Starting phenix.real_space_refine on Fri Sep 11 20:04:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.cif" model { file = "/net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7waz_32390/09_2026/7waz_32390.cif" } resolution = 3.4 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= -0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 196 atoms to isotropic. 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 157 5.49 5 S 28 5.16 5 C 6424 2.51 5 N 1966 2.21 5 O 2459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 11034 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7729 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 36, 'TRANS': 915} Chain breaks: 3 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNAv2': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 16, 'rna3p': 98} Chain breaks: 1 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Time building chain proxies: 2.55, per 1000 atoms: 0.23 Number of scatterers: 11034 At special positions: 0 Unit cell: (101.52, 144.76, 120.32, 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 28 16.00 P 157 15.00 O 2459 8.00 N 1966 7.00 C 6424 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: 1.01 Conformation dependent library (CDL) restraints added in 452.4 milliseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.1% alpha, 17.9% beta 42 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.540A pdb=" N SER A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.611A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.694A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 222 through 272 removed outlier: 4.280A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 343 through 368 removed outlier: 4.688A pdb=" N GLU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.794A pdb=" N GLU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 442 removed outlier: 3.756A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 472 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.541A pdb=" N ARG A 774 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 790 removed outlier: 3.924A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 920 through 936 removed outlier: 3.506A pdb=" N GLN A 924 " --> pdb=" O HIS A 920 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 954 through 973 removed outlier: 4.351A pdb=" N PHE A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 545 removed outlier: 4.375A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 532 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 530 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 529 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 586 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 34 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 542 through 545 removed outlier: 4.375A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 532 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 530 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 529 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 586 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 34 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 619 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.121A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 144 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 152 " --> pdb=" O GLN A 144 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.851A pdb=" N GLN A 135 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 693 removed outlier: 3.874A pdb=" N LEU A 692 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 668 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 754 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE A 658 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N ARG A 660 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER A 799 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 753 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 830 through 832 removed outlier: 3.854A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.821A pdb=" N ASN A 855 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 860 " --> pdb=" O ASN A 855 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2403 1.33 - 1.45: 3223 1.45 - 1.57: 5600 1.57 - 1.69: 310 1.69 - 1.81: 41 Bond restraints: 11577 Sorted by residual: bond pdb=" C1' DT C 6 " pdb=" N1 DT C 6 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" C3' DA C 10 " pdb=" C2' DA C 10 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DT C 6 " pdb=" C2' DT C 6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA B 24 " pdb=" C2' DA B 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C1' DT B 