Starting phenix.real_space_refine on Wed Nov 20 13:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgl_36238/11_2024/8jgl_36238_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgl_36238/11_2024/8jgl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgl_36238/11_2024/8jgl_36238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgl_36238/11_2024/8jgl_36238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgl_36238/11_2024/8jgl_36238_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgl_36238/11_2024/8jgl_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 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: 10.95, per 1000 atoms: 0.51 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: 6.97 Conformation dependent library (CDL) restraints added in 2.1 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: 1.23 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: 7.12 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10844 1.03 - 1.23: 45 1.23 - 1.43: 4655 1.43 - 1.62: 6288 1.62 - 1.82: 110 Bond restraints: 21942 Sorted by residual: bond pdb=" C4 AMP B 901 " pdb=" C5 AMP B 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 AMP A 901 " pdb=" C5 AMP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 AMP B 901 " pdb=" C6 AMP B 901 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 AMP A 901 " pdb=" C6 AMP A 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ LYS A 245 " pdb=" HZ2 LYS A 245 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 21937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 39433 2.12 - 4.25: 198 4.25 - 6.37: 21 6.37 - 8.49: 12 8.49 - 10.62: 6 Bond angle restraints: 39670 Sorted by residual: angle pdb=" CA PRO B 767 " pdb=" N PRO B 767 " pdb=" CD PRO B 767 " ideal model delta sigma weight residual 112.00 101.38 10.62 1.40e+00 5.10e-01 5.75e+01 angle pdb=" CA PRO A 767 " pdb=" N PRO A 767 " pdb=" CD PRO A 767 " ideal model delta sigma weight residual 112.00 101.80 10.20 1.40e+00 5.10e-01 5.31e+01 angle pdb=" N GLU B 631 " pdb=" CA GLU B 631 " pdb=" C GLU B 631 " ideal model delta sigma weight residual 113.55 106.64 6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" N GLU A 631 " pdb=" CA GLU A 631 " pdb=" C GLU A 631 " ideal model delta sigma weight residual 113.12 106.59 6.53 1.25e+00 6.40e-01 2.73e+01 angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 111.40 117.30 -5.90 1.22e+00 6.72e-01 2.34e+01 ... (remaining 39665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9253 17.98 - 35.96: 713 35.96 - 53.94: 255 53.94 - 71.91: 66 71.91 - 89.89: 17 Dihedral angle restraints: 10304 sinusoidal: 5472 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ARG B 659 " pdb=" C ARG B 659 " pdb=" N PRO B 660 " pdb=" CA PRO B 660 " ideal model delta harmonic sigma weight residual 180.00 139.72 40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA ARG A 659 " pdb=" C ARG A 659 " pdb=" N PRO A 660 " pdb=" CA PRO A 660 " ideal model delta harmonic sigma weight residual 180.00 140.46 39.54 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CB CYS A 161 " pdb=" SG CYS A 161 " pdb=" SG CYS A 172 " pdb=" CB CYS A 172 " ideal model delta sinusoidal sigma weight residual -86.00 -117.90 31.90 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 10301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1304 0.040 - 0.079: 285 0.079 - 0.119: 96 0.119 - 0.159: 11 0.159 - 0.199: 2 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C3' AMP A 901 " pdb=" C2' AMP A 901 " pdb=" C4' AMP A 901 " pdb=" O3' AMP A 901 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA PRO B 767 " pdb=" N PRO B 767 " pdb=" C PRO B 767 " pdb=" CB PRO B 767 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C2' AMP A 901 " pdb=" C1' AMP A 901 " pdb=" C3' AMP A 901 " pdb=" O2' AMP A 901 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1695 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 766 " 0.071 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B 767 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 767 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 767 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 766 " -0.070 5.00e-02 4.00e+02 9.86e-02 1.56e+01 pdb=" N PRO A 767 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 767 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 767 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 659 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO B 660 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 660 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 660 " 0.039 5.00e-02 4.00e+02 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1227 2.19 - 2.79: 44475 2.79 - 3.39: 62133 3.39 - 4.00: 78625 4.00 - 4.60: 123848 Nonbonded interactions: 310308 Sorted by model distance: nonbonded pdb=" O PHE B 443 " pdb="HH11 ARG B 449 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP A 86 " pdb=" H ASP A 87 " model vdw 1.591 2.450 nonbonded pdb=" O ALA B 150 " pdb=" HG1 THR B 154 " model vdw 1.606 2.450 nonbonded pdb=" O ALA A 150 " pdb=" HG1 THR A 154 " model vdw 1.613 2.450 nonbonded pdb=" O ILE A 264 " pdb=" HG1 THR A 268 " model vdw 1.617 2.450 ... (remaining 310303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.970 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: 0.300 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 47.080 Find NCS groups from input model: 0.500 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.430 ------------------------------------------------------------------------------- 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 11074 Z= 0.265 Angle : 0.622 10.618 15038 Z= 0.346 Chirality : 0.039 0.199 1698 Planarity : 0.005 0.100 1844 Dihedral : 14.099 89.892 3916 