Starting phenix.real_space_refine on Sun Aug 24 17:16:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgl_36238/08_2025/8jgl_36238_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgl_36238/08_2025/8jgl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2025/8jgl_36238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2025/8jgl_36238.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2025/8jgl_36238_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgl_36238/08_2025/8jgl_36238_trim.cif" } 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-2.0-5787/lib/python3.9/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: 3.65, per 1000 atoms: 0.17 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: 1.43 Conformation dependent library (CDL) restraints added in 422.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.44 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: 4.87 Time building geometry restraints manager: 1.92 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 - 2.14: 39427 2.14 - 4.29: 197 4.29 - 6.43: 25 6.43 - 8.58: 13 8.58 - 10.72: 8 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: 9252 17.98 - 35.96: 714 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 - 0.035: 1235 0.035 - 0.070: 319 0.070 - 0.106: 113 0.106 - 0.141: 25 0.141 - 0.176: 6 Chirality restraints: 1698 Sorted by residual: 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=" 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 -2.51 -2.68 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA PRO A 767 " pdb=" N PRO A 767 " pdb=" C PRO A 767 " pdb=" CB PRO A 767 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-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: 1.170 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.250 Find NCS groups from input model: 0.200 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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= 0.217 Angle : 0.647 10.720 15050 Z= 0.348 Chirality : 0.039 0.176 1698 Planarity : 0.005 0.100 1844 Dihedral : 14.089 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 aren 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 covalent geometry : bond 0.00450 (11074) covalent geometry : angle 0.64639 (15038) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.09383 ( 12) hydrogen bonds : bond 0.15284 ( 658) hydrogen bonds : angle 6.53742 ( 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 : 0.392 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: 0.8009 (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: 0.2130 time to fit residues: 43.9317 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 : 0.439 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.218544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.165210 restraints weight = 31380.653| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.48 r_work: 0.3475 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1030 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= 0.145 Angle : 0.545 7.023 15050 Z= 0.281 Chirality : 0.038 0.147 1698 Planarity : 0.005 0.074 1844 Dihedral : 4.876 40.398 1494 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.42 % 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 aren not related in a simple way. whole: 1.03 (0.22), residues: 1348 helix: 1.69 (0.17), residues: 832 sheet: -1.28 (0.77), residues: 42 loop : -0.94 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.014 0.001 TYR A 343 PHE 0.016 0.001 PHE B 407 TRP 0.012 0.001 TRP A 403 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00331 (11074) covalent geometry : angle 0.54491 (15038) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.96578 ( 12) hydrogen bonds : bond 0.04424 ( 658) hydrogen bonds : angle 4.76116 ( 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 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8590 (mt) cc_final: 0.8355 (mt) REVERT: A 574 TYR cc_start: 0.7905 (m-80) cc_final: 0.7222 (m-80) REVERT: B 209 MET cc_start: 0.7738 (tpp) cc_final: 0.7307 (tpt) REVERT: B 416 ARG cc_start: 0.7535 (ttm-80) cc_final: 0.7159 (ttm170) REVERT: B 423 PHE cc_start: 0.6426 (m-10) cc_final: 0.6175 (m-80) REVERT: B 574 TYR cc_start: 0.7905 (m-80) cc_final: 0.7244 (m-80) outliers start: 2 outliers final: 2 residues processed: 128 average time/residue: 0.2466 time to fit residues: 44.0562 Evaluate side-chains 121 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 0.3980 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: 8.