Starting phenix.real_space_refine on Wed Mar 4 11:17:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vef_21156/03_2026/6vef_21156.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vef_21156/03_2026/6vef_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_21156/03_2026/6vef_21156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vef_21156/03_2026/6vef_21156.map" model { file = "/net/cci-nas-00/data/ceres_data/6vef_21156/03_2026/6vef_21156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vef_21156/03_2026/6vef_21156.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.93, per 1000 atoms: 0.22 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: 0.84 Conformation dependent library (CDL) restraints added in 395.6 milliseconds 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: 0.28 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: 1.65 Time building geometry restraints manager: 1.08 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: 0.02 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.080 ------------------------------------------------------------------------------- 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 : 12.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG A 456 TYR 0.022 0.004 TYR A 849 PHE 0.041 0.004 PHE B 203 TRP 0.031 0.004 TRP A 708 HIS 0.017 0.003 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00937 (13722) covalent geometry : angle 1.19714 (18578) hydrogen bonds : bond 0.18523 ( 486) hydrogen bonds : angle 7.68701 ( 1398) *********************** 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 : 0.450 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: 0.7636 (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: 0.8179 (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: 0.8602 (mmp) cc_final: 0.8153 (mmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1020 time to fit residues: 37.9070 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.0764 ------------------------------------------------------------------------------- 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 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 B 631 HIS ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102731 restraints weight = 27588.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104873 restraints weight = 17729.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106348 restraints weight = 12984.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107213 restraints weight = 10513.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107630 restraints weight = 9202.255| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13722 Z= 0.152 Angle : 0.708 7.092 18578 Z= 0.360 Chirality : 0.046 0.192 1990 Planarity : 0.006 0.054 2454 Dihedral : 7.461 117.203 1864 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.18), residues: 1684 helix: -1.35 (0.18), residues: 674 sheet: -2.60 (0.32), residues: 202 loop : -2.74 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 510 TYR 0.017 0.002 TYR B 883 PHE 0.014 0.002 PHE B 279 TRP 0.021 0.002 TRP A 871 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00329 (13722) covalent geometry : angle 0.70822 (18578) hydrogen bonds : bond 0.04316 ( 486) hydrogen bonds : angle 5.44228 ( 1398) *********************** 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 224 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7509 (tpp) cc_final: 0.7231 (tpp) REVERT: A 211 GLU cc_start: 0.6774 (pp20) cc_final: 0.6528 (pp20) REVERT: A 503 THR cc_start: 0.8996 (p) cc_final: 0.8706 (t) REVERT: A 509 TYR cc_start: 0.8272 (t80) cc_final: 0.8049 (t80) REVERT: A 576 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8355 (mttp) REVERT: A 584 MET cc_start: 0.7386 (mtp) cc_final: 0.7094 (mtp) REVERT: A 659 LEU cc_start: 0.7553 (tt) cc_final: 0.7263 (mp) REVERT: B 101 PHE cc_start: 0.7141 (m-80) cc_final: 0.6444 (m-80) REVERT: B 173 MET cc_start: 0.8043 (tpp) cc_final: 0.6514 (tpp) REVERT: B 503 THR cc_start: 0.9008 (p) cc_final: 0.8721 (t) REVERT: B 509 TYR cc_start: 0.8234 (t80) cc_final: 0.8021 (t80) REVERT: B 576 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8316 (mttp) REVERT: B 581 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.7040 (ptp-170) REVERT: B 584 MET cc_start: 0.7390 (mtp) cc_final: 0.7059 (mtp) REVERT: B 659 LEU cc_start: 0.7618 (tt) cc_final: 0.7383 (mt) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1070 time to fit residues: 36.1889 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 : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A 879 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN B 739 GLN B 879 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101090 restraints weight = 27854.