Starting phenix.real_space_refine on Wed Jun 18 19:22:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgl_36238/06_2025/8jgl_36238_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgl_36238/06_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_36238/06_2025/8jgl_36238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgl_36238/06_2025/8jgl_36238.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgl_36238/06_2025/8jgl_36238_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgl_36238/06_2025/8jgl_36238_trim.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.68, per 1000 atoms: 0.49 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: 5.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.63 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: 8.60 Time building geometry restraints manager: 6.99 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: 0.06 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: 1.210 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: 0.400 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 47.750 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP B 166 HIS 0.004 0.001 HIS B 287 PHE 0.011 0.001 PHE B 377 TYR 0.019 0.001 TYR A 211 ARG 0.008 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.15284 ( 658) hydrogen bonds : angle 6.53742 ( 1944) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.09383 ( 12) covalent geometry : bond 0.00450 (11074) covalent geometry : angle 0.64639 (15038) *********************** 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 : 1.614 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: 0.7464 (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: 0.8345 (mt) REVERT: A 574 TYR cc_start: 0.7604 (m-80) cc_final: 0.6989 (m-80) REVERT: B 433 ILE cc_start: 0.8527 (mt) cc_final: 0.8306 (mt) REVERT: B 574 TYR cc_start: 0.7635 (m-80) cc_final: 0.6995 (m-80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.5072 time to fit residues: 104.0217 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 : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.214671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.161734 restraints weight = 31338.134| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.62 r_work: 0.3415 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11080 Z= 0.198 Angle : 0.585 6.694 15050 Z= 0.303 Chirality : 0.039 0.157 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.980 40.928 1494 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.26 % Allowed : 5.28 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1348 helix: 1.46 (0.17), residues: 828 sheet: -1.56 (0.77), residues: 42 loop : -1.05 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 403 HIS 0.007 0.001 HIS B 287 PHE 0.015 0.002 PHE B 407 TYR 0.015 0.002 TYR A 343 ARG 0.005 0.001 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 658) hydrogen bonds : angle 4.80990 ( 1944) SS BOND : bond 0.00441 ( 6) SS BOND : angle 1.11779 ( 12) covalent geometry : bond 0.00466 (11074) covalent geometry : angle 0.58409 (15038) *********************** 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: 3 poor density : 126 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8578 (mt) cc_final: 0.8343 (mt) REVERT: B 209 MET cc_start: 0.7858 (tpp) cc_final: 0.7410 (tpt) REVERT: B 423 PHE cc_start: 0.6172 (m-10) cc_final: 0.5948 (m-80) REVERT: B 433 ILE cc_start: 0.8518 (mt) cc_final: 0.8305 (mt) outliers start: 3 outliers final: 3 residues processed: 128 average time/residue: 0.6123 time to fit residues: 114.3323 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 : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 783 CYS Chi-restraints excluded: chain B residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.215206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162802 restraints weight = 31338.114| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.50 r_work: 0.3430 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11080 Z= 0.137 Angle : 0.523 5.957 15050 Z= 0.264 Chirality : 0.037 0.137 1698 Planarity : 0.005 0.074 1844 Dihedral : 4.645 40.202 1494 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.35 % Allowed : 6.34 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1348 helix: 1.73 (0.17), residues: 838 sheet: -1.87 (0.78), residues: 42 loop : -0.88 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 403 HIS 0.005 0.001 HIS B 287 PHE 0.012 0.001 PHE A 407 TYR 0.013 0.001 TYR A 343 ARG 0.004 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 658) hydrogen bonds : angle 4.47744 ( 1944) SS BOND : bond 0.00332 ( 6) SS BOND : angle 0.92032 ( 12) covalent geometry : bond 0.00313 (11074) covalent geometry : angle 0.52224 (15038) *********************** 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 133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8531 (mt) cc_final: 0.8296 (mt) REVERT: B 433 ILE cc_start: 0.8520 (mt) cc_final: 0.8299 (mt) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.5271 time to fit residues: 96.8382 Evaluate side-chains 120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 48 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.213544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.160508 restraints weight = 31445.012| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.54 r_work: 0.3425 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 0.045 11080 Z= 0.149 Angle : 0.529 5.759 15050 Z= 0.267 Chirality : 0.037 0.135 1698 Planarity : 0.005 0.074 1844 Dihedral : 4.551 40.402 1494 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.26 % Allowed : 7.66 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1348 helix: 1.77 (0.17), residues: 840 sheet: -1.89 (0.83), residues: 42 loop : -0.85 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.005 0.001 HIS B 287 PHE 0.011 0.001 PHE A 407 TYR 0.013 0.001 TYR A 343 ARG 0.004 0.000 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 658) hydrogen bonds : angle 4.35327 ( 1944) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.90734 ( 12) covalent geometry : bond 0.00348 (11074) covalent geometry : angle 0.52864 (15038) *********************** 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 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6591 (mtpt) cc_final: 0.6122 (tttp) REVERT: A 433 ILE cc_start: 0.8546 (mt) cc_final: 0.8312 (mt) REVERT: B 433 ILE cc_start: 0.8526 (mt) cc_final: 0.8303 (mt) outliers start: 3 outliers final: 3 residues processed: 127 average time/residue: 0.5946 time to fit residues: 109.8897 Evaluate side-chains 118 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.207005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155652 restraints weight = 31649.185| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.28 r_work: 0.3352 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11080 Z= 0.223 Angle : 0.614 7.264 15050 Z= 0.315 Chirality : 0.040 0.152 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.932 41.344 1494 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.70 % Allowed : 8.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1348 helix: 1.44 (0.17), residues: 830 sheet: -1.86 (1.26), residues: 22 loop : -1.06 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 403 HIS 0.009 0.002 HIS A 287 PHE 0.016 0.002 PHE B 598 TYR 0.016 0.002 TYR A 343 ARG 0.010 0.001 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 658) hydrogen bonds : angle 4.57444 ( 1944) SS BOND : bond 0.00622 ( 6) SS BOND : angle 1.13994 ( 12) covalent geometry : bond 0.00527 (11074) covalent geometry : angle 0.61380 (15038) *********************** 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: 8 poor density : 115 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7982 (p-90) cc_final: 0.7710 (p90) REVERT: A 683 MET cc_start: 0.5079 (ttt) cc_final: 0.4825 (ttm) REVERT: B 433 ILE cc_start: 0.8519 (mt) cc_final: 0.8286 (mt) outliers start: 8 outliers final: 7 residues processed: 119 average time/residue: 0.5616 time to fit residues: 98.1572 Evaluate side-chains 117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 570 THR 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 64 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.209426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158387 restraints weight = 31318.147| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.45 r_work: 0.3382 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2716 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= 0.131 Angle : 0.531 5.926 15050 Z= 0.267 Chirality : 0.037 0.134 1698 Planarity : 0.005 0.076 1844 Dihedral : 4.602 41.099 1494 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.70 % Allowed : 9.42 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1348 helix: 1.81 (0.17), residues: 828 sheet: -1.91 (1.26), residues: 22 loop : -0.91 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.003 0.001 HIS A 633 PHE 0.009 0.001 PHE B 598 TYR 0.013 0.001 TYR A 343 ARG 0.002 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 658) hydrogen bonds : angle 4.32464 ( 1944) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.83048 ( 12) covalent geometry : bond 0.00301 (11074) covalent geometry : angle 0.53046 (15038) *********************** 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 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6614 (mtpt) cc_final: 0.6104 (tttp) REVERT: A 166 TRP cc_start: 0.7952 (p-90) cc_final: 0.7634 (p90) REVERT: A 570 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7760 (t) REVERT: A 683 MET cc_start: 0.5230 (ttt) cc_final: 0.4869 (ttm) REVERT: B 166 TRP cc_start: 0.8015 (p-90) cc_final: 0.7785 (p90) REVERT: B 433 ILE cc_start: 0.8472 (mt) cc_final: 0.8239 (mt) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.5346 time to fit residues: 94.4681 Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 58 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.206672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156270 restraints weight = 31627.663| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.36 r_work: 0.3354 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11080 Z= 0.178 Angle : 0.556 5.811 15050 Z= 0.282 Chirality : 0.038 0.139 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.692 41.805 1494 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.88 % Allowed : 9.