Starting phenix.real_space_refine on Sat Sep 12 02:48:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vef_21156/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vef_21156/09_2026/6vef_21156.map" } 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-2.2.1-6174/lib/python3.11/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: {'OAA': 1} Classifications: {'RNAv2': 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: {'OAA': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 2.88, per 1000 atoms: 0.21 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: 0.85 Conformation dependent library (CDL) restraints added in 501.7 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: 0.50 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: 1.98 Time building geometry restraints manager: 1.19 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: 0.03 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.790 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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/Z covalent geometry : bond 0.00937 / 0.43 (13722) covalent geometry : angle 1.19728 / 0.64 (18578) hydrogen bonds : bond 0.18523 / 11.45 ( 486) hydrogen bonds : angle 7.68701 / 5.35 ( 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 : 0.414 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: 0.0910 time to fit residues: 34.2379 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 : 0.348 ------------------------------------------------------------------------------- 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... 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101948 restraints weight = 27649.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104369 restraints weight = 16975.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106010 restraints weight = 12101.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106932 restraints weight = 9627.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107808 restraints weight = 8362.774| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1827 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= 0.151 Angle : 0.708 7.136 18578 Z= 0.360 Chirality : 0.046 0.188 1990 Planarity : 0.006 0.055 2454 Dihedral : 7.446 117.048 1864 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % 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: -3.24 (0.18), residues: 1684 helix: -1.35 (0.18), residues: 674 sheet: -2.60 (0.32), residues: 202 loop : -2.73 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 510 TYR 0.016 0.002 TYR B 883 PHE 0.014 0.002 PHE A 591 TRP 0.020 0.002 TRP A 871 HIS 0.004 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13722) covalent geometry : angle 0.70841 / 0.36 (18578) hydrogen bonds : bond 0.04301 / 2.75 ( 486) hydrogen bonds : angle 5.42394 / 3.79 ( 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 225 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7514 (tpp) cc_final: 0.7241 (tpp) REVERT: A 211 GLU cc_start: 0.6778 (pp20) cc_final: 0.6532 (pp20) REVERT: A 503 THR cc_start: 0.8981 (p) cc_final: 0.8686 (t) REVERT: A 509 TYR cc_start: 0.8239 (t80) cc_final: 0.8020 (t80) REVERT: A 576 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8348 (mttp) REVERT: A 584 MET cc_start: 0.7367 (mtp) cc_final: 0.7038 (mtp) REVERT: A 659 LEU cc_start: 0.7554 (tt) cc_final: 0.7201 (mp) REVERT: B 101 PHE cc_start: 0.7157 (m-80) cc_final: 0.6459 (m-80) REVERT: B 173 MET cc_start: 0.8046 (tpp) cc_final: 0.6516 (tpp) REVERT: B 503 THR cc_start: 0.8992 (p) cc_final: 0.8702 (t) REVERT: B 509 TYR cc_start: 0.8212 (t80) cc_final: 0.7995 (t80) REVERT: B 576 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8327 (mttp) REVERT: B 581 ARG cc_start: 0.7272 (ptp-170) cc_final: 0.7043 (ptp-170) REVERT: B 584 MET cc_start: 0.7368 (mtp) cc_final: 0.7019 (mtp) REVERT: B 659 LEU cc_start: 0.7618 (tt) cc_final: 0.7385 (mt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1097 time to fit residues: 37.5921 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 : 0.501 ------------------------------------------------------------------------------- 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: 2.9990 chunk 115 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 87 optimal weight: 0.0020 chunk 69 optimal weight: 9.