Starting phenix.real_space_refine on Thu Jul 31 07:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vef_21156/07_2025/6vef_21156.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vef_21156/07_2025/6vef_21156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vef_21156/07_2025/6vef_21156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vef_21156/07_2025/6vef_21156.map" model { file = "/net/cci-nas-00/data/ceres_data/6vef_21156/07_2025/6vef_21156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vef_21156/07_2025/6vef_21156.cif" } resolution = 4.08 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= 0.004 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 2 5.49 5 S 66 5.16 5 C 8434 2.51 5 N 2400 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6675 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 39, 'TRANS': 804} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6675 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 39, 'TRANS': 804} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'AMP%rna2p': 1, 'OAA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'AMP%rna2p': 1, 'OAA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 8.92, per 1000 atoms: 0.66 Number of scatterers: 13414 At special positions: 0 Unit cell: (116.641, 106.117, 127.165, 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 66 16.00 P 2 15.00 O 2512 8.00 N 2400 7.00 C 8434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 40.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.807A pdb=" N GLN A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.518A pdb=" N GLN A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.633A pdb=" N GLU A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.823A pdb=" N VAL A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.846A pdb=" N VAL A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.766A pdb=" N GLU A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 426 through 445 removed outlier: 3.698A pdb=" N VAL A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.550A pdb=" N GLY A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 592 through 608 removed outlier: 3.599A pdb=" N ALA A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 673 Processing helix chain 'A' and resid 687 through 692 removed outlier: 4.318A pdb=" N GLY A 692 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 753 through 766 Processing helix chain 'A' and resid 779 through 784 removed outlier: 3.605A pdb=" N ARG A 783 " --> pdb=" O SER A 780 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 852 through 859 removed outlier: 3.586A pdb=" N MET A 856 " --> pdb=" O PRO A 852 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 893 removed outlier: 5.009A pdb=" N ARG A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 930 Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.807A pdb=" N GLN B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 162 removed outlier: 3.518A pdb=" N GLN B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.570A pdb=" N GLU B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 221 Processing helix chain 'B' and resid 234 through 249 Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.823A pdb=" N VAL B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 325 through 340 removed outlier: 3.845A pdb=" N VAL B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.767A pdb=" N GLU B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 426 through 445 removed outlier: 3.698A pdb=" N VAL B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 498 through 516 removed outlier: 3.551A pdb=" N GLY B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 563 Processing helix chain 'B' and resid 571 through 586 Processing helix chain 'B' and resid 592 through 608 removed outlier: 3.599A pdb=" N ALA B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 607 " --> pdb=" O THR B 603 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 673 Processing helix chain 'B' and resid 687 through 692 removed outlier: 4.318A pdb=" N GLY B 692 " --> pdb=" O PHE B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 700 Processing helix chain 'B' and resid 703 through 708 Processing helix chain 'B' and resid 734 through 738 Processing helix chain 'B' and resid 753 through 766 Processing helix chain 'B' and resid 779 through 784 removed outlier: 3.605A pdb=" N ARG B 783 " --> pdb=" O SER B 780 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS B 784 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 823 through 833 Processing helix chain 'B' and resid 852 through 859 removed outlier: 3.587A pdb=" N MET B 856 " --> pdb=" O PRO B 852 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 893 removed outlier: 5.009A pdb=" N ARG B 890 " --> pdb=" O GLN B 886 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 930 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 3.621A pdb=" N PHE A 420 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N VAL A 384 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE A 386 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A 353 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 388 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A 355 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU A 253 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 352 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 255 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE A 354 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 257 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 254 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 315 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 611 through 613 removed outlier: 6.407A pdb=" N ARG A 612 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLU A 683 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN A 747 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET A 776 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N CYS A 749 " --> pdb=" O MET A 776 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 631 Processing sheet with id=AA4, first strand: chain 'A' and resid 840 through 843 removed outlier: 6.540A pdb=" N ARG A 816 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 843 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 818 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 817 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.621A pdb=" N PHE B 420 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N VAL B 384 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE B 386 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR B 353 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 388 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS B 355 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU B 253 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE B 352 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL B 255 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE B 354 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY B 257 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 254 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 315 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 611 through 613 removed outlier: 6.406A pdb=" N ARG B 612 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLU B 683 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLN B 747 " --> pdb=" O VAL B 774 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET B 776 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 749 " --> pdb=" O MET B 776 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 630 through 631 Processing sheet with id=AA8, first strand: chain 'B' and resid 840 through 843 removed outlier: 6.541A pdb=" N ARG B 816 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 843 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL B 818 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 817 " --> pdb=" O ASP B 868 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4485 1.34 - 1.46: 2920 1.46 - 1.58: 6201 1.58 - 1.70: 2 1.70 - 1.82: 114 Bond restraints: 13722 Sorted by residual: bond pdb=" C3 OAA A1002 " pdb=" O3 OAA A1002 " ideal model delta sigma weight residual 1.214 1.305 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C3 OAA B1001 " pdb=" O3 OAA B1001 " ideal model delta sigma weight residual 1.214 1.304 -0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C4 OAA B1001 " pdb=" O4 OAA B1001 " ideal model delta sigma weight residual 1.241 1.305 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C4 OAA A1002 " pdb=" O4 OAA A1002 " ideal model delta sigma weight residual 1.241 1.305 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA TRP B 871 " pdb=" CB TRP B 871 " ideal model delta sigma weight residual 1.527 1.451 0.076 2.48e-02 1.63e+03 9.47e+00 ... (remaining 13717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 17394 