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103486 restraints weight = 16970.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104961 restraints weight = 12044.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106218 restraints weight = 9646.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106838 restraints weight = 8189.214| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13722 Z= 0.173 Angle : 0.709 7.644 18578 Z= 0.353 Chirality : 0.047 0.159 1990 Planarity : 0.005 0.045 2454 Dihedral : 7.078 116.130 1864 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.20), residues: 1684 helix: -0.65 (0.20), residues: 672 sheet: -2.50 (0.32), residues: 204 loop : -2.55 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 620 TYR 0.015 0.002 TYR A 722 PHE 0.031 0.002 PHE A 624 TRP 0.010 0.001 TRP B 871 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00385 (13722) covalent geometry : angle 0.70911 (18578) hydrogen bonds : bond 0.03915 ( 486) hydrogen bonds : angle 5.32099 ( 1398) *********************** 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 225 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.457 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 173 MET cc_start: 0.7814 (tpp) cc_final: 0.6620 (tpp) REVERT: A 408 MET cc_start: 0.4619 (mmp) cc_final: 0.4177 (mmp) REVERT: A 503 THR cc_start: 0.8985 (p) cc_final: 0.8672 (t) REVERT: A 675 GLU cc_start: 0.8287 (tp30) cc_final: 0.7495 (mm-30) REVERT: A 875 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 173 MET cc_start: 0.8033 (tpp) cc_final: 0.6431 (tpp) REVERT: B 211 GLU cc_start: 0.6959 (pp20) cc_final: 0.6755 (pp20) REVERT: B 408 MET cc_start: 0.4626 (mmp) cc_final: 0.4276 (mmp) REVERT: B 503 THR cc_start: 0.9009 (p) cc_final: 0.8700 (t) REVERT: B 659 LEU cc_start: 0.8011 (tt) cc_final: 0.7756 (tp) REVERT: B 675 GLU cc_start: 0.8303 (tp30) cc_final: 0.7490 (mm-30) REVERT: B 680 THR cc_start: 0.8706 (p) cc_final: 0.8465 (p) REVERT: B 776 MET cc_start: 0.8555 (mmm) cc_final: 0.8337 (mmm) outliers start: 2 outliers final: 0 residues processed: 223 average time/residue: 0.1008 time to fit residues: 34.6758 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 : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 5 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 627 HIS ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 HIS ** B 739 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 = 0.3622 r_free = 0.3622 target = 0.120416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100981 restraints weight = 28269.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103174 restraints weight = 18078.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104512 restraints weight = 13288.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105643 restraints weight = 10906.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106198 restraints weight = 9452.480| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13722 Z= 0.166 Angle : 0.691 7.345 18578 Z= 0.344 Chirality : 0.047 0.156 1990 Planarity : 0.005 0.041 2454 Dihedral : 6.829 114.507 1864 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.20), residues: 1684 helix: -0.45 (0.20), residues: 672 sheet: -2.33 (0.33), residues: 204 loop : -2.45 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 620 TYR 0.015 0.002 TYR A 849 PHE 0.018 0.002 PHE A 624 TRP 0.009 0.001 TRP A 871 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00371 (13722) covalent geometry : angle 0.69126 (18578) hydrogen bonds : bond 0.03721 ( 486) hydrogen bonds : angle 5.18922 ( 1398) *********************** 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 222 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.499 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: 0.7016 (pp20) cc_final: 0.6767 (pp20) REVERT: A 271 LEU cc_start: 0.8563 (mp) cc_final: 0.7789 (tt) REVERT: A 299 MET cc_start: 0.8637 (mpp) cc_final: 0.8187 (mpp) REVERT: A 408 MET cc_start: 0.4681 (mmp) cc_final: 0.4196 (mmp) REVERT: A 503 THR cc_start: 0.8939 (p) cc_final: 0.8597 (t) REVERT: A 581 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7575 (ttm170) REVERT: A 584 MET cc_start: 0.7510 (mtp) cc_final: 0.7019 (mtp) REVERT: B 189 GLU cc_start: 0.3998 (tm-30) cc_final: 0.3780 (tm-30) REVERT: B 211 GLU cc_start: 0.7007 (pp20) cc_final: 0.6772 (pp20) REVERT: B 271 LEU cc_start: 0.8552 (mp) cc_final: 0.7800 (tt) REVERT: B 408 MET cc_start: 0.4687 (mmp) cc_final: 