3 " pdb=" N1 DT B 3 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 ... (remaining 11572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 15817 2.20 - 4.41: 480 4.41 - 6.61: 34 6.61 - 8.81: 1 8.81 - 11.01: 1 Bond angle restraints: 16333 Sorted by residual: angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT B 3 " pdb=" C4 DT B 3 " pdb=" O4 DT B 3 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT B 26 " pdb=" C4 DT B 26 " pdb=" O4 DT B 26 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 16328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6154 35.75 - 71.50: 483 71.50 - 107.25: 16 107.25 - 143.00: 1 143.00 - 178.75: 3 Dihedral angle restraints: 6657 sinusoidal: 3878 harmonic: 2779 Sorted by residual: dihedral pdb=" C4' C D 111 " pdb=" C3' C D 111 " pdb=" C2' C D 111 " pdb=" C1' C D 111 " ideal model delta sinusoidal sigma weight residual 36.34 -37.41 73.75 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A D 15 " pdb=" C3' A D 15 " pdb=" C2' A D 15 " pdb=" C1' A D 15 " ideal model delta sinusoidal sigma weight residual 36.34 -37.27 73.61 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' A D 42 " pdb=" C3' A D 42 " pdb=" C2' A D 42 " pdb=" C1' A D 42 " ideal model delta sinusoidal sigma weight residual 36.35 -37.14 73.49 1 3.10e+00 1.04e-01 7.15e+02 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1566 0.064 - 0.127: 158 0.127 - 0.191: 9 0.191 - 0.255: 117 0.255 - 0.319: 30 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C2' C D 111 " pdb=" C3' C D 111 " pdb=" O2' C D 111 " pdb=" C1' C D 111 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1' A D 109 " pdb=" O4' A D 109 " pdb=" C2' A D 109 " pdb=" N9 A D 109 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C2' A D 114 " pdb=" C3' A D 114 " pdb=" O2' A D 114 " pdb=" C1' A D 114 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1877 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 109 " 0.029 2.00e-02 2.50e+03 1.44e-02 5.69e+00 pdb=" N9 A D 109 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A D 109 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A D 109 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A D 109 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 109 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 109 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A D 109 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 109 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 109 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 109 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 110 " 0.032 2.00e-02 2.50e+03 1.37e-02 5.67e+00 pdb=" N9 G D 110 " -0.033 2.00e-02 2.50e+03 pdb=" C8 G D 110 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G D 110 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G D 110 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G D 110 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G D 110 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G D 110 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G D 110 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G D 110 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 110 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G D 110 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 96 " 0.025 2.00e-02 2.50e+03 1.07e-02 3.18e+00 pdb=" N9 A D 96 " -0.021 2.00e-02 2.50e+03 pdb=" C8 A D 96 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A D 96 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 96 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A D 96 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A D 96 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A D 96 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 96 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 96 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 96 " -0.004 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 544 2.71 - 3.26: 10465 3.26 - 3.80: 19316 3.80 - 4.35: 22749 4.35 - 4.90: 35295 Nonbonded interactions: 88369 Sorted by model distance: nonbonded pdb=" OG SER A 171 " pdb=" OG SER A 185 " model vdw 2.160 3.040 nonbonded pdb=" O2' A D 114 " pdb=" O5' A D 115 " model vdw 2.166 3.040 nonbonded pdb=" O2' A D 109 " pdb=" O4' G D 110 " model vdw 2.167 3.040 nonbonded pdb=" O THR A 946 " pdb=" OG1 THR A 949 " model vdw 2.234 3.040 nonbonded pdb=" NE1 TRP A 836 " pdb=" OD1 ASP A 871 " model vdw 2.243 3.120 ... (remaining 88364 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 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 : 0.003 0.051 11577 Z= 0.266 Angle : 0.756 11.013 16333 Z= 0.447 Chirality : 0.078 0.319 1880 Planarity : 0.003 0.035 1513 Dihedral : 19.878 178.745 4861 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.03 % Favored : 95.76 % Rotamer: Outliers : 5.53 % Allowed : 6.73 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.74 (0.28), residues: 944 helix: 2.27 (0.26), residues: 420 sheet: -1.43 (0.43), residues: 135 loop : -0.77 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.014 0.001 TYR A 85 PHE 0.007 0.001 PHE A 240 TRP 0.009 0.001 TRP A 344 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.27 (11577) covalent geometry : angle 0.75580 / 0.45 (16333) hydrogen bonds : bond 0.14887 / 10.68 ( 494) hydrogen bonds : angle 5.96334 / 4.19 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7218 (p0) REVERT: A 142 LEU cc_start: 0.5693 (tp) cc_final: 0.5411 (tp) REVERT: A 485 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4690 (pttp) REVERT: A 517 PHE cc_start: 0.4740 (OUTLIER) cc_final: 0.4171 (t80) REVERT: A 551 PHE cc_start: 0.6445 (m-80) cc_final: 0.6183 (m-80) REVERT: A 591 ARG cc_start: 0.6476 (ttt90) cc_final: 0.6193 (ttt180) REVERT: A 601 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 604 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.4159 (mp) REVERT: A 621 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7152 (tt) REVERT: A 660 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.4984 (mtt-85) outliers start: 46 outliers final: 10 residues processed: 172 average time/residue: 0.1327 time to fit residues: 30.6473 Evaluate side-chains 89 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 512 GLN A 534 ASN A 924 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.177697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.142710 restraints weight = 33571.632| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 4.46 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11577 Z= 0.225 Angle : 1.249 23.600 16333 Z= 0.523 Chirality : 0.115 1.989 1880 Planarity : 0.005 0.045 1513 Dihedral : 20.928 179.250 2907 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.87 % Favored : 94.81 % Rotamer: Outliers : 3.12 % Allowed : 11.54 % Favored : 85.34 % 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: 0.37 (0.28), residues: 944 helix: 1.71 (0.25), residues: 432 sheet: -1.29 (0.45), residues: 134 loop : -0.86 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 478 TYR 0.033 0.002 TYR A 966 PHE 0.032 0.002 PHE A 935 TRP 0.015 0.002 TRP A 962 HIS 0.007 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (11577) covalent geometry : angle 1.24875 / 0.52 (16333) hydrogen bonds : bond 0.06294 / 4.60 ( 494) hydrogen bonds : angle 5.07302 / 3.59 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.6238 (mtm) cc_final: 0.5674 (mtm) REVERT: A 517 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.4378 (t80) REVERT: A 551 PHE cc_start: 0.7397 (m-80) cc_final: 0.6954 (m-80) REVERT: A 621 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 728 LYS cc_start: 0.9127 (tttt) cc_final: 0.8818 (tppt) REVERT: A 771 MET cc_start: 0.1420 (tmm) cc_final: -0.1208 (mmt) REVERT: A 797 TYR cc_start: 0.6175 (m-10) cc_final: 0.5974 (m-10) REVERT: A 945 GLN cc_start: 0.6585 (mt0) cc_final: 0.6332 (mt0) outliers start: 26 outliers final: 19 residues processed: 111 average time/residue: 0.1196 time to fit residues: 18.0485 Evaluate side-chains 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.173848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.137640 restraints weight = 33745.342| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 4.25 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11577 Z= 0.248 Angle : 1.051 14.173 16333 Z= 0.462 Chirality : 0.085 1.096 1880 Planarity : 0.005 0.045 1513 Dihedral : 21.223 174.900 2895 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.25 % Favored : 93.64 % Rotamer: Outliers : 4.69 % Allowed : 11.42 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.28), residues: 944 helix: 1.42 (0.25), residues: 431 sheet: -1.47 (0.45), residues: 135 loop : -1.14 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 6 TYR 0.019 0.002 TYR A 776 PHE 0.050 0.003 PHE A 935 TRP 0.018 0.002 TRP A 782 HIS 0.005 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.25 (11577) covalent geometry : angle 1.05075 / 0.46 (16333) hydrogen bonds : bond 0.06675 / 4.81 ( 494) hydrogen bonds : angle 5.01988 / 3.55 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6856 (tpp) cc_final: 0.6567 (tpp) REVERT: A 347 MET cc_start: 0.5878 (mtm) cc_final: 0.5666 (mtm) REVERT: A 517 PHE cc_start: 0.4777 (OUTLIER) cc_final: 0.4334 (t80) REVERT: A 529 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3684 (mm) REVERT: A 551 PHE cc_start: 