2.19 - 4.39: 972 4.39 - 6.58: 145 6.58 - 8.78: 49 8.78 - 10.97: 18 Bond angle restraints: 18578 Sorted by residual: angle pdb=" CA SER B 373 " pdb=" C SER B 373 " pdb=" N LYS B 374 " ideal model delta sigma weight residual 116.84 125.79 -8.95 1.71e+00 3.42e-01 2.74e+01 angle pdb=" CA SER A 373 " pdb=" C SER A 373 " pdb=" N LYS A 374 " ideal model delta sigma weight residual 116.84 125.78 -8.94 1.71e+00 3.42e-01 2.74e+01 angle pdb=" C GLY A 393 " pdb=" N PHE A 394 " pdb=" CA PHE A 394 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" N GLY B 142 " pdb=" CA GLY B 142 " pdb=" C GLY B 142 " ideal model delta sigma weight residual 113.18 102.21 10.97 2.37e+00 1.78e-01 2.14e+01 angle pdb=" CA TYR A 883 " pdb=" CB TYR A 883 " pdb=" CG TYR A 883 " ideal model delta sigma weight residual 113.90 105.78 8.12 1.80e+00 3.09e-01 2.03e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.90: 8015 25.90 - 51.79: 195 51.79 - 77.69: 12 77.69 - 103.58: 0 103.58 - 129.48: 2 Dihedral angle restraints: 8224 sinusoidal: 3362 harmonic: 4862 Sorted by residual: dihedral pdb=" CA GLU A 728 " pdb=" C GLU A 728 " pdb=" N HIS A 729 " pdb=" CA HIS A 729 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU B 728 " pdb=" C GLU B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA TYR A 883 " pdb=" C TYR A 883 " pdb=" N CYS A 884 " pdb=" CA CYS A 884 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1523 0.075 - 0.150: 412 0.150 - 0.225: 48 0.225 - 0.300: 5 0.300 - 0.375: 2 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE B 609 " pdb=" CA ILE B 609 " pdb=" CG1 ILE B 609 " pdb=" CG2 ILE B 609 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASN A 140 " pdb=" N ASN A 140 " pdb=" C ASN A 140 " pdb=" CB ASN A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1987 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 829 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LEU A 829 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 829 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 830 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 829 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C LEU B 829 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 829 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 830 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 398 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 399 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " 0.037 5.00e-02 4.00e+02 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 107 2.47 - 3.08: 8841 3.08 - 3.69: 21726 3.69 - 4.29: 30522 4.29 - 4.90: 49232 Nonbonded interactions: 110428 Sorted by model distance: nonbonded pdb=" OE1 GLU B 368 " pdb=" OG SER B 660 " model vdw 1.866 3.040 nonbonded pdb=" O LEU B 740 " pdb=" OH TYR B 849 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A 740 " pdb=" OH TYR A 849 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 164 " pdb=" OE1 GLU B 189 " model vdw 2.256 3.040 nonbonded pdb=" OG SER B 909 " pdb=" O ALA B 911 " model vdw 2.264 3.040 ... (remaining 110423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and resid 84 through 933) selection = (chain 'B' and resid 84 through 933) } 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 group one per residue 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.330 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.009 0.091 13722 Z= 0.427 Angle : 1.197 10.973 18578 Z= 0.642 Chirality : 0.066 0.375 1990 Planarity : 0.008 0.066 2454 Dihedral : 11.750 129.480 5100 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -4.48 (0.16), residues: 1684 helix: -2.88 (0.15), residues: 654 sheet: -2.70 (0.32), residues: 190 loop : -3.12 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 708 HIS 0.017 0.003 HIS B 460 PHE 0.041 0.004 PHE B 203 TYR 0.022 0.004 TYR A 849 ARG 0.010 0.001 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.18523 ( 486) hydrogen bonds : angle 7.68701 ( 1398) covalent geometry : bond 0.00937 (13722) covalent geometry : angle 1.19714 (18578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.501 Fit side-chains REVERT: A 173 MET cc_start: 0.7556 (tpp) cc_final: 0.6183 (tpp) REVERT: A 624 PHE cc_start: 0.7877 (t80) cc_final: 0.7635 (t80) REVERT: A 659 LEU cc_start: 0.8176 (tt) cc_final: 0.7969 (tp) REVERT: A 776 MET cc_start: 0.8625 (mmp) cc_final: 0.8178 (mmm) REVERT: B 101 PHE cc_start: 0.7334 (m-80) cc_final: 0.6576 (m-80) REVERT: B 173 MET cc_start: 0.7558 (tpp) cc_final: 