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (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 *********************** 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 : 1.463 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: 0.5537 time to fit residues: 114.0075 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 : 1.828 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11074 Z= 0.299 Angle : 0.572 6.066 15038 Z= 0.301 Chirality : 0.039 0.148 1698 Planarity : 0.005 0.075 1844 Dihedral : 5.475 54.073 1494 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.26 % Allowed : 5.11 % Favored : 94.63 % 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: 0.75 (0.22), residues: 1348 helix: 1.49 (0.17), residues: 828 sheet: -1.55 (0.77), residues: 42 loop : -1.06 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.007 0.001 HIS B 287 PHE 0.015 0.001 PHE B 407 TYR 0.015 0.002 TYR A 343 ARG 0.005 0.001 ARG B 416 *********************** 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 126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ILE cc_start: 0.8570 (mt) cc_final: 0.8337 (mt) REVERT: B 209 MET cc_start: 0.7532 (tpp) cc_final: 0.7060 (tpt) REVERT: B 423 PHE cc_start: 0.6070 (m-10) cc_final: 0.5819 (m-80) outliers start: 3 outliers final: 3 residues processed: 125 average time/residue: 0.5676 time to fit residues: 100.7837 Evaluate side-chains 121 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 68 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11074 Z= 0.167 Angle : 0.500 5.806 15038 Z= 0.255 Chirality : 0.036 0.137 1698 Planarity : 0.005 0.073 1844 Dihedral : 5.213 54.086 1494 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.35 % Allowed : 6.25 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.23), residues: 1348 helix: 1.82 (0.17), residues: 840 sheet: -1.77 (0.77), residues: 42 loop : -0.82 (0.29), residues: 466 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 0.011 0.001 PHE B 598 TYR 0.012 0.001 TYR A 343 ARG 0.006 0.000 ARG A 351 *********************** 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 138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 TYR cc_start: 0.7651 (m-80) cc_final: 0.7208 (m-80) REVERT: B 423 PHE cc_start: 0.5953 (m-10) cc_final: 0.5730 (m-80) outliers start: 4 outliers final: 3 residues processed: 134 average time/residue: 0.5491 time to fit residues: 104.4534 Evaluate side-chains 126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 658 MET 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 122 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 chunk 124 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11074 Z= 0.172 Angle : 0.495 5.750 15038 Z= 0.251 Chirality : 0.036 0.141 1698 Planarity : 0.004 0.072 1844 Dihedral : 5.045 53.455 1494 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.09 % Allowed : 7.04 % Favored : 92.87 % 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: 1.39 (0.23), residues: 1348 helix: 2.00 (0.17), residues: 840 sheet: -1.97 (0.79), residues: 42 loop : -0.80 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.004 0.001 HIS B 287 PHE 0.010 0.001 PHE B 407 TYR 0.012 0.001 TYR B 211 ARG 0.004 0.000 ARG B 351 *********************** 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 132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 TYR cc_start: 0.7592 (m-80) cc_final: 0.7338 (m-80) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.5447 time to fit residues: 100.7782 Evaluate side-chains 123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11074 Z= 0.173 Angle : 0.495 5.985 15038 Z= 0.248 Chirality : 0.036 0.132 1698 Planarity : 0.004 0.072 1844 Dihedral : 4.977 53.962 1494 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.26 % Allowed : 8.27 % Favored : 91.46 % 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: 1.54 (0.23), residues: 1348 helix: 2.12 (0.17), residues: 840 sheet: -1.81 (0.83), residues: 42 loop : -0.76 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS B 287 PHE 0.009 0.001 PHE A 407 TYR 0.011 0.001 TYR B 211 ARG 0.004 0.000 ARG B 351 *********************** 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 126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 124 average time/residue: 0.6081 time to fit residues: 106.5524 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain B residue 449 ARG 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 118 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11074 Z= 0.216 Angle : 0.510 5.786 15038 Z= 0.257 Chirality : 0.036 0.136 1698 Planarity : 0.005 0.073 1844 Dihedral : 5.028 55.233 1494 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.62 % Allowed : 8.19 % Favored : 91.20 % 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: 1.46 (0.23), residues: 1348 helix: 2.03 (0.17), residues: 844 sheet: -1.87 (0.85), residues: 42 loop : -0.78 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 403 HIS 0.005 0.001 HIS B 287 PHE 0.010 0.001 PHE A 407 TYR 0.012 0.001 TYR A 343 ARG 0.004 0.000 ARG B 351 *********************** 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 125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6624 (mtpt) cc_final: 0.6294 (tttp) outliers start: 7 outliers final: 5 residues processed: 121 average time/residue: 0.5926 time to fit residues: 100.0987 Evaluate side-chains 120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11074 Z= 0.283 Angle : 0.557 7.873 15038 Z= 0.283 Chirality : 0.038 0.144 1698 Planarity : 0.005 0.073 1844 Dihedral : 5.280 58.332 1494 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.62 % Allowed : 8.63 % Favored : 90.76 % 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: 1.24 (0.23), residues: 1348 helix: 1.87 (0.17), residues: 