0.7515 (m-80) cc_final: 0.7027 (m-80) REVERT: A 595 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 621 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7607 (tt) REVERT: A 728 LYS cc_start: 0.9113 (tttt) cc_final: 0.8701 (ptmm) REVERT: A 797 TYR cc_start: 0.6316 (m-10) cc_final: 0.6106 (m-10) REVERT: A 945 GLN cc_start: 0.6676 (mt0) cc_final: 0.6387 (mt0) outliers start: 39 outliers final: 27 residues processed: 106 average time/residue: 0.1193 time to fit residues: 17.5120 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 512 GLN A 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.174523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.138002 restraints weight = 33352.012| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 4.30 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11577 Z= 0.195 Angle : 0.963 12.285 16333 Z= 0.422 Chirality : 0.075 0.852 1880 Planarity : 0.005 0.042 1513 Dihedral : 21.101 174.230 2895 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.51 % Favored : 94.39 % Rotamer: Outliers : 4.09 % Allowed : 14.30 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.28), residues: 944 helix: 1.53 (0.25), residues: 428 sheet: -1.56 (0.44), residues: 135 loop : -1.11 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 627 TYR 0.021 0.001 TYR A 294 PHE 0.039 0.002 PHE A 965 TRP 0.016 0.002 TRP A 422 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (11577) covalent geometry : angle 0.96260 / 0.42 (16333) hydrogen bonds : bond 0.06024 / 4.26 ( 494) hydrogen bonds : angle 4.88380 / 3.47 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.6667 (p0) REVERT: A 40 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6563 (p0) REVERT: A 347 MET cc_start: 0.5939 (mtm) cc_final: 0.5735 (mtm) REVERT: A 412 GLU cc_start: 0.1792 (OUTLIER) cc_final: 0.1404 (mt-10) REVERT: A 517 PHE cc_start: 0.4748 (OUTLIER) cc_final: 0.4274 (t80) REVERT: A 551 PHE cc_start: 0.7504 (m-80) cc_final: 0.6985 (m-80) REVERT: A 595 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 621 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7603 (tt) REVERT: A 728 LYS cc_start: 0.9161 (tttt) cc_final: 0.8728 (ptmm) REVERT: A 729 ASN cc_start: 0.8111 (m110) cc_final: 0.7641 (m-40) outliers start: 34 outliers final: 23 residues processed: 99 average time/residue: 0.1119 time to fit residues: 15.4872 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 528 ASN A 914 ASN A 920 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.171786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.134946 restraints weight = 33353.144| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 4.17 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11577 Z= 0.238 Angle : 0.991 13.662 16333 Z= 0.439 Chirality : 0.073 0.844 1880 Planarity : 0.005 0.052 1513 Dihedral : 21.051 173.354 2893 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.10 % Favored : 92.80 % Rotamer: Outliers : 4.81 % Allowed : 13.70 % Favored : 81.49 % 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: -0.16 (0.27), residues: 944 helix: 1.50 (0.25), residues: 417 sheet: -1.70 (0.44), residues: 135 loop : -1.25 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 721 TYR 0.021 0.002 TYR A 140 PHE 0.035 0.002 PHE A 935 TRP 0.039 0.003 TRP A 344 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.24 (11577) covalent geometry : angle 0.99140 / 0.44 (16333) hydrogen bonds : bond 0.06644 / 4.68 ( 494) hydrogen bonds : angle 5.01562 / 3.57 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6666 (p0) REVERT: A 347 MET cc_start: 0.5918 (mtm) cc_final: 0.5695 (mtm) REVERT: A 412 GLU cc_start: 0.1799 (OUTLIER) cc_final: 0.1415 (mt-10) REVERT: A 517 PHE cc_start: 0.4843 (OUTLIER) cc_final: 0.4204 (t80) REVERT: A 551 PHE cc_start: 0.7553 (m-80) cc_final: 0.6997 (m-80) REVERT: A 595 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 621 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7644 (tt) REVERT: A 628 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: A 728 LYS cc_start: 0.9139 (tttt) cc_final: 0.8711 (ptmm) REVERT: A 729 ASN cc_start: 0.8024 (m110) cc_final: 0.7545 (m110) REVERT: A 775 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6513 (pp30) REVERT: A 962 TRP cc_start: 0.1298 (OUTLIER) cc_final: -0.0159 (t-100) outliers start: 40 outliers final: 23 residues processed: 99 average time/residue: 0.1047 time to fit residues: 14.7194 Evaluate side-chains 92 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 528 ASN A 914 ASN A 924 GLN A 928 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.174192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.142242 restraints weight = 33296.237| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 4.25 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11577 Z= 0.164 Angle : 0.906 12.702 16333 Z= 0.399 Chirality : 0.067 0.690 1880 Planarity : 0.004 0.053 1513 Dihedral : 20.904 173.848 2890 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.72 % Favored : 94.17 % Rotamer: Outliers : 3.12 % Allowed : 16.59 % Favored : 80.29 % 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: 0.14 (0.28), residues: 944 helix: 1.74 (0.25), residues: 416 sheet: -1.46 (0.45), residues: 126 loop : -1.14 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.017 0.001 TYR A 140 PHE 0.068 0.002 PHE A 965 TRP 0.019 0.002 TRP A 344 HIS 0.007 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (11577) covalent geometry : angle 0.90636 / 0.40 (16333) hydrogen bonds : bond 0.05749 / 4.07 ( 494) hydrogen bonds : angle 4.71236 / 3.37 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 PHE cc_start: 0.4733 (OUTLIER) cc_final: 0.4089 (t80) REVERT: A 551 PHE cc_start: 0.7391 (m-80) cc_final: 0.6949 (m-80) REVERT: A 621 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7638 (tt) REVERT: A 728 LYS cc_start: 0.9056 (tttt) cc_final: 0.8686 (ptmm) REVERT: A 729 ASN cc_start: 0.8044 (m110) cc_final: 0.7563 (m110) REVERT: A 775 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6275 (pp30) outliers start: 26 outliers final: 19 residues processed: 95 average time/residue: 0.1102 time to fit residues: 15.0860 Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 512 GLN A 914 ASN A 947 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.172860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.136088 restraints weight = 33127.764| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 4.36 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11577 Z= 0.186 Angle : 0.914 12.708 16333 Z= 0.402 Chirality : 0.066 0.659 1880 Planarity : 0.004 0.055 1513 Dihedral : 20.828 173.957 2888 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 3.49 % Allowed : 16.95 % Favored : 79.57 % 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: 0.07 (0.27), residues: 944 helix: 1.68 (0.25), residues: 417 sheet: -1.65 (0.43), residues: 133 loop : -1.10 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.016 0.001 TYR A 140 PHE 0.019 0.002 PHE A 935 TRP 0.021 0.002 TRP A 422 HIS 0.014 0.002 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (11577) covalent geometry : angle 0.91384 / 0.40 (16333) hydrogen bonds : bond 0.06046 / 4.27 ( 494) hydrogen bonds : angle 4.71554 / 3.37 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 PHE cc_start: 0.7459 (m-80) cc_final: 0.6923 (m-80) REVERT: A 621 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7708 (tt) REVERT: A 628 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: A 728 LYS cc_start: 0.9143 (tttt) cc_final: 0.8739 (ptmm) REVERT: A 729 ASN cc_start: 0.8123 (m110) cc_final: 0.7633 (m110) REVERT: A 775 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6393 (pp30) outliers start: 29 outliers final: 24 residues processed: 88 average time/residue: 0.1170 time to fit residues: 14.3878 Evaluate side-chains 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 44 optimal weight: 40.0000 chunk 5 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 512 GLN A 528 ASN A 914 ASN A 920 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.171060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.138737 restraints weight = 33392.744| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 4.71 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11577 Z= 0.242 Angle : 0.980 17.033 16333 Z= 0.432 Chirality : 0.068 0.761 1880 Planarity : 0.005 0.056 1513 Dihedral : 20.867 174.129 2888 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.31 % Favored : 92.58 % Rotamer: Outliers : 3.85 % Allowed : 17.19 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 944 helix: 1.34 (0.25), residues: 417 sheet: -1.81 (0.42), residues: 133 loop : -1.26 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 660 TYR 0.038 0.002 TYR A 776 PHE 0.062 0.002 PHE A 965 TRP 0.024 0.002 TRP A 782 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 (11577) covalent geometry : angle 0.97953 / 0.43 (16333) hydrogen bonds : bond 0.06576 / 4.56 ( 494) hydrogen bonds : angle 4.94899 / 3.54 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6680 (p0) REVERT: A 412 GLU cc_start: 0.1875 (OUTLIER) cc_final: 0.1479 (mt-10) REVERT: A 621 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 628 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: A 728 LYS cc_start: 0.8955 (tttt) cc_final: 0.8709 (ptmt) REVERT: A 729 ASN