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102914 restraints weight = 27941.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105303 restraints weight = 17181.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106961 restraints weight = 12282.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107944 restraints weight = 9749.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108816 restraints weight = 8432.226| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13722 Z= 0.150 Angle : 0.689 7.174 18578 Z= 0.343 Chirality : 0.046 0.151 1990 Planarity : 0.005 0.045 2454 Dihedral : 7.039 116.190 1864 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.14 % Allowed : 3.31 % Favored : 96.55 % 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: -2.69 (0.19), residues: 1684 helix: -0.68 (0.20), residues: 672 sheet: -2.56 (0.31), residues: 216 loop : -2.54 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 620 TYR 0.014 0.002 TYR A 722 PHE 0.031 0.002 PHE A 624 TRP 0.011 0.001 TRP B 871 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13722) covalent geometry : angle 0.68926 / 0.34 (18578) hydrogen bonds : bond 0.03861 / 2.50 ( 486) hydrogen bonds : angle 5.28007 / 3.72 ( 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 229 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.531 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: 0.7754 (tpp) cc_final: 0.6593 (tpp) REVERT: A 408 MET cc_start: 0.4578 (mmp) cc_final: 0.4189 (mmp) REVERT: A 503 THR cc_start: 0.8974 (p) cc_final: 0.8650 (t) REVERT: A 581 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6980 (ttm170) REVERT: A 675 GLU cc_start: 0.8234 (tp30) cc_final: 0.7424 (mm-30) REVERT: A 776 MET cc_start: 0.8534 (mmm) cc_final: 0.8289 (mmm) REVERT: B 173 MET cc_start: 0.8013 (tpp) cc_final: 0.6652 (tpp) REVERT: B 408 MET cc_start: 0.4579 (mmp) cc_final: 0.4289 (mmp) REVERT: B 503 THR cc_start: 0.8996 (p) cc_final: 0.8689 (t) REVERT: B 509 TYR cc_start: 0.8300 (t80) cc_final: 0.8014 (t80) REVERT: B 659 LEU cc_start: 0.7949 (tt) cc_final: 0.7354 (mt) REVERT: B 680 THR cc_start: 0.8671 (p) cc_final: 0.8431 (p) REVERT: B 776 MET cc_start: 0.8524 (mmm) cc_final: 0.8270 (mmm) REVERT: B 875 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7801 (mt-10) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.1049 time to fit residues: 36.7813 Evaluate side-chains 159 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 10.0000 chunk 117 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** 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 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 = 0.3635 r_free = 0.3635 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102068 restraints weight = 27894.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104314 restraints weight = 17849.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105647 restraints weight = 13008.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106764 restraints weight = 10644.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107527 restraints weight = 9191.656| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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= 0.158 Angle : 0.689 7.228 18578 Z= 0.343 Chirality : 0.046 0.153 1990 Planarity : 0.005 0.041 2454 Dihedral : 6.778 115.049 1864 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -0.47 (0.20), residues: 672 sheet: -2.28 (0.33), residues: 204 loop : -2.48 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 581 TYR 0.016 0.002 TYR A 849 PHE 0.019 0.002 PHE A 449 TRP 0.009 0.001 TRP B 871 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13722) covalent geometry : angle 0.68934 / 0.34 (18578) hydrogen bonds : bond 0.03773 / 2.45 ( 486) hydrogen bonds : angle 5.13450 / 3.62 ( 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 220 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.437 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: A 189 GLU cc_start: 0.5864 (tt0) cc_final: 0.5596 (tt0) REVERT: A 211 GLU cc_start: 0.7040 (pp20) cc_final: 0.6801 (pp20) REVERT: A 271 LEU cc_start: 0.8562 (mp) cc_final: 0.7812 (tt) REVERT: A 299 MET cc_start: 0.8658 (mpp) cc_final: 0.8371 (mpp) REVERT: A 408 MET cc_start: 0.4625 (mmp) cc_final: 0.4072 (mmp) REVERT: A 581 ARG cc_start: 0.7307 (ptp-170) cc_final: 0.6863 (ttm170) REVERT: A 584 MET