Starting phenix.real_space_refine on Fri Aug 7 12:13:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgl_36238/08_2026/8jgl_36238_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgl_36238/08_2026/8jgl_36238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2026/8jgl_36238_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2026/8jgl_36238_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2026/8jgl_36238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2026/8jgl_36238.map" } resolution = 3.14 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= 0.038 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 72 5.16 5 C 7060 2.51 5 N 1780 2.21 5 O 1880 1.98 5 H 10868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21662 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10807 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 28, 'TRANS': 655} Chain breaks: 4 Chain: "B" Number of atoms: 10807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10807 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 28, 'TRANS': 655} Chain breaks: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.86, per 1000 atoms: 0.18 Number of scatterers: 21662 At special positions: 0 Unit cell: (86.49, 121.83, 108.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 2 15.00 O 1880 8.00 N 1780 7.00 C 7060 6.00 H 10868 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 568 " distance=2.03 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: 2.12 Conformation dependent library (CDL) restraints added in 514.2 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 68.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.654A pdb=" N GLU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.501A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 4.112A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.656A pdb=" N THR A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 removed outlier: 4.287A pdb=" N LEU A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.658A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 4.145A pdb=" N HIS A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.504A pdb=" N THR A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 347 through 365 removed outlier: 4.150A pdb=" N ARG A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 420 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 443 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.549A pdb=" N LEU A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.910A pdb=" N ASP A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 518 removed outlier: 3.864A pdb=" N TYR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.555A pdb=" N GLU A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.679A pdb=" N TYR A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 601 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 653 through 658 removed outlier: 4.028A pdb=" N VAL A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 767 through 779 Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'B' and resid 92 through 112 removed outlier: 3.535A pdb=" N GLU B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 157 removed outlier: 4.408A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 4.111A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.602A pdb=" N THR B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.507A pdb=" N TYR B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 257' Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.638A pdb=" N LEU B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 298 removed outlier: 4.130A pdb=" N HIS B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.651A pdb=" N THR B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 347 through 365 removed outlier: 4.165A pdb=" N ARG B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 418 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.593A pdb=" N LEU B 450 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.880A pdb=" N ASP B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 518 removed outlier: 3.864A pdb=" N TYR B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.544A pdb=" N GLU B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.669A pdb=" N TYR B 574 " --> pdb=" O THR B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 601 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.501A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 691 through 695 removed outlier: 6.840A pdb=" N PHE A 692 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE A 706 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 