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1348 helix: 1.72 (0.17), residues: 828 sheet: -2.02 (1.21), residues: 22 loop : -0.96 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.006 0.001 HIS B 287 PHE 0.011 0.001 PHE B 407 TYR 0.014 0.002 TYR A 343 ARG 0.005 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 658) hydrogen bonds : angle 4.36994 ( 1944) SS BOND : bond 0.00491 ( 6) SS BOND : angle 0.95669 ( 12) covalent geometry : bond 0.00421 (11074) covalent geometry : angle 0.55597 (15038) *********************** 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: 10 poor density : 114 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.7954 (p-90) cc_final: 0.7659 (p90) REVERT: A 200 GLN cc_start: 0.6993 (pt0) cc_final: 0.6625 (pt0) REVERT: A 683 MET cc_start: 0.5453 (ttt) cc_final: 0.5097 (ttm) REVERT: B 166 TRP cc_start: 0.7994 (p-90) cc_final: 0.7717 (p90) REVERT: B 167 TYR cc_start: 0.6716 (m-80) cc_final: 0.6481 (m-80) REVERT: B 200 GLN cc_start: 0.6906 (pt0) cc_final: 0.6656 (pt0) REVERT: B 402 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 416 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7217 (ttm170) outliers start: 10 outliers final: 9 residues processed: 120 average time/residue: 0.5142 time to fit residues: 92.3260 Evaluate side-chains 119 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 653 LEU Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 ASP 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 111 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.207312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156974 restraints weight = 31606.322| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.35 r_work: 0.3362 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11080 Z= 0.154 Angle : 0.541 7.126 15050 Z= 0.273 Chirality : 0.037 0.138 1698 Planarity : 0.005 0.076 1844 Dihedral : 4.602 41.512 1494 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.32 % Allowed : 9.95 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1348 helix: 1.81 (0.17), residues: 830 sheet: -2.03 (1.20), residues: 22 loop : -0.90 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.003 0.001 HIS B 287 PHE 0.010 0.001 PHE B 598 TYR 0.013 0.001 TYR A 343 ARG 0.004 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 658) hydrogen bonds : angle 4.28745 ( 1944) SS BOND : bond 0.00430 ( 6) SS BOND : angle 0.87814 ( 12) covalent geometry : bond 0.00360 (11074) covalent geometry : angle 0.54081 (15038) *********************** 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: 15 poor density : 116 time to evaluate : 2.039 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: 0.6651 (mtpt) cc_final: 0.6143 (tttp) REVERT: A 166 TRP cc_start: 0.7984 (p-90) cc_final: 0.7688 (p90) REVERT: A 200 GLN cc_start: 0.7030 (pt0) cc_final: 0.6682 (pt0) REVERT: A 402 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 570 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7785 (t) REVERT: A 683 MET cc_start: 0.5489 (ttt) cc_final: 0.5092 (ttm) REVERT: B 166 TRP cc_start: 0.7957 (p-90) cc_final: 0.7669 (p90) REVERT: B 402 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8075 (mp) outliers start: 15 outliers final: 11 residues processed: 127 average time/residue: 0.5146 time to fit residues: 96.8912 Evaluate side-chains 125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 402 LEU 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 A residue 653 LEU Chi-restraints excluded: chain A residue 783 CYS Chi-restraints excluded: chain B residue 402 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 64 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.207684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.157954 restraints weight = 31534.096| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.33 r_work: 0.3372 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3231 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= 0.134 Angle : 0.527 7.049 15050 Z= 0.264 Chirality : 0.037 0.133 1698 Planarity : 0.005 0.073 1844 Dihedral : 4.464 41.409 1494 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 9.