cc_start: 0.7466 (mtp) cc_final: 0.6901 (mtp) REVERT: A 870 VAL cc_start: 0.8926 (p) cc_final: 0.8709 (m) REVERT: B 189 GLU cc_start: 0.3994 (tm-30) cc_final: 0.3785 (tm-30) REVERT: B 211 GLU cc_start: 0.7073 (pp20) cc_final: 0.6818 (pp20) REVERT: B 271 LEU cc_start: 0.8565 (mp) cc_final: 0.7857 (tt) REVERT: B 299 MET cc_start: 0.8634 (mpp) cc_final: 0.8396 (mpp) REVERT: B 408 MET cc_start: 0.4726 (mmp) cc_final: 0.4334 (mmp) REVERT: B 581 ARG cc_start: 0.7089 (ptp-170) cc_final: 0.6815 (ttm170) REVERT: B 584 MET cc_start: 0.7442 (mtp) cc_final: 0.6893 (mtp) REVERT: B 659 LEU cc_start: 0.8031 (tt) cc_final: 0.7432 (mt) REVERT: B 680 THR cc_start: 0.8650 (p) cc_final: 0.8418 (p) REVERT: B 776 MET cc_start: 0.8554 (mmm) cc_final: 0.8330 (mmm) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0989 time to fit residues: 34.0680 Evaluate side-chains 146 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 0.9980 chunk 163 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 29 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101156 restraints weight = 28005.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103688 restraints weight = 16940.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105285 restraints weight = 11891.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106598 restraints weight = 9402.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107092 restraints weight = 7922.930| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2727 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= 0.167 Angle : 0.688 7.022 18578 Z= 0.343 Chirality : 0.047 0.262 1990 Planarity : 0.005 0.041 2454 Dihedral : 6.693 114.099 1864 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.30 (0.20), residues: 1684 helix: -0.33 (0.20), residues: 674 sheet: -2.20 (0.33), residues: 204 loop : -2.41 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 900 TYR 0.021 0.002 TYR B 849 PHE 0.031 0.002 PHE A 449 TRP 0.008 0.001 TRP B 871 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (13722) covalent geometry : angle 0.68840 / 0.34 (18578) hydrogen bonds : bond 0.03647 / 2.38 ( 486) hydrogen bonds : angle 5.05966 / 3.57 ( 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 228 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.519 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: 0.7158 (pp20) cc_final: 0.6872 (pp20) REVERT: A 299 MET cc_start: 0.8662 (mpp) cc_final: 0.8337 (mpp) REVERT: A 408 MET cc_start: 0.4651 (mmp) cc_final: 0.4085 (mmp) REVERT: A 584 MET cc_start: 0.7502 (mtp) cc_final: 0.7294 (mtp) REVERT: A 675 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 871 TRP cc_start: 0.8948 (t60) cc_final: 0.8460 (t60) REVERT: A 875 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 189 GLU cc_start: 0.3816 (tm-30) cc_final: 0.3395 (tm-30) REVERT: B 211 GLU cc_start: 0.7163 (pp20) cc_final: 0.6856 (pp20) REVERT: B 299 MET cc_start: 0.8597 (mpp) cc_final: 0.8324 (mpp) REVERT: B 408 MET cc_start: 0.4620 (mmp) cc_final: 0.4099 (mmp) REVERT: B 584 MET cc_start: 0.7484 (mtp) cc_final: 0.7240 (mtp) REVERT: B 680 THR cc_start: 0.8629 (p) cc_final: 0.8382 (p) REVERT: B 875 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8007 (mt-10) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1080 time to fit residues: 37.3349 Evaluate side-chains 163 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 9.9990 chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 0.0050 chunk 131 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 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 = 0.3673 r_free = 0.3673 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104744 restraints weight = 27457.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107035 restraints weight = 17797.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108401 restraints weight = 12975.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109619 restraints weight = 10562.