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.211506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158573 restraints weight = 31568.754| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.57 r_work: 0.3401 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11080 Z= 0.209 Angle : 0.593 6.018 15050 Z= 0.304 Chirality : 0.039 0.159 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.859 40.758 1494 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.62 % Allowed : 6.43 % Favored : 92.96 % 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 aren not related in a simple way. whole: 0.76 (0.22), residues: 1348 helix: 1.47 (0.17), residues: 840 sheet: -2.04 (0.79), residues: 42 loop : -1.01 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 588 TYR 0.015 0.002 TYR B 639 PHE 0.015 0.002 PHE A 407 TRP 0.014 0.001 TRP A 403 HIS 0.011 0.002 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00493 (11074) covalent geometry : angle 0.59211 (15038) SS BOND : bond 0.00520 ( 6) SS BOND : angle 1.17845 ( 12) hydrogen bonds : bond 0.04413 ( 658) hydrogen bonds : angle 4.60994 ( 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 : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8565 (mt) cc_final: 0.8334 (mt) REVERT: B 423 PHE cc_start: 0.6407 (m-10) cc_final: 0.6205 (m-80) outliers start: 7 outliers final: 5 residues processed: 131 average time/residue: 0.2314 time to fit residues: 43.4057 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 : 0.361 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.0040 chunk 86 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.214513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163329 restraints weight = 31572.449| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.33 r_work: 0.3437 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11080 Z= 0.115 Angle : 0.516 5.722 15050 Z= 0.259 Chirality : 0.036 0.130 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.492 40.154 1494 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.26 % Allowed : 7.75 % Favored : 91.99 % 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 aren not related in a simple way. whole: 1.26 (0.23), residues: 1348 helix: 1.85 (0.17), residues: 840 sheet: -1.74 (0.84), residues: 42 loop : -0.79 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.011 0.001 TYR A 343 PHE 0.009 0.001 PHE B 598 TRP 0.011 0.001 TRP A 403 HIS 0.002 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00260 (11074) covalent geometry : angle 0.51609 (15038) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.86167 ( 12) hydrogen bonds : bond 0.03732 ( 658) hydrogen bonds : angle 4.32870 ( 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 138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8502 (mt) cc_final: 0.8275 (mt) outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.2325 time to fit residues: 44.8542 Evaluate side-chains 125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET 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: 0.8980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 93 optimal weight: 0.0010 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.212084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.161425 restraints weight = 31303.220| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.22 r_work: 0.3412 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11080 Z= 0.147 Angle : 0.534 6.236 15050 Z= 0.268 Chirality : 0.037 0.147 1698 Planarity : 0.005 0.072 1844 Dihedral : 4.503 40.320 1494 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.35 % Allowed : 9.15 % Favored : 90.49 % 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 aren not related in a simple way. whole: 1.26 (0.23), residues: 1348 helix: 1.86 (0.17), residues: 840 sheet: -1.83 (0.85), residues: 42 loop : -0.81 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.012 0.001 TYR A 343 PHE 0.011 0.001 PHE B 407 TRP 0.011 0.001 TRP A 403 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00346 (11074) covalent geometry : angle 0.53352 (15038) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.90545 ( 12) hydrogen bonds : bond 0.03796 ( 658) hydrogen bonds : angle 4.28219 ( 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 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6674 (mtpt) cc_final: 0.6188 (tttp) REVERT: A 433 ILE cc_start: 0.8547 (mt) cc_final: 0.8324 (mt) outliers start: 4 outliers final: 4 residues processed: 119 average time/residue: 0.2353 time to fit residues: 39.5229 Evaluate side-chains 116 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.205730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154511 restraints weight = 31681.336| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.25 r_work: 0.3348 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11080 Z= 0.261 Angle : 0.621 5.970 15050 Z= 0.319 Chirality : 0.040 0.166 1698 Planarity : 0.005 0.078 1844 Dihedral : 4.909 42.068 1494 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.79 % Allowed : 9.68 % Favored : 89.52 % 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 aren not related in a simple way. whole: 0.73 (0.23), residues: 1348 helix: 1.44 (0.17), residues: 830 sheet: -1.85 (1.29), residues: 22 loop : -1.05 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 351 TYR 0.016 0.002 TYR B 639 PHE 0.014 0.002 PHE B 598 TRP 0.014 0.001 TRP B 403 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00633 (11074) covalent geometry : angle 0.62043 (15038) SS BOND : bond 0.00574 ( 6) SS BOND : angle 0.97719 ( 12) hydrogen bonds : bond 0.04353 ( 658) hydrogen bonds : angle 4.56970 ( 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 