cc_start: 0.8058 (m110) cc_final: 0.7684 (m110) outliers start: 32 outliers final: 24 residues processed: 91 average time/residue: 0.0968 time to fit residues: 12.9860 Evaluate side-chains 91 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 52 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 528 ASN A 920 HIS A 947 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.174664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.136703 restraints weight = 32858.144| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 4.25 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11577 Z= 0.148 Angle : 0.895 17.424 16333 Z= 0.397 Chirality : 0.063 0.569 1880 Planarity : 0.004 0.056 1513 Dihedral : 20.854 174.435 2886 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 2.28 % Allowed : 19.35 % Favored : 78.37 % 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: 0.10 (0.27), residues: 944 helix: 1.65 (0.25), residues: 418 sheet: -1.51 (0.46), residues: 120 loop : -1.11 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 774 TYR 0.017 0.001 TYR A 776 PHE 0.017 0.001 PHE A 755 TRP 0.022 0.002 TRP A 422 HIS 0.008 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (11577) covalent geometry : angle 0.89497 / 0.40 (16333) hydrogen bonds : bond 0.05554 / 3.94 ( 494) hydrogen bonds : angle 4.56678 / 3.28 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8520 (tt0) cc_final: 0.8130 (mt0) REVERT: A 551 PHE cc_start: 0.7645 (m-80) cc_final: 0.7055 (m-80) REVERT: A 621 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7777 (tt) REVERT: A 728 LYS cc_start: 0.9154 (tttt) cc_final: 0.8789 (ptmm) REVERT: A 729 ASN cc_start: 0.8202 (m110) cc_final: 0.7430 (m110) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.1060 time to fit residues: 12.5819 Evaluate side-chains 79 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN A 512 GLN A 914 ASN A 920 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.175117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.138883 restraints weight = 33218.915| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 4.26 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11577 Z= 0.141 Angle : 0.873 17.484 16333 Z= 0.387 Chirality : 0.061 0.524 1880 Planarity : 0.004 0.058 1513 Dihedral : 20.771 174.076 2886 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 2.04 % Allowed : 19.83 % Favored : 78.12 % 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: 0.26 (0.28), residues: 944 helix: 1.71 (0.25), residues: 417 sheet: -1.31 (0.47), residues: 120 loop : -0.97 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 703 TYR 0.019 0.001 TYR A 776 PHE 0.053 0.001 PHE A 965 TRP 0.025 0.002 TRP A 422 HIS 0.005 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (11577) covalent geometry : angle 0.87303 / 0.39 (16333) hydrogen bonds : bond 0.05420 / 3.86 ( 494) hydrogen bonds : angle 4.50950 / 3.28 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8408 (tt0) cc_final: 0.8042 (mt0) REVERT: A 240 PHE cc_start: 0.6476 (t80) cc_final: 0.6252 (t80) REVERT: A 551 PHE cc_start: 0.7567 (m-80) cc_final: 0.7006 (m-80) REVERT: A 571 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6315 (pp20) REVERT: A 621 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 728 LYS cc_start: 0.9056 (tttt) cc_final: 0.8747 (ptmm) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.1013 time to fit residues: 12.4355 Evaluate side-chains 79 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 107 optimal weight: 40.0000 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 914 ASN A 947 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.174174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.136757 restraints weight = 33788.084| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 4.40 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11577 Z= 0.154 Angle : 0.877 17.272 16333 Z= 0.388 Chirality : 0.060 0.525 1880 Planarity : 0.004 0.055 1513 Dihedral : 20.720 173.935 2884 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 1.92 % Allowed : 20.07 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.28), residues: 944 helix: 1.73 (0.25), residues: 417 sheet: -1.35 (0.45), residues: 133 loop : -0.95 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.021 0.001 TYR A 776 PHE 0.040 0.002 PHE A 965 TRP 0.025 0.002 TRP A 422 HIS 0.004 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (11577) covalent geometry : angle 0.87667 / 0.39 (16333) hydrogen bonds : bond 0.05515 / 3.89 ( 494) hydrogen bonds : angle 4.47780 / 3.25 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.51 seconds wall clock time: 43 minutes 26.23 seconds (2606.23 seconds total)