694 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 763 removed outlier: 5.937A pdb=" N VAL A 762 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS A 783 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 794 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 785 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 691 through 695 removed outlier: 6.786A pdb=" N PHE B 692 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 706 " --> pdb=" O PHE B 692 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 694 " --> pdb=" O VAL B 704 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 787 removed outlier: 6.648A pdb=" N CYS B 783 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE B 794 " --> pdb=" O CYS B 783 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 785 " --> pdb=" O LEU B 792 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10844 1.03 - 1.23: 45 1.23 - 1.43: 4655 1.43 - 1.62: 6288 1.62 - 1.82: 110 Bond restraints: 21942 Sorted by residual: bond pdb=" C4 AMP B 901 " pdb=" C5 AMP B 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 AMP A 901 " pdb=" C5 AMP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 AMP B 901 " pdb=" C6 AMP B 901 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 AMP A 901 " pdb=" C6 AMP A 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ LYS A 245 " pdb=" HZ2 LYS A 245 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 21937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 39431 2.12 - 4.25: 200 4.25 - 6.37: 21 6.37 - 8.49: 12 8.49 - 10.62: 6 Bond angle restraints: 39670 Sorted by residual: angle pdb=" CA PRO B 767 " pdb=" N PRO B 767 " pdb=" CD PRO B 767 " ideal model delta sigma weight residual 112.00 101.38 10.62 1.40e+00 5.10e-01 5.75e+01 angle pdb=" CA PRO A 767 " pdb=" N PRO A 767 " pdb=" CD PRO A 767 " ideal model delta sigma weight residual 112.00 101.80 10.20 1.40e+00 5.10e-01 5.31e+01 angle pdb=" N GLU B 631 " pdb=" CA GLU B 631 " pdb=" C GLU B 631 " ideal model delta sigma weight residual 113.55 106.64 6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" N GLU A 631 " pdb=" CA GLU A 631 " pdb=" C GLU A 631 " ideal model delta sigma weight residual 113.12 106.59 6.53 1.25e+00 6.40e-01 2.73e+01 angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 111.40 117.30 -5.90 1.22e+00 6.72e-01 2.34e+01 ... (remaining 39665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9253 17.98 - 35.96: 713 35.96 - 53.94: 255 53.94 - 71.91: 66 71.91 - 89.89: 17 Dihedral angle restraints: 10304 sinusoidal: 5472 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ARG B 659 " pdb=" C ARG B 659 " pdb=" N PRO B 660 " pdb=" CA PRO B 660 " ideal model delta harmonic sigma weight residual 180.00 139.72 40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA ARG A 659 " pdb=" C ARG A 659 " pdb=" N PRO A 660 " pdb=" CA PRO A 660 " ideal model delta harmonic sigma weight residual 180.00 140.46 39.54 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CB CYS A 161 " pdb=" SG CYS A 161 " pdb=" SG CYS A 172 " pdb=" CB CYS A 172 " ideal model delta sinusoidal sigma weight residual -86.00 -117.90 31.90 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 10301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1304 0.040 - 0.079: 285 0.079 - 0.119: 96 0.119 - 0.159: 11 0.159 - 0.199: 2 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C3' AMP A 901 " pdb=" C2' AMP A 901 " pdb=" C4' AMP A 901 " pdb=" O3' AMP A 901 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA PRO B 767 " pdb=" N PRO B 767 " pdb=" C PRO B 767 " pdb=" CB PRO B 767 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C2' AMP A 901 " pdb=" C1' AMP A 901 " pdb=" C3' AMP A 901 " pdb=" O2' AMP A 901 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1695 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 766 " 0.071 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B 767 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 767 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 767 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 766 " -0.070 5.00e-02 4.00e+02 9.86e-02 1.56e+01 pdb=" N PRO A 767 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 767 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 767 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 659 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO B 660 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 660 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 660 " 0.039 5.00e-02 4.00e+02 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1227 2.19 - 2.79: 44475 2.79 - 3.39: 