120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7965 (p-90) cc_final: 0.7738 (p90) REVERT: A 574 TYR cc_start: 0.8060 (m-80) cc_final: 0.7794 (m-80) REVERT: A 683 MET cc_start: 0.5251 (ttt) cc_final: 0.4940 (ttm) REVERT: B 683 MET cc_start: 0.4841 (ttt) cc_final: 0.4557 (ttm) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.2231 time to fit residues: 37.4924 Evaluate side-chains 114 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 A residue 783 CYS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL 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: 0.6980 chunk 129 optimal weight: 5.9990 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: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.207446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156960 restraints weight = 31484.303| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.23 r_work: 0.3377 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11080 Z= 0.156 Angle : 0.544 5.808 15050 Z= 0.273 Chirality : 0.037 0.137 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.676 41.798 1494 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.97 % Allowed : 9.77 % Favored : 89.26 % 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 aren not related in a simple way. whole: 1.04 (0.23), residues: 1348 helix: 1.72 (0.17), residues: 828 sheet: -1.93 (1.25), residues: 22 loop : -0.95 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 416 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 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00366 (11074) covalent geometry : angle 0.54318 (15038) SS BOND : bond 0.00402 ( 6) SS BOND : angle 0.90376 ( 12) hydrogen bonds : bond 0.03869 ( 658) hydrogen bonds : angle 4.37377 ( 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 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7919 (p-90) cc_final: 0.7657 (p90) REVERT: A 200 GLN cc_start: 0.6793 (pt0) cc_final: 0.6461 (pt0) REVERT: A 570 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7752 (t) REVERT: A 574 TYR cc_start: 0.7926 (m-80) cc_final: 0.7696 (m-80) REVERT: A 683 MET cc_start: 0.5492 (ttt) cc_final: 0.5163 (ttm) REVERT: B 166 TRP cc_start: 0.8035 (p-90) cc_final: 0.7767 (p90) REVERT: B 167 TYR cc_start: 0.6659 (m-80) cc_final: 0.6390 (m-80) REVERT: B 200 GLN cc_start: 0.6718 (pt0) cc_final: 0.6493 (pt0) REVERT: B 570 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7567 (t) REVERT: B 683 MET cc_start: 0.4891 (ttt) cc_final: 0.4620 (ttm) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.1963 time to fit residues: 35.5821 Evaluate side-chains 120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 71 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.207921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157254 restraints weight = 31513.575| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.44 r_work: 0.3370 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2993 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= 0.142 Angle : 0.531 6.311 15050 Z= 0.266 Chirality : 0.037 0.134 1698 Planarity : 0.005 0.076 1844 Dihedral : 4.527 41.465 1494 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.79 % Allowed : 10.56 % Favored : 88.64 % 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 aren not related in a simple way. whole: 1.22 (0.23), residues: 1348 helix: 1.87 (0.17), residues: 830 sheet: -2.00 (1.23), residues: 22 loop : -0.91 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 449 TYR 0.012 0.001 TYR A 343 PHE 0.009 0.001 PHE B 598 TRP 0.011 0.001 TRP B 403 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00331 (11074) covalent geometry : angle 0.53060 (15038) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.84690 ( 12) hydrogen bonds : bond 0.03705 ( 658) hydrogen bonds : angle 4.26415 ( 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 131 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6656 (mtpt) cc_final: 0.6150 (tttp) REVERT: A 166 TRP cc_start: 0.7932 (p-90) cc_final: 0.7699 (p90) REVERT: A 200 GLN cc_start: 0.6959 (pt0) cc_final: 0.6572 (pt0) REVERT: A 570 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7780 (t) REVERT: A 574 TYR cc_start: 0.7905 (m-80) cc_final: 0.7659 (m-80) REVERT: A 683 MET cc_start: 0.5614 (ttt) cc_final: 0.5251 (ttm) REVERT: B 166 TRP cc_start: 0.7957 (p-90) cc_final: 0.7689 (p90) REVERT: B 200 GLN cc_start: 0.6949 (pt0) cc_final: 0.6729 (pt0) REVERT: B 570 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7550 (t) REVERT: B 574 TYR cc_start: 0.7963 (m-80) cc_final: 0.7612 (m-80) REVERT: B 683 MET cc_start: 0.5080 (ttt) cc_final: 0.4779 (ttm) REVERT: B 757 MET cc_start: 0.6738 (mmp) cc_final: 0.6512 (mmp) outliers start: 9 outliers final: 7 residues processed: 127 average time/residue: 0.2067 time to fit residues: 37.9249 Evaluate side-chains 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 570 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 658 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 607 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.208733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.158864 