0.4253 (mmp) REVERT: B 503 THR cc_start: 0.8980 (p) cc_final: 0.8669 (t) REVERT: B 581 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6836 (ttm170) REVERT: B 584 MET cc_start: 0.7448 (mtp) cc_final: 0.6875 (mtp) REVERT: B 680 THR cc_start: 0.8655 (p) cc_final: 0.8421 (p) REVERT: B 875 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7788 (mt-10) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0994 time to fit residues: 34.0446 Evaluate side-chains 155 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 87 optimal weight: 0.0070 chunk 74 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- 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 269 ASN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 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 269 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 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 = 0.3597 r_free = 0.3597 target = 0.118640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099080 restraints weight = 28347.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101216 restraints weight = 18239.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102608 restraints weight = 13494.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103694 restraints weight = 11049.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104257 restraints weight = 9582.610| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13722 Z= 0.218 Angle : 0.736 7.065 18578 Z= 0.367 Chirality : 0.049 0.264 1990 Planarity : 0.005 0.040 2454 Dihedral : 6.844 113.666 1864 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.20), residues: 1684 helix: -0.46 (0.20), residues: 674 sheet: -2.37 (0.32), residues: 224 loop : -2.44 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 900 TYR 0.017 0.002 TYR A 849 PHE 0.034 0.003 PHE A 449 TRP 0.008 0.002 TRP B 871 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00496 (13722) covalent geometry : angle 0.73560 (18578) hydrogen bonds : bond 0.03824 ( 486) hydrogen bonds : angle 5.22276 ( 1398) *********************** 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 219 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.504 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 189 GLU cc_start: 0.5804 (tt0) cc_final: 0.5590 (tt0) REVERT: A 211 GLU cc_start: 0.7107 (pp20) cc_final: 0.6776 (pp20) REVERT: A 299 MET cc_start: 0.8474 (mpp) cc_final: 0.8195 (mpp) REVERT: A 408 MET cc_start: 0.4758 (mmp) cc_final: 0.4274 (mmp) REVERT: A 503 THR cc_start: 0.8956 (p) cc_final: 0.8621 (t) REVERT: A 598 ASN cc_start: 0.8303 (p0) cc_final: 0.7874 (t0) REVERT: A 675 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 712 CYS cc_start: 0.8023 (t) cc_final: 0.7786 (t) REVERT: A 875 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 189 GLU cc_start: 0.3996 (tm-30) cc_final: 0.3649 (tm-30) REVERT: B 211 GLU cc_start: 0.7098 (pp20) cc_final: 0.6818 (pp20) REVERT: B 408 MET cc_start: 0.4765 (mmp) cc_final: 0.4187 (mmp) REVERT: B 581 ARG cc_start: 0.7331 (ptp-170) cc_final: 0.6978 (ttm170) REVERT: B 584 MET cc_start: 0.7580 (mtp) cc_final: 0.7271 (mtp) REVERT: B 598 ASN cc_start: 0.8219 (p0) cc_final: 0.7760 (t0) REVERT: B 659 LEU cc_start: 0.8178 (tt) cc_final: 0.7459 (mp) REVERT: B 680 THR cc_start: 0.8676 (p) cc_final: 0.8437 (p) REVERT: B 875 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7867 (mt-10) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.0998 time to fit residues: 34.0012 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 139 optimal weight: 0.1980 chunk 128 optimal weight: 7.9990 overall best weight: 2.0022 ------------------------------------------------------------------------------- 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 739 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 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 = 0.3637 r_free = 0.3637 target = 0.121338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101008 restraints weight = 27766.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103520 restraints weight = 17007.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105125 restraints weight = 12062.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106321 restraints weight = 9639.