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110252 restraints weight = 9043.121| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13722 Z= 0.125 Angle : 0.663 7.310 18578 Z= 0.326 Chirality : 0.045 0.192 1990 Planarity : 0.004 0.039 2454 Dihedral : 6.517 113.170 1864 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: -2.08 (0.20), residues: 1684 helix: -0.12 (0.20), residues: 668 sheet: -2.20 (0.32), residues: 224 loop : -2.24 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 900 TYR 0.016 0.002 TYR A 883 PHE 0.032 0.002 PHE B 449 TRP 0.014 0.001 TRP B 871 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13722) covalent geometry : angle 0.66272 / 0.33 (18578) hydrogen bonds : bond 0.03445 / 2.25 ( 486) hydrogen bonds : angle 4.89944 / 3.46 ( 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 248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.505 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: 0.5534 (tt0) cc_final: 0.4755 (tm-30) REVERT: A 211 GLU cc_start: 0.7067 (pp20) cc_final: 0.6823 (pp20) REVERT: A 271 LEU cc_start: 0.8554 (mp) cc_final: 0.7807 (tt) REVERT: A 299 MET cc_start: 0.8567 (mpp) cc_final: 0.8252 (mpp) REVERT: A 408 MET cc_start: 0.4430 (mmp) cc_final: 0.3979 (mmp) REVERT: A 675 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 871 TRP cc_start: 0.8888 (t60) cc_final: 0.8326 (t60) REVERT: B 173 MET cc_start: 0.7000 (tpp) cc_final: 0.5228 (tpp) REVERT: B 189 GLU cc_start: 0.3765 (tm-30) cc_final: 0.3381 (mm-30) REVERT: B 211 GLU cc_start: 0.7066 (pp20) cc_final: 0.6748 (pp20) REVERT: B 271 LEU cc_start: 0.8533 (mp) cc_final: 0.7784 (tt) REVERT: B 299 MET cc_start: 0.8510 (mpp) cc_final: 0.8265 (mpp) REVERT: B 408 MET cc_start: 0.4456 (mmp) cc_final: 0.3986 (mmp) REVERT: B 680 THR cc_start: 0.8594 (p) cc_final: 0.8343 (p) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.0996 time to fit residues: 38.5292 Evaluate side-chains 162 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 chunk 121 optimal weight: 0.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 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 = 0.3673 r_free = 0.3673 target = 0.124054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105897 restraints weight = 27817.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106653 restraints weight = 20288.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108738 restraints weight = 16317.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108899 restraints weight = 12832.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109047 restraints weight = 11718.382| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13722 Z= 0.137 Angle : 0.674 8.367 18578 Z= 0.331 Chirality : 0.046 0.177 1990 Planarity : 0.004 0.044 2454 Dihedral : 6.455 113.860 1864 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % 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: -2.04 (0.20), residues: 1684 helix: -0.10 (0.20), residues: 668 sheet: -2.18 (0.31), residues: 224 loop : -2.21 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 581 TYR 0.019 0.002 TYR B 849 PHE 0.022 0.002 PHE B 869 TRP 0.009 0.001 TRP B 871 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13722) covalent geometry : angle 0.67414 / 0.33 (18578) hydrogen bonds : bond 0.03419 / 2.22 ( 486) hydrogen bonds : angle 4.86378 / 3.45 ( 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 228 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.413 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: 0.5270 (tt0) cc_final: 0.4609 (tm-30) REVERT: A 211 GLU cc_start: 0.7095 (pp20) cc_final: 0.6824 (pp20) REVERT: A 408 MET cc_start: 0.4447 (mmp) cc_final: 0.3971 (mmp) REVERT: A 675 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 857 GLN cc_start: 0.8619 (pp30) cc_final: 0.7799 (tm-30) REVERT: A 871 TRP cc_start: 0.8914 (t60) cc_final: 0.8597 (t60) REVERT: B 189 GLU cc_start: 0.3565 (tm-30) cc_final: 0.3148 (mm-30) REVERT: B 211 GLU cc_start: 0.7073 (pp20) cc_final: 0.6736 (pp20) REVERT: B 408 MET cc_start: 0.4437 (mmp) cc_final: 0.3955 (mmp) REVERT: B 492 GLU cc_start: 0.8397 (tt0) cc_final: 0.8077 (tt0) REVERT: B 680 THR cc_start: 0.8520 (p) cc_final: 0.8309 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.0958 time to fit residues: 34.3302 Evaluate side-chains 172 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 460 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 857 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 = 0.3704 r_free = 0.3704 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107361 restraints weight = 27614.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109528 restraints weight = 17490.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111225 restraints weight = 12841.