restraints weight = 31348.227| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.35 r_work: 0.3386 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11080 Z= 0.120 Angle : 0.517 6.604 15050 Z= 0.258 Chirality : 0.036 0.134 1698 Planarity : 0.005 0.073 1844 Dihedral : 4.405 41.122 1494 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.97 % Allowed : 11.00 % Favored : 88.03 % 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 aren not related in a simple way. whole: 1.42 (0.23), residues: 1348 helix: 2.04 (0.17), residues: 832 sheet: -2.03 (1.22), residues: 22 loop : -0.86 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 416 TYR 0.011 0.001 TYR A 343 PHE 0.008 0.001 PHE B 598 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00277 (11074) covalent geometry : angle 0.51691 (15038) SS BOND : bond 0.00273 ( 6) SS BOND : angle 0.83818 ( 12) hydrogen bonds : bond 0.03564 ( 658) hydrogen bonds : angle 4.15477 ( 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 128 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6695 (mtpt) cc_final: 0.6170 (tttp) REVERT: A 166 TRP cc_start: 0.7901 (p-90) cc_final: 0.7698 (p90) REVERT: A 200 GLN cc_start: 0.7002 (pt0) cc_final: 0.6638 (pt0) REVERT: A 365 SER cc_start: 0.6535 (t) cc_final: 0.6274 (m) REVERT: A 570 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7828 (t) REVERT: A 683 MET cc_start: 0.5494 (ttt) cc_final: 0.5229 (ttm) REVERT: B 200 GLN cc_start: 0.6964 (pt0) cc_final: 0.6715 (pt0) REVERT: B 570 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7534 (t) REVERT: B 683 MET cc_start: 0.5214 (ttt) cc_final: 0.4935 (ttm) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.1876 time to fit residues: 34.3178 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 658 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 607 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 0.0000 chunk 73 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.200951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149713 restraints weight = 31769.321| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.28 r_work: 0.3403 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3207 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= 0.140 Angle : 0.540 7.124 15050 Z= 0.268 Chirality : 0.037 0.132 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.436 41.152 1494 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.88 % Allowed : 11.18 % Favored : 87.94 % 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 aren not related in a simple way. whole: 1.40 (0.23), residues: 1348 helix: 2.03 (0.17), residues: 830 sheet: -2.13 (1.20), residues: 22 loop : -0.85 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 351 TYR 0.012 0.001 TYR A 343 PHE 0.009 0.001 PHE A 407 TRP 0.011 0.001 TRP B 403 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00329 (11074) covalent geometry : angle 0.53950 (15038) SS BOND : bond 0.00353 ( 6) SS BOND : angle 0.87028 ( 12) hydrogen bonds : bond 0.03637 ( 658) hydrogen bonds : angle 4.17479 ( 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 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6660 (mtpt) cc_final: 0.6122 (tttp) REVERT: A 166 TRP cc_start: 0.7921 (p-90) cc_final: 0.7714 (p90) REVERT: A 200 GLN cc_start: 0.7240 (pt0) cc_final: 0.6894 (pt0) REVERT: A 365 SER cc_start: 0.6469 (t) cc_final: 0.6196 (m) REVERT: A 570 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7942 (t) REVERT: A 683 MET cc_start: 0.5612 (ttt) cc_final: 0.5302 (ttm) REVERT: B 189 GLN cc_start: 0.5068 (pt0) cc_final: 0.4865 (pm20) REVERT: B 200 GLN cc_start: 0.6950 (pt0) cc_final: 0.6680 (pt0) REVERT: B 570 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 574 TYR cc_start: 0.8004 (m-80) cc_final: 0.7586 (m-80) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 0.1865 time to fit residues: 33.1720 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.196267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145473 restraints weight = 31736.270| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.15 r_work: 0.3357 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11080 Z= 0.218 Angle : 0.591 6.476 15050 Z= 0.299 Chirality : 0.039 0.151 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.752 42.634 1494 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.88 % Allowed : 11.18 % Favored : 87.94 % 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 aren not related in a simple way. whole: 0.98 (0.23), residues: 1348 helix: 1.66 (0.17), residues: 830 sheet: -2.15 (1.20), residues: 22 loop : -0.96 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 416 TYR 0.016 0.002 TYR B 639 PHE 0.013 0.001 PHE B 598 TRP 0.013 0.001 TRP A 403 HIS 0.007 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00524 (11074) covalent geometry : angle 0.59080 (15038) SS BOND : bond 0.00606 ( 6) SS BOND : angle 1.04481 ( 12) hydrogen bonds : bond 0.04036 ( 658) hydrogen bonds : angle 4.40436 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4970.16 seconds wall clock time: 84 minutes 56.53 seconds (5096.53 seconds total)