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107015 restraints weight = 8229.096| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13722 Z= 0.147 Angle : 0.691 7.669 18578 Z= 0.340 Chirality : 0.046 0.205 1990 Planarity : 0.004 0.040 2454 Dihedral : 6.686 113.085 1864 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.20), residues: 1684 helix: -0.24 (0.20), residues: 670 sheet: -2.36 (0.32), residues: 224 loop : -2.38 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 385 TYR 0.017 0.002 TYR A 849 PHE 0.036 0.002 PHE B 449 TRP 0.013 0.001 TRP B 871 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00340 (13722) covalent geometry : angle 0.69071 (18578) hydrogen bonds : bond 0.03638 ( 486) hydrogen bonds : angle 5.04580 ( 1398) *********************** 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 237 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.497 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: 0.5625 (tt0) cc_final: 0.5421 (tt0) REVERT: A 211 GLU cc_start: 0.7142 (pp20) cc_final: 0.6827 (pp20) REVERT: A 271 LEU cc_start: 0.8525 (mp) cc_final: 0.7761 (tt) REVERT: A 299 MET cc_start: 0.8563 (mpp) cc_final: 0.8090 (mpp) REVERT: A 408 MET cc_start: 0.4770 (mmp) cc_final: 0.4121 (mmp) REVERT: A 581 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7458 (ttm170) REVERT: A 584 MET cc_start: 0.7586 (mtp) cc_final: 0.7006 (mtp) REVERT: A 675 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 871 TRP cc_start: 0.8906 (t60) cc_final: 0.8530 (t60) REVERT: B 189 GLU cc_start: 0.3777 (tm-30) cc_final: 0.3384 (tm-30) REVERT: B 211 GLU cc_start: 0.7133 (pp20) cc_final: 0.6830 (pp20) REVERT: B 271 LEU cc_start: 0.8552 (mp) cc_final: 0.7817 (tt) REVERT: B 408 MET cc_start: 0.4616 (mmp) cc_final: 0.3969 (mmp) REVERT: B 659 LEU cc_start: 0.7814 (tt) cc_final: 0.7253 (mt) REVERT: B 680 THR cc_start: 0.8571 (p) cc_final: 0.8314 (p) REVERT: B 871 TRP cc_start: 0.8896 (t60) cc_final: 0.8489 (t60) REVERT: B 875 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7700 (mt-10) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1002 time to fit residues: 36.5171 Evaluate side-chains 169 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 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 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 739 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102079 restraints weight = 28075.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103390 restraints weight = 19709.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105007 restraints weight = 14293.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105256 restraints weight = 13033.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105363 restraints weight = 11056.036| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13722 Z= 0.180 Angle : 0.709 8.136 18578 Z= 0.352 Chirality : 0.048 0.186 1990 Planarity : 0.005 0.039 2454 Dihedral : 6.659 113.124 1864 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.20), residues: 1684 helix: -0.22 (0.20), residues: 674 sheet: -2.30 (0.32), residues: 224 loop : -2.40 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 620 TYR 0.019 0.002 TYR B 849 PHE 0.026 0.002 PHE B 449 TRP 0.010 0.001 TRP B 871 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00413 (13722) covalent geometry : angle 0.70862 (18578) hydrogen bonds : bond 0.03737 ( 486) hydrogen bonds : angle 5.04355 ( 1398) *********************** 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 209 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.386 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: 0.5548 (tt0) cc_final: 0.5336 (tt0) REVERT: A 211 GLU cc_start: 0.7162 (pp20) cc_final: 0.6787 (pp20) REVERT: A 299 MET cc_start: 0.8610 (mpp) cc_final: 0.8185 (mpp) REVERT: A 408 MET cc_start: 0.4750 (mmp) cc_final: 0.4166 (mmp) REVERT: A 584 MET cc_start: 0.7676 (mtp) cc_final: 0.7136 (mtp) REVERT: A 675 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 189 GLU cc_start: 0.3804 (tm-30) cc_final: 0.3375 (mm-30) REVERT: B 211 GLU cc_start: 0.7145 (pp20) cc_final: 0.6766 (pp20) REVERT: B 408 MET cc_start: 0.4736 (mmp) cc_final: 0.4193 (mmp) REVERT: B 581 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7345 (ttm170) REVERT: B 584 MET cc_start: 0.7436 (mtp) cc_final: 0.6671 (mtp) REVERT: B 659 LEU cc_start: 0.7848 (tt) cc_final: 0.7352 (mt) REVERT: B 680 THR cc_start: 0.8610 (p) cc_final: 0.8371 (p) REVERT: B 875 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7721 (mt-10) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0934 time to fit residues: 30.7554 Evaluate side-chains 155 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 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 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 = 0.3612 r_free = 0.3612 target = 0.120074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101070 restraints weight = 27966.