0.6344 (tpp) REVERT: B 624 PHE cc_start: 0.7858 (t80) cc_final: 0.7647 (t80) REVERT: B 776 MET cc_start: 0.8601 (mmp) cc_final: 0.8153 (mmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2499 time to fit residues: 92.5915 Evaluate side-chains 141 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 185 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 313 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 694 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 89 GLN B 185 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 313 HIS ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 HIS B 694 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100249 restraints weight = 27706.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102771 restraints weight = 16740.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104420 restraints weight = 11779.941| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13722 Z= 0.186 Angle : 0.742 7.312 18578 Z= 0.378 Chirality : 0.048 0.202 1990 Planarity : 0.006 0.055 2454 Dihedral : 7.572 116.571 1864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -3.27 (0.18), residues: 1684 helix: -1.34 (0.18), residues: 672 sheet: -2.67 (0.32), residues: 204 loop : -2.76 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 871 HIS 0.005 0.001 HIS B 888 PHE 0.014 0.002 PHE B 279 TYR 0.017 0.002 TYR A 669 ARG 0.004 0.001 ARG B 510 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 486) hydrogen bonds : angle 5.52708 ( 1398) covalent geometry : bond 0.00411 (13722) covalent geometry : angle 0.74197 (18578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7599 (tpp) cc_final: 0.7328 (tpp) REVERT: A 211 GLU cc_start: 0.6816 (pp20) cc_final: 0.6573 (pp20) REVERT: A 503 THR cc_start: 0.9042 (p) cc_final: 0.8753 (t) REVERT: A 509 TYR cc_start: 0.8312 (t80) cc_final: 0.8035 (t80) REVERT: A 576 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8347 (mttp) REVERT: A 584 MET cc_start: 0.7523 (mtp) cc_final: 0.7217 (mtp) REVERT: A 659 LEU cc_start: 0.7703 (tt) cc_final: 0.7382 (mp) REVERT: B 101 PHE cc_start: 0.7138 (m-80) cc_final: 0.6442 (m-80) REVERT: B 173 MET cc_start: 0.8108 (tpp) cc_final: 0.6536 (tpp) REVERT: B 503 THR cc_start: 0.9051 (p) cc_final: 0.8760 (t) REVERT: B 509 TYR cc_start: 0.8323 (t80) cc_final: 0.8009 (t80) REVERT: B 576 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8331 (mttp) REVERT: B 584 MET cc_start: 0.7495 (mtp) cc_final: 0.7179 (mtp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2400 time to fit residues: 78.3786 Evaluate side-chains 156 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 39 optimal weight: 0.0470 chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 739 GLN A 879 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN B 627 HIS B 739 GLN B 879 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100497 restraints weight = 28188.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102615 restraints weight = 18006.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104092 restraints weight = 13223.103| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13722 Z= 0.184 Angle : 0.722 7.132 18578 Z= 0.361 Chirality : 0.048 0.155 1990 Planarity : 0.005 0.045 2454 Dihedral : 7.138 114.485 1864 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.14 % Allowed : 2.82 % Favored : 97.04 % 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: -2.76 (0.19), residues: 1684 helix: -0.74 (0.20), residues: 672 sheet: -2.57 (0.32), residues: 204 loop : -2.61 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 871 HIS 0.004 0.001 HIS B 322 PHE 0.032 0.002 PHE A 624 TYR 0.015 0.002 TYR A 509 ARG 0.005 0.001 ARG B 385 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 486) hydrogen bonds : angle 5.40053 ( 1398) covalent geometry : bond 0.00413 (13722) covalent geometry : angle 0.72182 (18578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 1.649 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7885 (tpp) cc_final: 0.6655 (tpp) REVERT: A 408 MET cc_start: 0.4704 (mmp) cc_final: 0.4210 (mmp) REVERT: A 503 THR cc_start: 0.8983 (p) cc_final: 0.8673 (t) REVERT: A 624 PHE cc_start: 0.8023 (t80) cc_final: 0.7790 (t80) REVERT: B 173 MET cc_start: 0.8080 (tpp) cc_final: 0.6471 (tpp) REVERT: B 211 GLU cc_start: 0.6967 (pp20) cc_final: 0.6763 (pp20) REVERT: B 408 MET cc_start: 0.4711 (mmp) cc_final: 0.4378 (mmp) REVERT: B 503 THR cc_start: 0.9014 (p) cc_final: 0.8713 (t) REVERT: B 875 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7864 (mt-10) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.2303 time to fit residues: 75.1806 Evaluate side-chains 164 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 0.0570 chunk 126 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 0.0980 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106420 restraints weight = 27527.