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112409 restraints weight = 10278.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113129 restraints weight = 8732.410| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13722 Z= 0.119 Angle : 0.655 8.753 18578 Z= 0.323 Chirality : 0.045 0.158 1990 Planarity : 0.004 0.046 2454 Dihedral : 6.323 112.039 1864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % 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: -1.99 (0.20), residues: 1684 helix: -0.07 (0.20), residues: 680 sheet: -2.07 (0.32), residues: 220 loop : -2.24 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.018 0.002 TYR B 849 PHE 0.018 0.002 PHE B 869 TRP 0.012 0.001 TRP A 871 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13722) covalent geometry : angle 0.65515 / 0.32 (18578) hydrogen bonds : bond 0.03389 / 2.20 ( 486) hydrogen bonds : angle 4.74488 / 3.37 ( 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 238 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.491 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: 0.5100 (tt0) cc_final: 0.4558 (tm-30) REVERT: A 211 GLU cc_start: 0.7143 (pp20) cc_final: 0.6665 (pp20) REVERT: A 271 LEU cc_start: 0.8475 (mp) cc_final: 0.7712 (tt) REVERT: A 408 MET cc_start: 0.4353 (mmp) cc_final: 0.3932 (mmp) REVERT: A 584 MET cc_start: 0.7333 (mtp) cc_final: 0.6589 (mtp) REVERT: A 675 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 871 TRP cc_start: 0.8869 (t60) cc_final: 0.8367 (t60) REVERT: B 271 LEU cc_start: 0.8459 (mp) cc_final: 0.7741 (tt) REVERT: B 408 MET cc_start: 0.4391 (mmp) cc_final: 0.3868 (mmp) REVERT: B 492 GLU cc_start: 0.8243 (tt0) cc_final: 0.7948 (tt0) REVERT: B 584 MET cc_start: 0.7376 (mtp) cc_final: 0.6588 (mtp) REVERT: B 680 THR cc_start: 0.8509 (p) cc_final: 0.8277 (p) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1020 time to fit residues: 37.2999 Evaluate side-chains 172 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 6.9990 chunk 144 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 174 HIS ** 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 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** 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 = 0.3716 r_free = 0.3716 target = 0.127230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.107878 restraints weight = 27934.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110443 restraints weight = 17266.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112184 restraints weight = 12194.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113310 restraints weight = 9573.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113949 restraints weight = 8125.623| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13722 Z= 0.119 Angle : 0.665 9.379 18578 Z= 0.324 Chirality : 0.045 0.159 1990 Planarity : 0.004 0.039 2454 Dihedral : 6.231 110.261 1864 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.08 % 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: -1.93 (0.20), residues: 1684 helix: -0.03 (0.20), residues: 684 sheet: -1.97 (0.31), residues: 232 loop : -2.21 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 710 TYR 0.017 0.002 TYR B 849 PHE 0.019 0.001 PHE A 624 TRP 0.015 0.001 TRP B 523 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13722) covalent geometry : angle 0.66460 / 0.32 (18578) hydrogen bonds : bond 0.03321 / 2.16 ( 486) hydrogen bonds : angle 4.74195 / 3.36 ( 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 222 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.346 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: 0.4948 (tt0) cc_final: 0.4494 (tm-30) REVERT: A 408 MET cc_start: 0.4411 (mmp) cc_final: 0.3883 (mmp) REVERT: A 419 ILE cc_start: 0.7998 (mm) cc_final: 0.7692 (mm) REVERT: A 584 MET cc_start: 0.7436 (mtp) cc_final: 0.6767 (mtp) REVERT: A 675 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 871 TRP cc_start: 0.8852 (t60) cc_final: 0.8426 (t60) REVERT: A 875 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 408 MET cc_start: 0.4322 (mmp) cc_final: 0.3824 (mmp) REVERT: B 492 GLU cc_start: 0.8263 (tt0) cc_final: 0.7980 (tt0) REVERT: B 584 MET cc_start: 0.7410 (mtp) cc_final: 0.6756 (mtp) REVERT: B 680 THR cc_start: 0.8503 (p) cc_final: 0.8259 (p) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.1008 time to fit residues: 34.5062 Evaluate side-chains 166 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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: 0.0470 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 108 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 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 = 0.3696 r_free = 0.3696 target = 0.125523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106377 restraints weight = 27730.