 1780 helix: 1.51 (0.15), residues: 1178 sheet: -0.35 (0.84), residues: 36 loop : -0.43 (0.27), residues: 566 *********************** 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 166 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.841 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 160 average time/residue: 1.2034 time to fit residues: 221.5647 Evaluate side-chains 149 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 1.2283 time to fit residues: 6.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 169 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19938 Z= 0.186 Angle : 0.595 10.896 27872 Z= 0.328 Chirality : 0.037 0.170 3096 Planarity : 0.004 0.043 2804 Dihedral : 24.994 115.965 4134 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.81 % 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: 1.52 (0.20), residues: 1780 helix: 1.71 (0.15), residues: 1178 sheet: -0.15 (0.87), residues: 36 loop : -0.35 (0.27), residues: 566 ********************** 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 164 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.835 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 161 average time/residue: 1.1742 time to fit residues: 218.1041 Evaluate side-chains 154 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 1 average time/residue: 0.3141 time to fit residues: 2.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 764 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5361 r_free = 0.5361 target = 0.257049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5301 r_free = 0.5301 target = 0.248330 restraints weight = 20527.828| |-----------------------------------------------------------------------------| r_work (start): 0.5304 rms_B_bonded: 0.22 r_work: 0.5105 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.5054 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.5025 rms_B_bonded: 1.68 restraints_weight: 0.1250 r_work (final): 0.5025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19938 Z= 0.196 Angle : 0.586 11.914 27872 Z= 0.327 Chirality : 0.037 0.165 3096 Planarity : 0.004 0.043 2804 Dihedral : 24.967 118.247 4134 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.74 % 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: 1.55 (0.20), residues: 1780 helix: 1.73 (0.15), residues: 1176 sheet: -0.09 (0.88), residues: 36 loop : -0.31 (0.27), residues: 568 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.02 seconds wall clock time: 94 minutes 17.92 seconds (5657.92 seconds total)