62133 3.39 - 4.00: 78625 4.00 - 4.60: 123848 Nonbonded interactions: 310308 Sorted by model distance: nonbonded pdb=" O PHE B 443 " pdb="HH11 ARG B 449 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP A 86 " pdb=" H ASP A 87 " model vdw 1.591 2.450 nonbonded pdb=" O ALA B 150 " pdb=" HG1 THR B 154 " model vdw 1.606 2.450 nonbonded pdb=" O ALA A 150 " pdb=" HG1 THR A 154 " model vdw 1.613 2.450 nonbonded pdb=" O ILE A 264 " pdb=" HG1 THR A 268 " model vdw 1.617 2.450 ... (remaining 310303 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' selection = chain 'B' } 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: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.940 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.004 0.148 11080 Z= 0.216 Angle : 0.623 10.618 15050 Z= 0.346 Chirality : 0.039 0.199 1698 Planarity : 0.005 0.100 1844 Dihedral : 14.099 89.892 3916 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 0.40 (0.22), residues: 1348 helix: 1.08 (0.17), residues: 832 sheet: -0.65 (0.79), residues: 42 loop : -1.06 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 416 TYR 0.019 0.001 TYR A 211 PHE 0.011 0.001 PHE B 377 TRP 0.011 0.001 TRP B 166 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (11074) covalent geometry : angle 0.62247 / 0.35 (15038) SS BOND : bond 0.00219 / 0.15 ( 6) SS BOND : angle 1.09383 / 0.56 ( 12) hydrogen bonds : bond 0.15284 / 10.39 ( 658) hydrogen bonds : angle 6.53742 / 4.91 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8010 (mtt) cc_final: 0.7462 (mtt) REVERT: A 423 PHE cc_start: 0.6180 (m-10) cc_final: 0.5974 (m-80) REVERT: A 433 ILE cc_start: 0.8571 (mt) cc_final: 0.8344 (mt) REVERT: A 574 TYR cc_start: 0.7604 (m-80) cc_final: 0.6990 (m-80) REVERT: B 433 ILE cc_start: 0.8527 (mt) cc_final: 0.8312 (mt) REVERT: B 574 TYR cc_start: 0.7635 (m-80) cc_final: 0.6996 (m-80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2303 time to fit residues: 47.9674 Evaluate side-chains 110 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.218637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.165211 restraints weight = 31399.869| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.68 r_work: 0.3463 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11080 Z= 0.146 Angle : 0.534 5.969 15050 Z= 0.278 Chirality : 0.037 0.147 1698 Planarity : 0.005 0.073 1844 Dihedral : 5.393 60.380 1494 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.18 % Allowed : 4.31 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.00 (0.22), residues: 1348 helix: 1.62 (0.17), residues: 840 sheet: -1.23 (0.76), residues: 42 loop : -0.92 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 416 TYR 0.014 0.001 TYR A 343 PHE 0.015 0.001 PHE B 407 TRP 0.012 0.001 TRP B 403 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11074) covalent geometry : angle 0.53310 / 0.28 (15038) SS BOND : bond 0.00303 / 0.22 ( 6) SS BOND : angle 0.97148 / 0.51 ( 12) hydrogen bonds : bond 0.04604 / 3.11 ( 658) hydrogen bonds : angle 4.78948 / 3.58 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8567 (mt) cc_final: 0.8334 (mt) REVERT: A 574 TYR cc_start: 0.7825 (m-80) cc_final: 0.7140 (m-80) REVERT: B 209 MET cc_start: 0.7616 (tpp) cc_final: 0.7176 (tpt) REVERT: B 416 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7163 (ttm170) REVERT: B 423 PHE cc_start: 0.6333 (m-10) cc_final: 0.6071 (m-80) REVERT: B 441 ILE cc_start: 0.8507 (tt) cc_final: 0.8301 (mt) REVERT: B 574 TYR cc_start: 0.7837 (m-80) cc_final: 0.7183 (m-80) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.2613 time to fit residues: 46.8214 Evaluate side-chains 118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 783 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.212653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.161432 restraints weight = 31369.054| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.33 r_work: 0.3415 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11080 Z= 0.183 Angle : 0.558 6.087 15050 Z= 0.288 Chirality : 0.038 0.144 1698 Planarity : 0.005 0.074 1844 Dihedral : 5.340 54.505 1494 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.62 % Allowed : 5.99 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 0.91 (0.23), residues: 1348 helix: 1.59 (0.17), residues: 840 sheet: -2.04 (0.78), residues: 42 loop : -0.95 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 351 TYR 0.014 0.002 TYR A 343 PHE 0.014 0.001 PHE B 407 TRP 0.011 0.001 TRP A 403 HIS 0.009 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (11074) covalent geometry : angle 0.55735 / 0.29 (15038) SS BOND : bond 0.00424 / 0.31 ( 6) SS BOND : angle 1.10949 / 0.58 ( 12) hydrogen bonds : bond 0.04263 / 2.87 ( 658) hydrogen bonds : angle 4.54014 / 3.40 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8591 (mt) cc_final: 0.8373 (mt) REVERT: B 416 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7178 (ttm170) REVERT: B 423 PHE cc_start: 0.6357 (m-10) cc_final: 0.6148 (m-80) outliers start: 7 outliers final: 5 residues processed: 131 average time/residue: 0.2453 time to fit residues: 46.5233 Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 783 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.212470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.160687 restraints weight = 31710.396| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.45 r_work: 0.3401 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11080 Z= 0.162 Angle : 0.539 6.267 15050 Z= 0.275 Chirality : 0.037 0.138 1698 Planarity : 0.005 0.075 1844 Dihedral : 5.287 55.369 1494 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.53 % Allowed : 7.66 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.07 (0.23), residues: 1348 helix: 1.71 (0.17), residues: 840 sheet: -1.82 (0.83), residues: 42 loop : -0.87 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 351 TYR 0.013 0.001 TYR A 343 PHE 0.010 0.001 PHE A 407 TRP 0.011 0.001 TRP A 403 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (11074) covalent geometry : angle 0.53891 / 0.28 (15038) SS BOND : bond 0.00382 / 0.27 ( 6) SS BOND : angle 0.94211 / 0.49 ( 12) hydrogen bonds : bond 0.03972 / 2.68 ( 658) hydrogen bonds : angle 4.41831 / 3.30 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6639 (mtpt) cc_final: 0.6151 (tttp) REVERT: A 433 ILE cc_start: 0.8537 (mt) cc_final: 0.8308 (mt) REVERT: B 416 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7189 (ttm170) REVERT: B 423 PHE cc_start: 0.6458 (m-10) cc_final: 0.6257 (m-80) outliers start: 6 outliers final: 6 residues processed: 127 average time/residue: 0.2623 time to fit residues: 47.3442 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.211125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.159474 restraints weight = 31254.946| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.44 r_work: 0.3403 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11080 Z= 0.149 Angle : 0.525 6.008 15050 Z= 0.267 Chirality : 0.037 0.135 1698 Planarity : 0.005 0.074 1844 Dihedral : 5.210 56.073 1494 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.44 % Allowed : 8.98 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.24 (0.23), residues: 1348 helix: 1.91 (0.17), residues: 828 sheet: -1.85 (0.86), residues: 42 loop : -0.87 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 351 TYR 0.013 0.001 TYR A 343 PHE 0.010 0.001 PHE B 706 TRP 0.011 0.001 TRP A 403 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (11074) covalent geometry : angle 0.52419 / 0.27 (15038) SS BOND : bond 0.00294 / 0.19 ( 6) SS BOND : angle 0.94128 / 0.46 ( 12) hydrogen bonds : bond 0.03819 / 2.58 ( 658) hydrogen bonds : angle 4.30572 / 3.22 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6663 (mtpt) cc_final: 0.6181 (tttp) REVERT: A 433 ILE cc_start: 0.8481 (mt) cc_final: 0.8246 (mt) REVERT: A 683 MET cc_start: 0.4783 (ttt) cc_final: 0.4572 (ttm) outliers start: 5 outliers final: 5 residues processed: 123 average time/residue: 0.2493 time to fit residues: 44.4397 Evaluate side-chains 121 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 788 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.205732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155012 restraints weight = 31635.480| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.29 r_work: 0.3340 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11080 Z= 0.234 Angle : 0.601 7.259 15050 Z= 0.310 Chirality : 0.039 0.142 1698 Planarity : 0.005 0.079 1844 Dihedral : 5.529 59.309 1494 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.88 % Allowed : 9.42 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 0.77 (0.23), residues: 1348 helix: 1.50 (0.17), residues: 830 sheet: -2.03 (1.23), residues: 22 loop : -1.07 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 351 TYR 0.018 0.002 TYR B 639 PHE 0.014 0.002 PHE B 598 TRP 0.014 0.001 TRP B 403 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (11074) covalent geometry : angle 0.60023 / 0.31 (15038) SS BOND : bond 0.00621 / 0.45 ( 6) SS BOND : angle 0.90569 / 0.48 ( 12) hydrogen bonds : bond 0.04240 / 2.85 ( 658) hydrogen bonds : angle 4.53859 / 3.39 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7914 (p-90) cc_final: 