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1348 helix: 1.97 (0.17), residues: 830 sheet: -2.06 (1.19), residues: 22 loop : -0.85 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.003 0.001 HIS A 633 PHE 0.008 0.001 PHE B 598 TYR 0.012 0.001 TYR A 343 ARG 0.012 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 658) hydrogen bonds : angle 4.18677 ( 1944) SS BOND : bond 0.00356 ( 6) SS BOND : angle 0.83487 ( 12) covalent geometry : bond 0.00311 (11074) covalent geometry : angle 0.52635 (15038) *********************** 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 133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6645 (mtpt) cc_final: 0.6124 (tttp) REVERT: A 200 GLN cc_start: 0.7252 (pt0) cc_final: 0.6891 (pt0) REVERT: A 402 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 570 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (t) REVERT: A 683 MET cc_start: 0.5485 (ttt) cc_final: 0.5102 (ttm) REVERT: B 99 LYS cc_start: 0.6665 (mtpt) cc_final: 0.6143 (tttp) REVERT: B 166 TRP cc_start: 0.7905 (p-90) cc_final: 0.7584 (p90) REVERT: B 200 GLN cc_start: 0.6969 (pt0) cc_final: 0.6632 (pt0) REVERT: B 402 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 574 TYR cc_start: 0.7967 (m-80) cc_final: 0.7619 (m-80) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 0.4520 time to fit residues: 87.8342 Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 402 LEU 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 A residue 658 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL 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 112 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.206895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157222 restraints weight = 31705.837| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.28 r_work: 0.3365 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3339 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= 0.142 Angle : 0.534 6.782 15050 Z= 0.268 Chirality : 0.037 0.135 1698 Planarity : 0.005 0.075 1844 Dihedral : 4.479 41.407 1494 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 10.56 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1348 helix: 1.99 (0.17), residues: 830 sheet: -2.21 (1.16), residues: 22 loop : -0.83 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.003 0.001 HIS B 287 PHE 0.009 0.001 PHE B 598 TYR 0.012 0.001 TYR A 343 ARG 0.007 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 658) hydrogen bonds : angle 4.17952 ( 1944) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.81551 ( 12) covalent geometry : bond 0.00333 (11074) covalent geometry : angle 0.53333 (15038) ********************** 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 137 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6618 (mtpt) cc_final: 0.6098 (tttp) REVERT: A 166 TRP cc_start: 0.7887 (p-90) cc_final: 0.7620 (p90) REVERT: A 200 GLN cc_start: 0.7240 (pt0) cc_final: 0.6933 (pt0) REVERT: A 402 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 570 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 683 MET cc_start: 0.5610 (ttt) cc_final: 0.5237 (ttm) REVERT: B 99 LYS cc_start: 0.6679 (mtpt) cc_final: 0.6158 (tttp) REVERT: B 166 TRP cc_start: 0.7956 (p-90) cc_final: 0.7672 (p90) REVERT: B 200 GLN cc_start: 0.7048 (pt0) cc_final: 0.6721 (pt0) REVERT: B 402 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8061 (mp) outliers start: 13 outliers final: 8 residues processed: 134 average time/residue: 0.4588 time to fit residues: 91.7103 Evaluate side-chains 132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 402 LEU 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 402 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 522 VAL 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 74 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.205784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155643 restraints weight = 31745.903| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.32 r_work: 0.3354 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11080 Z= 0.161 Angle : 0.544 6.620 15050 Z= 0.274 Chirality : 0.037 0.134 1698 Planarity : 0.005 0.077 1844 Dihedral : 4.547 42.165 1494 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.06 % Allowed : 10.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1348 helix: 1.92 (0.17), residues: 830 sheet: -2.27 (1.15), residues: 22 loop : -0.88 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.004 0.001 HIS B 287 PHE 0.010 0.001 PHE B 598 TYR 0.013 0.001 TYR A 343 ARG 0.009 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 658) hydrogen bonds : angle 4.21746 ( 1944) SS BOND : bond 0.00404 ( 6) SS BOND : angle 0.83542 ( 12) covalent geometry : bond 0.00379 (11074) covalent geometry : angle 0.54330 (15038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11373.17 seconds wall clock time: 198 minutes 9.05 seconds (11889.05 seconds total)