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108895 restraints weight = 16857.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110619 restraints weight = 11953.550| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13722 Z= 0.114 Angle : 0.651 7.540 18578 Z= 0.322 Chirality : 0.045 0.136 1990 Planarity : 0.004 0.041 2454 Dihedral : 6.620 112.866 1864 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -2.39 (0.20), residues: 1684 helix: -0.47 (0.20), residues: 672 sheet: -2.28 (0.32), residues: 202 loop : -2.38 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 871 HIS 0.002 0.000 HIS A 918 PHE 0.021 0.002 PHE A 624 TYR 0.014 0.002 TYR A 849 ARG 0.003 0.000 ARG B 385 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 486) hydrogen bonds : angle 5.01881 ( 1398) covalent geometry : bond 0.00249 (13722) covalent geometry : angle 0.65090 (18578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.535 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7737 (tpp) cc_final: 0.6427 (tpp) REVERT: A 238 MET cc_start: 0.8120 (ttp) cc_final: 0.7911 (ttt) REVERT: A 271 LEU cc_start: 0.8498 (mp) cc_final: 0.7751 (tt) REVERT: A 408 MET cc_start: 0.4476 (mmp) cc_final: 0.3958 (mmp) REVERT: A 503 THR cc_start: 0.8958 (p) cc_final: 0.8635 (t) REVERT: A 624 PHE cc_start: 0.8003 (t80) cc_final: 0.7784 (t80) REVERT: A 776 MET cc_start: 0.8373 (mmp) cc_final: 0.8112 (mmm) REVERT: A 871 TRP cc_start: 0.8880 (t60) cc_final: 0.8476 (t60) REVERT: A 875 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 189 GLU cc_start: 0.3884 (tm-30) cc_final: 0.3547 (tm-30) REVERT: B 408 MET cc_start: 0.4458 (mmp) cc_final: 0.3998 (mmp) REVERT: B 503 THR cc_start: 0.9001 (p) cc_final: 0.8689 (t) REVERT: B 776 MET cc_start: 0.8357 (mmp) cc_final: 0.8108 (mmm) REVERT: B 871 TRP cc_start: 0.8885 (t60) cc_final: 0.8468 (t60) REVERT: B 875 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7708 (mt-10) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2367 time to fit residues: 88.1990 Evaluate side-chains 158 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 86 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 248 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103236 restraints weight = 27982.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105657 restraints weight = 17456.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107144 restraints weight = 12585.329| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13722 Z= 0.155 Angle : 0.669 6.896 18578 Z= 0.332 Chirality : 0.046 0.252 1990 Planarity : 0.004 0.041 2454 Dihedral : 6.539 113.975 1864 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: -2.17 (0.20), residues: 1684 helix: -0.24 (0.20), residues: 668 sheet: -2.12 (0.33), residues: 210 loop : -2.31 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 882 HIS 0.004 0.001 HIS B 322 PHE 0.031 0.002 PHE A 449 TYR 0.014 0.002 TYR A 849 ARG 0.014 0.000 ARG B 763 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 486) hydrogen bonds : angle 4.98421 ( 1398) covalent geometry : bond 0.00350 (13722) covalent geometry : angle 0.66927 (18578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.483 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7154 (pp20) cc_final: 0.6851 (pp20) REVERT: A 408 MET cc_start: 0.4590 (mmp) cc_final: 0.4085 (mmp) REVERT: A 509 TYR cc_start: 0.8302 (t80) cc_final: 0.8074 (t80) REVERT: A 584 MET cc_start: 0.7882 (mtm) cc_final: 0.7510 (mtp) REVERT: A 624 PHE cc_start: 0.8021 (t80) cc_final: 0.7821 (t80) REVERT: A 680 THR cc_start: 0.8630 (p) cc_final: 0.8421 (p) REVERT: A 776 MET cc_start: 0.8472 (mmp) cc_final: 0.8193 (mmm) REVERT: A 871 TRP cc_start: 0.8951 (t60) cc_final: 0.8458 (t60) REVERT: A 875 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 189 GLU cc_start: 0.3910 (tm-30) cc_final: 0.3485 (tm-30) REVERT: B 271 LEU cc_start: 0.8530 (mp) cc_final: 0.7831 (tt) REVERT: B 408 MET cc_start: 0.4530 (mmp) cc_final: 0.4043 (mmp) REVERT: B 584 MET cc_start: 0.7817 (mtm) cc_final: 0.7496 (mtp) REVERT: B 675 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 680 THR cc_start: 0.8647 (p) cc_final: 0.8420 (p) REVERT: B 776 MET cc_start: 0.8463 (mmp) cc_final: 0.8209 (mmm) REVERT: B 871 TRP cc_start: 0.8958 (t60) cc_final: 0.8449 (t60) REVERT: B 875 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8082 (mt-10) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2286 time to fit residues: 80.2922 Evaluate side-chains 166 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 40.0000 chunk 4 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101214 restraints weight = 28442.