832 sheet: -1.96 (0.85), residues: 42 loop : -0.81 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.007 0.001 HIS A 287 PHE 0.011 0.001 PHE B 706 TYR 0.033 0.002 TYR A 574 ARG 0.003 0.000 ARG A 95 *********************** 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 126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6652 (mtpt) cc_final: 0.6285 (tttp) REVERT: A 570 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7919 (t) REVERT: A 683 MET cc_start: 0.4791 (ttt) cc_final: 0.4574 (ttm) REVERT: B 570 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7712 (t) outliers start: 7 outliers final: 4 residues processed: 122 average time/residue: 0.5861 time to fit residues: 99.4618 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.950 ------------------------------------------------------------------------------- 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 658 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11074 Z= 0.198 Angle : 0.514 6.088 15038 Z= 0.259 Chirality : 0.036 0.133 1698 Planarity : 0.005 0.075 1844 Dihedral : 5.116 56.165 1494 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 1.40 (0.23), residues: 1348 helix: 2.02 (0.17), residues: 832 sheet: -1.81 (0.86), residues: 42 loop : -0.79 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.003 0.001 HIS A 553 PHE 0.008 0.001 PHE B 598 TYR 0.012 0.001 TYR A 343 ARG 0.005 0.000 ARG B 416 *********************** 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: 8 poor density : 123 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6633 (mtpt) cc_final: 0.6275 (tttp) REVERT: A 570 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7836 (t) REVERT: A 683 MET cc_start: 0.5039 (ttt) cc_final: 0.4760 (ttm) REVERT: B 570 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7624 (t) REVERT: B 574 TYR cc_start: 0.7705 (m-80) cc_final: 0.7292 (m-80) outliers start: 8 outliers final: 6 residues processed: 127 average time/residue: 0.5229 time to fit residues: 95.0514 Evaluate side-chains 120 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 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 122 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11074 Z= 0.161 Angle : 0.501 5.867 15038 Z= 0.250 Chirality : 0.036 0.131 1698 Planarity : 0.005 0.072 1844 Dihedral : 5.010 55.214 1494 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.70 % Allowed : 9.51 % Favored : 89.79 % 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: 1.62 (0.23), residues: 1348 helix: 2.21 (0.17), residues: 832 sheet: -1.81 (0.87), residues: 42 loop : -0.73 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.003 0.001 HIS A 553 PHE 0.007 0.001 PHE B 598 TYR 0.011 0.001 TYR A 343 ARG 0.004 0.000 ARG B 351 *********************** 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 126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.591 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: 0.6665 (mtpt) cc_final: 0.6300 (tttp) REVERT: A 570 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7871 (t) REVERT: A 683 MET cc_start: 0.5067 (ttt) cc_final: 0.4770 (ttm) REVERT: B 99 LYS cc_start: 0.6702 (mtpt) cc_final: 0.6323 (tttp) REVERT: B 570 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7598 (t) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 0.5444 time to fit residues: 94.3931 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11074 Z= 0.161 Angle : 0.495 6.496 15038 Z= 0.247 Chirality : 0.036 0.130 1698 Planarity : 0.005 0.074 1844 Dihedral : 4.960 55.620 1494 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.62 % Allowed : 9.68 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.23), residues: 1348 helix: 2.33 (0.17), residues: 832 sheet: -2.10 (1.20), residues: 22 loop : -0.73 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.002 0.001 HIS A 553 PHE 0.007 0.001 PHE B 598 TYR 0.011 0.001 TYR A 343 ARG 0.004 0.000 ARG B 416 ********************** 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 125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.624 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: 0.6644 (mtpt) cc_final: 0.6286 (tttp) REVERT: A 570 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7891 (t) REVERT: A 683 MET cc_start: 0.5185 (ttt) cc_final: 0.4896 (ttm) REVERT: A 787 HIS cc_start: 0.5967 (t-90) cc_final: 0.5762 (t-90) REVERT: B 200 GLN cc_start: 0.6336 (pt0) cc_final: 0.5972 (pp30) REVERT: B 365 SER cc_start: 0.6761 (t) cc_final: 0.6550 (m) REVERT: B 570 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7624 (t) outliers start: 7 outliers final: 5 residues processed: 121 average time/residue: 0.5307 time to fit residues: 92.1702 Evaluate side-chains 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 110 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.211256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.160923 restraints weight = 31368.104| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.33 r_work: 0.3414 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11074 Z= 0.169 Angle : 0.498 6.467 15038 Z= 0.248 Chirality : 0.036 0.132 1698 Planarity : 0.005 0.071 1844 Dihedral : 4.921 54.953 1494 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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 (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: 1.79 (0.23), residues: 1348 helix: 2.34 (0.17), residues: 834 sheet: -2.20 (1.18), residues: 22 loop : -0.70 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 403 HIS 0.003 0.001 HIS B 803 PHE 0.008 0.001 PHE B 598 TYR 0.011 0.001 TYR A 167 ARG 0.003 0.000 ARG B 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4684.51 seconds wall clock time: 84 minutes 52.27 seconds (5092.27 seconds total)