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108819 restraints weight = 17458.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110322 restraints weight = 12516.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111522 restraints weight = 10049.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112195 restraints weight = 8551.119| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13722 Z= 0.145 Angle : 0.689 11.089 18578 Z= 0.336 Chirality : 0.046 0.164 1990 Planarity : 0.006 0.188 2454 Dihedral : 6.304 110.351 1864 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.14 % Allowed : 0.07 % 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: -1.88 (0.20), residues: 1684 helix: 0.00 (0.20), residues: 684 sheet: -1.93 (0.31), residues: 232 loop : -2.18 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 763 TYR 0.018 0.002 TYR B 849 PHE 0.028 0.002 PHE B 101 TRP 0.010 0.001 TRP A 871 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13722) covalent geometry : angle 0.68921 / 0.34 (18578) hydrogen bonds : bond 0.03410 / 2.19 ( 486) hydrogen bonds : angle 4.77573 / 3.38 ( 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 215 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.579 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 271 LEU cc_start: 0.8455 (mp) cc_final: 0.7671 (tt) REVERT: A 324 GLU cc_start: 0.8207 (tp30) cc_final: 0.7884 (tp30) REVERT: A 408 MET cc_start: 0.4392 (mmp) cc_final: 0.3890 (mmp) REVERT: A 584 MET cc_start: 0.7519 (mtp) cc_final: 0.6879 (mtp) REVERT: A 675 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 762 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.7942 (mtp180) REVERT: A 871 TRP cc_start: 0.8910 (t60) cc_final: 0.8485 (t60) REVERT: B 271 LEU cc_start: 0.8424 (mp) cc_final: 0.7688 (tt) REVERT: B 408 MET cc_start: 0.4491 (mmp) cc_final: 0.3940 (mmp) REVERT: B 492 GLU cc_start: 0.8313 (tt0) cc_final: 0.8007 (tt0) REVERT: B 584 MET cc_start: 0.7532 (mtp) cc_final: 0.6866 (mtp) REVERT: B 680 THR cc_start: 0.8591 (p) cc_final: 0.8347 (p) REVERT: B 762 ARG cc_start: 0.8512 (mtp-110) cc_final: 0.8099 (mtp180) REVERT: B 875 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7523 (mt-10) outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.1030 time to fit residues: 33.8026 Evaluate side-chains 162 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 0.5980 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** B 108 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105611 restraints weight = 28249.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107955 restraints weight = 17863.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109588 restraints weight = 12943.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110743 restraints weight = 10348.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111204 restraints weight = 8812.848| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3639 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= 0.144 Angle : 0.685 9.677 18578 Z= 0.335 Chirality : 0.046 0.168 1990 Planarity : 0.004 0.042 2454 Dihedral : 6.246 108.928 1864 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.14 % Allowed : 0.21 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.83 (0.20), residues: 1684 helix: 0.04 (0.20), residues: 684 sheet: -1.94 (0.33), residues: 220 loop : -2.14 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 767 TYR 0.019 0.002 TYR B 849 PHE 0.020 0.002 PHE A 624 TRP 0.013 0.001 TRP A 523 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13722) covalent geometry : angle 0.68528 / 0.33 (18578) hydrogen bonds : bond 0.03369 / 2.18 ( 486) hydrogen bonds : angle 4.72282 / 3.34 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1922.10 seconds wall clock time: 34 minutes 19.65 seconds (2059.65 seconds total)