0.7662 (p90) REVERT: A 683 MET cc_start: 0.5264 (ttt) cc_final: 0.4935 (ttm) REVERT: B 166 TRP cc_start: 0.8057 (p-90) cc_final: 0.7803 (p90) REVERT: B 167 TYR cc_start: 0.6781 (m-80) cc_final: 0.6562 (m-80) REVERT: B 570 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7715 (t) outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 0.2187 time to fit residues: 37.3288 Evaluate side-chains 118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 783 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.206676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155580 restraints weight = 31542.358| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.41 r_work: 0.3354 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11080 Z= 0.174 Angle : 0.551 5.994 15050 Z= 0.281 Chirality : 0.037 0.138 1698 Planarity : 0.005 0.076 1844 Dihedral : 5.369 58.021 1494 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.14 % Allowed : 9.95 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 0.95 (0.23), residues: 1348 helix: 1.66 (0.17), residues: 828 sheet: -2.09 (1.20), residues: 22 loop : -1.01 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 351 TYR 0.014 0.001 TYR A 343 PHE 0.010 0.001 PHE B 598 TRP 0.011 0.001 TRP B 403 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (11074) covalent geometry : angle 0.55065 / 0.28 (15038) SS BOND : bond 0.00466 / 0.34 ( 6) SS BOND : angle 0.93016 / 0.50 ( 12) hydrogen bonds : bond 0.03920 / 2.65 ( 658) hydrogen bonds : angle 4.40780 / 3.30 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7902 (p-90) cc_final: 0.7643 (p90) REVERT: A 200 GLN cc_start: 0.6999 (pt0) cc_final: 0.6576 (pt0) REVERT: A 570 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7828 (t) REVERT: A 683 MET cc_start: 0.5474 (ttt) cc_final: 0.5134 (ttm) REVERT: B 166 TRP cc_start: 0.7976 (p-90) cc_final: 0.7682 (p90) REVERT: B 200 GLN cc_start: 0.6891 (pt0) cc_final: 0.6466 (pp30) REVERT: B 570 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7614 (t) REVERT: B 683 MET cc_start: 0.5126 (ttt) cc_final: 0.4903 (ttm) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.2019 time to fit residues: 39.2699 Evaluate side-chains 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 783 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 124 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.209262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159287 restraints weight = 31459.115| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.31 r_work: 0.3387 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11080 Z= 0.113 Angle : 0.512 6.671 15050 Z= 0.258 Chirality : 0.036 0.134 1698 Planarity : 0.005 0.074 1844 Dihedral : 5.136 55.895 1494 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.97 % Allowed : 10.48 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.35 (0.23), residues: 1348 helix: 1.99 (0.17), residues: 830 sheet: -2.00 (1.21), residues: 22 loop : -0.87 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.011 0.001 TYR A 343 PHE 0.007 0.001 PHE B 598 TRP 0.012 0.001 TRP A 403 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (11074) covalent geometry : angle 0.51124 / 0.26 (15038) SS BOND : bond 0.00257 / 0.18 ( 6) SS BOND : angle 0.83481 / 0.44 ( 12) hydrogen bonds : bond 0.03592 / 2.44 ( 658) hydrogen bonds : angle 4.22302 / 3.16 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6686 (mtpt) cc_final: 0.6159 (tttp) REVERT: A 166 TRP cc_start: 0.7905 (p-90) cc_final: 0.7674 (p90) REVERT: A 200 GLN cc_start: 0.6989 (pt0) cc_final: 0.6619 (pt0) REVERT: A 570 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7775 (t) REVERT: A 683 MET cc_start: 0.5511 (ttt) cc_final: 0.5152 (ttm) REVERT: B 99 LYS cc_start: 0.6668 (mtpt) cc_final: 0.6197 (tttp) REVERT: B 200 GLN cc_start: 0.6946 (pt0) cc_final: 0.6561 (pp30) REVERT: B 570 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7530 (t) REVERT: B 574 TYR cc_start: 0.7970 (m-80) cc_final: 0.7629 (m-80) REVERT: B 683 MET cc_start: 0.5174 (ttt) cc_final: 0.4951 (ttm) outliers start: 11 outliers final: 7 residues processed: 126 average time/residue: 0.2187 time to fit residues: 40.6935 Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.208815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158765 restraints weight = 31328.678| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.31 r_work: 0.3386 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11080 Z= 0.121 Angle : 0.513 6.851 15050 Z= 0.258 Chirality : 0.036 0.132 1698 Planarity : 0.005 0.074 1844 Dihedral : 5.063 56.247 1494 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.14 % Allowed : 10.30 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.46 (0.23), residues: 1348 helix: 2.08 (0.17), residues: 830 sheet: -2.10 (1.18), residues: 22 loop : -0.84 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.012 0.001 TYR A 343 PHE 0.008 0.001 PHE A 407 TRP 0.011 0.001 TRP B 403 HIS 0.002 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11074) covalent geometry : angle 0.51251 / 0.26 (15038) SS BOND : bond 0.00270 / 0.19 ( 6) SS BOND : angle 0.87810 / 0.46 ( 12) hydrogen bonds : bond 0.03557 / 2.41 ( 658) hydrogen bonds : angle 4.16997 / 3.12 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7929 (p-90) cc_final: 0.7707 (p90) REVERT: A 200 GLN cc_start: 0.7074 (pt0) cc_final: 0.6713 (pt0) REVERT: A 365 SER cc_start: 0.6564 (t) cc_final: 0.6292 (m) REVERT: A 570 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7845 (t) REVERT: A 576 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8256 (ttp) REVERT: A 683 MET cc_start: 0.5295 (ttt) cc_final: 0.4994 (ttm) REVERT: B 99 LYS cc_start: 0.6637 (mtpt) cc_final: 0.6150 (tttp) REVERT: B 166 TRP cc_start: 0.7874 (p-90) cc_final: 0.7633 (p90) REVERT: B 200 GLN cc_start: 0.6926 (pt0) cc_final: 0.6566 (pp30) REVERT: B 570 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7567 (t) outliers start: 13 outliers final: 6 residues processed: 131 average time/residue: 0.2198 time to fit residues: 42.2978 Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.199580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148420 restraints weight = 31848.572| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.19 r_work: 0.3427 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11080 Z= 0.141 Angle : 0.532 7.914 15050 Z= 0.267 Chirality : 0.036 0.133 1698 Planarity : 0.005 0.075 1844 Dihedral : 5.106 55.238 1494 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.97 % Allowed : 10.56 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.46 (0.23), residues: 1348 helix: 2.09 (0.17), residues: 828 sheet: -2.04 (0.84), residues: 42 loop : -0.76 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 351 TYR 0.012 0.001 TYR A 343 PHE 0.009 0.001 PHE B 598 TRP 0.011 0.001 TRP A 403 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11074) covalent geometry : angle 0.53211 / 0.27 (15038) SS BOND : bond 0.00334 / 0.23 ( 6) SS BOND : angle 0.85731 / 0.44 ( 12) hydrogen bonds : bond 0.03630 / 2.45 ( 658) hydrogen bonds : angle 4.17584 / 3.12 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7933 (p-90) cc_final: 0.7713 (p90) REVERT: A 200 GLN cc_start: 0.7188 (pt0) cc_final: 0.6833 (pt0) REVERT: A 365 SER cc_start: 0.6493 (t) cc_final: 0.6218 (m) REVERT: A 570 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7924 (t) REVERT: A 683 MET cc_start: 0.5617 (ttt) cc_final: 0.5279 (ttm) REVERT: A 787 HIS cc_start: 0.6246 (t-90) cc_final: 0.6022 (t-90) REVERT: B 99 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6143 (tttp) REVERT: B 166 TRP cc_start: 0.7867 (p-90) cc_final: 0.7640 (p90) REVERT: B 200 GLN cc_start: 0.6986 (pt0) cc_final: 0.6622 (pp30) REVERT: B 570 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7636 (t) REVERT: B 782 GLN cc_start: 0.7249 (pm20) cc_final: 0.6996 (pm20) outliers start: 11 outliers final: 7 residues processed: 122 average time/residue: 0.1956 time to fit residues: 36.6351 Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 607 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.202834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.152128 restraints weight = 31491.671| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.26 r_work: 0.3408 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11080 Z= 0.147 Angle : 0.530 6.395 15050 Z= 0.267 Chirality : 0.037 0.135 1698 Planarity : 0.005 0.074 1844 Dihedral : 5.133 56.910 1494 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.88 % Allowed : 10.30 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: 1.41 (0.23), residues: 1348 helix: 2.04 (0.17), residues: 832 sheet: -2.37 (1.10), residues: 22 loop : -0.84 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 351 TYR 0.013 0.001 TYR A 343 PHE 0.010 0.001 PHE B 598 TRP 0.010 0.001 TRP B 403 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11074) covalent geometry : angle 0.52969 / 0.27 (15038) SS BOND : bond 0.00389 / 0.28 ( 6) SS BOND : angle 0.92671 / 0.49 ( 12) hydrogen bonds : bond 0.03665 / 2.47 ( 658) hydrogen bonds : angle 4.19370 / 3.14 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5241.89 seconds wall clock time: 89 minutes 33.78 seconds (5373.78 seconds total)