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103403 restraints weight = 18274.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104746 restraints weight = 13500.995| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13722 Z= 0.164 Angle : 0.688 7.431 18578 Z= 0.338 Chirality : 0.046 0.211 1990 Planarity : 0.005 0.052 2454 Dihedral : 6.533 113.017 1864 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -2.08 (0.20), residues: 1684 helix: -0.11 (0.20), residues: 668 sheet: -2.13 (0.32), residues: 210 loop : -2.29 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 871 HIS 0.004 0.001 HIS A 888 PHE 0.034 0.002 PHE B 449 TYR 0.021 0.002 TYR A 849 ARG 0.007 0.000 ARG B 763 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 486) hydrogen bonds : angle 4.93414 ( 1398) covalent geometry : bond 0.00374 (13722) covalent geometry : angle 0.68847 (18578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.453 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.6045 (m-10) cc_final: 0.5755 (m-10) REVERT: A 189 GLU cc_start: 0.5506 (tt0) cc_final: 0.4957 (tt0) REVERT: A 211 GLU cc_start: 0.7191 (pp20) cc_final: 0.6877 (pp20) REVERT: A 271 LEU cc_start: 0.8547 (mp) cc_final: 0.7758 (tt) REVERT: A 408 MET cc_start: 0.4626 (mmp) cc_final: 0.4151 (mmp) REVERT: A 584 MET cc_start: 0.7904 (mtm) cc_final: 0.7553 (mtp) REVERT: A 624 PHE cc_start: 0.8079 (t80) cc_final: 0.7852 (t80) REVERT: A 680 THR cc_start: 0.8621 (p) cc_final: 0.8419 (p) REVERT: A 776 MET cc_start: 0.8514 (mmp) cc_final: 0.8295 (mmm) REVERT: A 871 TRP cc_start: 0.8945 (t60) cc_final: 0.8546 (t60) REVERT: A 875 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 189 GLU cc_start: 0.3758 (tm-30) cc_final: 0.3283 (mm-30) REVERT: B 211 GLU cc_start: 0.7078 (pp20) cc_final: 0.6854 (pp20) REVERT: B 408 MET cc_start: 0.4677 (mmp) cc_final: 0.4092 (mmp) REVERT: B 584 MET cc_start: 0.7818 (mtm) cc_final: 0.7520 (mtp) REVERT: B 675 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 680 THR cc_start: 0.8691 (p) cc_final: 0.8466 (p) REVERT: B 776 MET cc_start: 0.8518 (mmp) cc_final: 0.8276 (mmm) REVERT: B 871 TRP cc_start: 0.8955 (t60) cc_final: 0.8543 (t60) REVERT: B 875 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8049 (mt-10) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2293 time to fit residues: 79.4456 Evaluate side-chains 165 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098877 restraints weight = 28539.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101025 restraints weight = 17958.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102687 restraints weight = 13040.619| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13722 Z= 0.216 Angle : 0.735 8.036 18578 Z= 0.366 Chirality : 0.049 0.197 1990 Planarity : 0.005 0.047 2454 Dihedral : 6.646 112.329 1864 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -2.18 (0.20), residues: 1684 helix: -0.14 (0.20), residues: 668 sheet: -2.25 (0.32), residues: 210 loop : -2.38 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 523 HIS 0.006 0.001 HIS A 888 PHE 0.028 0.002 PHE B 449 TYR 0.022 0.002 TYR A 849 ARG 0.005 0.001 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 486) hydrogen bonds : angle 5.06400 ( 1398) covalent geometry : bond 0.00496 (13722) covalent geometry : angle 0.73453 (18578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.481 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 189 GLU cc_start: 0.5561 (tt0) cc_final: 0.4919 (tt0) REVERT: A 211 GLU cc_start: 0.7246 (pp20) cc_final: 0.6856 (pp20) REVERT: A 408 MET cc_start: 0.4821 (mmp) cc_final: 0.4220 (mmp) REVERT: A 581 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7555 (ttm170) REVERT: A 624 PHE cc_start: 0.8181 (t80) cc_final: 0.7978 (t80) REVERT: A 680 THR cc_start: 0.8705 (p) cc_final: 0.8499 (p) REVERT: A 776 MET cc_start: 0.8641 (mmp) cc_final: 0.8395 (mmm) REVERT: A 871 TRP cc_start: 0.8947 (t60) cc_final: 0.8480 (t60) REVERT: A 875 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 189 GLU cc_start: 0.3786 (tm-30) cc_final: 0.3357 (mm-30) REVERT: B 211 GLU cc_start: 0.7184 (pp20) cc_final: 0.6895 (pp20) REVERT: B 271 LEU cc_start: 0.8572 (mp) cc_final: 0.7807 (tt) REVERT: B 408 MET cc_start: 0.4879 (mmp) cc_final: 0.4310 (mmp) REVERT: B 581 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7405 (ttm170) REVERT: B 584 MET cc_start: 0.8014 (mtm) cc_final: 0.7645 (mtp) REVERT: B 675 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7640 (tm-30) REVERT: B 680 THR cc_start: 0.8756 (p) cc_final: 0.8540 (p) REVERT: B 776 MET cc_start: 0.8610 (mmp) cc_final: 0.8363 (mmm) REVERT: B 871 TRP cc_start: 0.8949 (t60) cc_final: 0.8498 (t60) REVERT: B 875 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7994 (mt-10) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2361 time to fit residues: 73.3098 Evaluate side-chains 151 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 82 optimal weight: 0.0010 chunk 145 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104259 restraints weight = 28146.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106715 restraints weight = 17375.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108180 restraints weight = 12347.263| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13722 Z= 0.122 Angle : 0.663 8.570 18578 Z= 0.325 Chirality : 0.045 0.166 1990 Planarity : 0.005 0.083 2454 Dihedral : 6.432 110.975 1864 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -2.00 (0.20), residues: 1684 helix: -0.02 (0.20), residues: 672 sheet: -2.07 (0.32), residues: 204 loop : -2.28 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 871 HIS 0.006 0.001 HIS A 720 PHE 0.022 0.002 PHE B 449 TYR 0.019 0.002 TYR A 825 ARG 0.008 0.000 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 486) hydrogen bonds : angle 4.84828 ( 1398) covalent geometry : bond 0.00275 (13722) covalent geometry : angle 0.66302 (18578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.423 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 271 LEU cc_start: 0.8520 (mp) cc_final: 0.7769 (tt) REVERT: A 299 MET cc_start: 0.8493 (mpp) cc_final: 0.8015 (mpp) REVERT: A 408 MET cc_start: 0.4518 (mmp) cc_final: 0.4043 (mmp) REVERT: A 503 THR cc_start: 0.8893 (p) cc_final: 0.8589 (t) REVERT: A 581 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7292 (ttm170) REVERT: A 599 LEU cc_start: 0.8910 (tp) cc_final: 0.8626 (tp) REVERT: A 624 PHE cc_start: 0.8123 (t80) cc_final: 0.7888 (t80) REVERT: A 680 THR cc_start: 0.8595 (p) cc_final: 0.8364 (p) REVERT: A 871 TRP cc_start: 0.8871 (t60) cc_final: 0.8496 (t60) REVERT: B 211 GLU cc_start: 0.7148 (pp20) cc_final: 0.6798 (pp20) REVERT: B 408 MET cc_start: 0.4547 (mmp) cc_final: 0.3967 (mmp) REVERT: B 492 GLU cc_start: 0.8442 (tt0) cc_final: 0.8103 (tt0) REVERT: B 503 THR cc_start: 0.8948 (p) cc_final: 0.8650 (t) REVERT: B 584 MET cc_start: 0.7772 (mtm) cc_final: 0.7458 (mtp) REVERT: B 680 THR cc_start: 0.8681 (p) cc_final: 0.8436 (p) REVERT: B 712 CYS cc_start: 0.8249 (t) cc_final: 0.8048 (t) REVERT: B 871 TRP cc_start: 0.8850 (t60) cc_final: 0.8553 (t60) REVERT: B 875 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7868 (mt-10) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2248 time to fit residues: 77.6046 Evaluate side-chains 165 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS A 756 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097474 restraints weight = 28668.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099763 restraints weight = 18339.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101336 restraints weight = 13337.916| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 13722 Z= 0.255 Angle : 0.779 9.077 18578 Z= 0.389 Chirality : 0.050 0.202 1990 Planarity : 0.005 0.054 2454 Dihedral : 6.692 111.022 1864 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -2.25 (0.20), residues: 1684 helix: -0.30 (0.20), residues: 682 sheet: -2.28 (0.32), residues: 210 loop : -2.36 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 523 HIS 0.007 0.001 HIS A 539 PHE 0.026 0.003 PHE B 449 TYR 0.023 0.002 TYR A 849 ARG 0.011 0.001 ARG B 763 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 486) hydrogen bonds : angle 5.07933 ( 1398) covalent geometry : bond 0.00581 (13722) covalent geometry : angle 0.77879 (18578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.485 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7455 (pp20) cc_final: 0.6682 (pp20) REVERT: A 408 MET cc_start: 0.4910 (mmp) cc_final: 0.4229 (mmp) REVERT: A 503 THR cc_start: 0.8908 (p) cc_final: 0.8582 (t) REVERT: A 581 ARG cc_start: 0.7898 (ttm170) cc_final: 0.7275 (ttm170) REVERT: A 584 MET cc_start: 0.7594 (mtp) cc_final: 0.6696 (mtp) REVERT: B 211 GLU cc_start: 0.7248 (pp20) cc_final: 0.6909 (pp20) REVERT: B 271 LEU cc_start: 0.8630 (mp) cc_final: 0.7794 (tt) REVERT: B 408 MET cc_start: 0.4896 (mmp) cc_final: 0.3904 (mmt) REVERT: B 503 THR cc_start: 0.8981 (p) cc_final: 0.8685 (t) REVERT: B 680 THR cc_start: 0.8768 (p) cc_final: 0.8559 (p) REVERT: B 767 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7779 (ttm110) REVERT: B 875 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7962 (mt-10) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2388 time to fit residues: 69.6265 Evaluate side-chains 139 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 chunk 127 optimal weight: 0.0970 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104084 restraints weight = 27995.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106254 restraints weight = 17897.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107906 restraints weight = 13018.939| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13722 Z= 0.133 Angle : 0.699 9.580 18578 Z= 0.343 Chirality : 0.046 0.185 1990 Planarity : 0.005 0.044 2454 Dihedral : 6.495 108.871 1864 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % 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: -2.06 (0.20), residues: 1684 helix: -0.09 (0.20), residues: 680 sheet: -2.19 (0.32), residues: 206 loop : -2.30 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 871 HIS 0.004 0.001 HIS A 888 PHE 0.029 0.002 PHE A 869 TYR 0.016 0.001 TYR A 825 ARG 0.011 0.000 ARG B 763 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 486) hydrogen bonds : angle 4.89399 ( 1398) covalent geometry : bond 0.00304 (13722) covalent geometry : angle 0.69894 (18578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.483 Fit side-chains TARDY: cannot create tardy model for: "GLN A 685 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 685 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.5333 (tt0) cc_final: 0.4602 (tm-30) REVERT: A 271 LEU cc_start: 0.8557 (mp) cc_final: 0.7782 (tt) REVERT: A 408 MET cc_start: 0.4499 (mmp) cc_final: 0.3982 (mmp) REVERT: A 503 THR cc_start: 0.8790 (p) cc_final: 0.8473 (t) REVERT: A 581 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7373 (ttm170) REVERT: A 584 MET cc_start: 0.7467 (mtp) cc_final: 0.6644 (mtp) REVERT: A 680 THR cc_start: 0.8605 (p) cc_final: 0.8404 (p) REVERT: A 712 CYS cc_start: 0.8195 (t) cc_final: 0.7978 (t) REVERT: B 211 GLU cc_start: 0.7168 (pp20) cc_final: 0.6814 (pp20) REVERT: B 408 MET cc_start: 0.4486 (mmp) cc_final: 0.3847 (mmp) REVERT: B 503 THR cc_start: 0.8916 (p) cc_final: 0.8598 (t) REVERT: B 584 MET cc_start: 0.7373 (mtp) cc_final: 0.6655 (mtp) REVERT: B 875 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7730 (mt-10) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.2217 time to fit residues: 74.9421 Evaluate side-chains 163 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 166 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** 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 = 0.3623 r_free = 0.3623 target = 0.120995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101827 restraints weight = 28316.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104023 restraints weight = 18146.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105310 restraints weight = 13319.268| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13722 Z= 0.172 Angle : 0.714 9.082 18578 Z= 0.352 Chirality : 0.047 0.176 1990 Planarity : 0.005 0.045 2454 Dihedral : 6.498 109.280 1864 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -2.05 (0.20), residues: 1684 helix: -0.12 (0.20), residues: 678 sheet: -2.20 (0.32), residues: 206 loop : -2.24 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 523 HIS 0.005 0.001 HIS A 888 PHE 0.022 0.002 PHE B 449 TYR 0.020 0.002 TYR A 849 ARG 0.010 0.000 ARG B 763 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 486) hydrogen bonds : angle 4.91915 ( 1398) covalent geometry : bond 0.00397 (13722) covalent geometry : angle 0.71350 (18578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3794.95 seconds wall clock time: 66 minutes 59.04 seconds (4019.04 seconds total)