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102925 restraints weight = 18812.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104393 restraints weight = 14330.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105205 restraints weight = 11782.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105906 restraints weight = 10415.095| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13722 Z= 0.185 Angle : 0.723 8.809 18578 Z= 0.358 Chirality : 0.048 0.177 1990 Planarity : 0.005 0.039 2454 Dihedral : 6.698 112.090 1864 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.20), residues: 1684 helix: -0.27 (0.20), residues: 686 sheet: -2.29 (0.32), residues: 210 loop : -2.42 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 763 TYR 0.021 0.002 TYR B 849 PHE 0.025 0.002 PHE A 869 TRP 0.031 0.002 TRP A 871 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00428 (13722) covalent geometry : angle 0.72313 (18578) hydrogen bonds : bond 0.03720 ( 486) hydrogen bonds : angle 5.07699 ( 1398) *********************** 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 213 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.357 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: A 189 GLU cc_start: 0.5433 (tt0) cc_final: 0.5231 (tt0) REVERT: A 211 GLU cc_start: 0.7124 (pp20) cc_final: 0.6722 (pp20) REVERT: A 271 LEU cc_start: 0.8558 (mp) cc_final: 0.7864 (tt) REVERT: A 299 MET cc_start: 0.8542 (mpp) cc_final: 0.8249 (mpp) REVERT: A 408 MET cc_start: 0.4697 (mmp) cc_final: 0.4088 (mmp) REVERT: A 584 MET cc_start: 0.7605 (mtp) cc_final: 0.7325 (mtp) REVERT: A 675 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 712 CYS cc_start: 0.7861 (t) cc_final: 0.7602 (t) REVERT: B 189 GLU cc_start: 0.3694 (tm-30) cc_final: 0.3259 (mm-30) REVERT: B 211 GLU cc_start: 0.7104 (pp20) cc_final: 0.6726 (pp20) REVERT: B 271 LEU cc_start: 0.8526 (mp) cc_final: 0.7858 (tt) REVERT: B 408 MET cc_start: 0.4635 (mmp) cc_final: 0.4067 (mmp) REVERT: B 503 THR cc_start: 0.8863 (p) cc_final: 0.8530 (t) REVERT: B 584 MET cc_start: 0.7586 (mtp) cc_final: 0.6964 (mtp) REVERT: B 598 ASN cc_start: 0.8175 (p0) cc_final: 0.7806 (t0) REVERT: B 659 LEU cc_start: 0.7868 (tt) cc_final: 0.7353 (mt) REVERT: B 875 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7837 (mt-10) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1011 time to fit residues: 32.7873 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 : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 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 363 GLN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 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 = 0.3634 r_free = 0.3634 target = 0.121615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102864 restraints weight = 28219.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104748 restraints weight = 18903.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106239 restraints weight = 14279.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106845 restraints weight = 11671.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107789 restraints weight = 10437.640| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13722 Z= 0.153 Angle : 0.710 8.250 18578 Z= 0.352 Chirality : 0.047 0.175 1990 Planarity : 0.005 0.062 2454 Dihedral : 6.605 111.130 1864 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.07 % Allowed : 0.70 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.20), residues: 1684 helix: -0.22 (0.20), residues: 686 sheet: -2.33 (0.32), residues: 220 loop : -2.37 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 763 TYR 0.017 0.002 TYR B 849 PHE 0.024 0.002 PHE A 869 TRP 0.035 0.002 TRP B 871 HIS 0.004 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00353 (13722) covalent geometry : angle 0.71036 (18578) hydrogen bonds : bond 0.03649 ( 486) hydrogen bonds : angle 5.03802 ( 1398) *********************** 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 221 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.358 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: A 211 GLU cc_start: 0.7087 (pp20) cc_final: 0.6669 (pp20) REVERT: A 299 MET cc_start: 0.8522 (mpp) cc_final: 0.8186 (mpp) REVERT: A 408 MET cc_start: 0.4568 (mmp) cc_final: 0.3912 (mmp) REVERT: A 584 MET cc_start: 0.7463 (mtp) cc_final: 0.7069 (mtp) REVERT: A 675 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 189 GLU cc_start: 0.3623 (tm-30) cc_final: 0.3181 (mm-30) REVERT: B 299 MET cc_start: 0.8750 (mpp) cc_final: 0.8258 (mpp) REVERT: B 408 MET cc_start: 0.4547 (mmp) cc_final: 0.3988 (mmp) REVERT: B 503 THR cc_start: 0.8774 (p) cc_final: 0.8430 (t) REVERT: B 581 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7704 (ttm170) REVERT: B 659 LEU cc_start: 0.7751 (tt) cc_final: 0.7297 (mt) REVERT: B 762 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7746 (mtp-110) REVERT: B 875 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7685 (mt-10) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.0933 time to fit residues: 31.5894 Evaluate side-chains 161 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 0.0050 chunk 117 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 131 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** 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 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 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 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106395 restraints weight = 27913.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107488 restraints weight = 19565.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109080 restraints weight = 14534.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109309 restraints weight = 12264.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109357 restraints weight = 11087.534| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13722 Z= 0.128 Angle : 0.694 9.611 18578 Z= 0.340 Chirality : 0.046 0.164 1990 Planarity : 0.005 0.056 2454 Dihedral : 6.419 109.265 1864 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.20), residues: 1684 helix: -0.18 (0.20), residues: 682 sheet: -2.28 (0.31), residues: 220 loop : -2.30 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 763 TYR 0.017 0.002 TYR B 849 PHE 0.024 0.002 PHE B 449 TRP 0.037 0.002 TRP B 871 HIS 0.003 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00291 (13722) covalent geometry : angle 0.69389 (18578) hydrogen bonds : bond 0.03568 ( 486) hydrogen bonds : angle 4.92848 ( 1398) ********************** 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 228 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.468 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: A 238 MET cc_start: 0.7941 (ttp) cc_final: 0.7668 (ttt) REVERT: A 271 LEU cc_start: 0.8439 (mp) cc_final: 0.7753 (tt) REVERT: A 299 MET cc_start: 0.8401 (mpp) cc_final: 0.8065 (mpp) REVERT: A 408 MET cc_start: 0.4344 (mmp) cc_final: 0.3855 (mmp) REVERT: A 584 MET cc_start: 0.7382 (mtp) cc_final: 0.7060 (mtp) REVERT: A 675 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 189 GLU cc_start: 0.3517 (tm-30) cc_final: 0.3072 (mm-30) REVERT: B 271 LEU cc_start: 0.8437 (mp) cc_final: 0.7792 (tt) REVERT: B 299 MET cc_start: 0.8686 (mpp) cc_final: 0.8211 (mpp) REVERT: B 408 MET cc_start: 0.4299 (mmp) cc_final: 0.3817 (mmp) REVERT: B 492 GLU cc_start: 0.8091 (tt0) cc_final: 0.7765 (tt0) REVERT: B 503 THR cc_start: 0.8707 (p) cc_final: 0.8421 (t) REVERT: B 584 MET cc_start: 0.7175 (mtp) cc_final: 0.6558 (mtp) REVERT: B 875 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7623 (mt-10) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0942 time to fit residues: 33.3963 Evaluate side-chains 168 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 0.0050 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 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 298 HIS ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104729 restraints weight = 28311.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106881 restraints weight = 18576.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108260 restraints weight = 13762.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109102 restraints weight = 11213.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109829 restraints weight = 9868.004| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13722 Z= 0.136 Angle : 0.686 9.215 18578 Z= 0.336 Chirality : 0.046 0.159 1990 Planarity : 0.004 0.043 2454 Dihedral : 6.337 108.830 1864 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.07 % Allowed : 0.77 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1684 helix: -0.09 (0.20), residues: 684 sheet: -2.30 (0.31), residues: 222 loop : -2.30 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 763 TYR 0.021 0.002 TYR B 825 PHE 0.020 0.002 PHE A 624 TRP 0.024 0.002 TRP B 871 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00311 (13722) covalent geometry : angle 0.68578 (18578) hydrogen bonds : bond 0.03444 ( 486) hydrogen bonds : angle 4.83833 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.25 seconds wall clock time: 31 minutes 6.05 seconds (1866.05 seconds total)