Starting phenix.real_space_refine on Fri Oct 23 16:00:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36jb_77609/10_2026/36jb_77609.cif Found real_map, /net/cci-nas-00/data/ceres_data/36jb_77609/10_2026/36jb_77609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36jb_77609/10_2026/36jb_77609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36jb_77609/10_2026/36jb_77609.map" model { file = "/net/cci-nas-00/data/ceres_data/36jb_77609/10_2026/36jb_77609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36jb_77609/10_2026/36jb_77609.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.101 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Cu 1 5.60 5 P 2 5.49 5 S 49 5.16 5 C 6413 2.51 5 N 1690 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10077 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1225, 9916 Classifications: {'peptide': 1225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1164} Chain breaks: 9 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 44 Unusual residues: {' CA': 2, 'CU1': 1, 'NAG': 1} Inner-chain residues flagged as termini: ['pdbres="SEP A3005 "', 'pdbres="SEP A3006 "'] Classifications: {'peptide': 2, 'undetermined': 4, 'water': 5} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1, None: 9} Not linked: pdbres="NAG A3001 " pdbres=" CA A3002 " Not linked: pdbres=" CA A3002 " pdbres=" CA A3003 " Not linked: pdbres=" CA A3003 " pdbres="CU1 A3004 " Not linked: pdbres="CU1 A3004 " pdbres="SEP A3005 " Not linked: pdbres="SEP A3006 " pdbres="HOH A3101 " ... (remaining 4 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.10, per 1000 atoms: 0.21 Number of scatterers: 10077 At special positions: 0 Unit cell: (80.25, 110.21, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 1 28.99 Ca 2 19.99 S 49 16.00 P 2 15.00 O 1920 8.00 N 1690 7.00 C 6413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.05 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A1697 " - pdb=" SG CYS A1723 " distance=2.03 Simple disulfide: pdb=" SG CYS A1879 " - pdb=" SG CYS A2033 " distance=2.03 Simple disulfide: pdb=" SG CYS A2038 " - pdb=" SG CYS A2193 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A3001 " - " ASN A1675 " " NAG B 1 " - " ASN A 269 " " NAG C 1 " - " ASN A1982 " " NAG D 1 " - " ASN A 211 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 345.4 milliseconds 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 17 sheets defined 10.0% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.867A pdb=" N MET A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.514A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.506A pdb=" N GLU A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.588A pdb=" N ILE A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1544 removed outlier: 3.656A pdb=" N ILE A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1614 removed outlier: 3.903A pdb=" N GLY A1614 " --> pdb=" O GLU A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1667 Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1707 through 1714 Processing helix chain 'A' and resid 1751 through 1753 No H-bonds generated for 'chain 'A' and resid 1751 through 1753' Processing helix chain 'A' and resid 1860 through 1867 Processing helix chain 'A' and resid 1891 through 1893 No H-bonds generated for 'chain 'A' and resid 1891 through 1893' Processing helix chain 'A' and resid 1905 through 1909 Processing helix chain 'A' and resid 2069 through 2073 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 6 current: chain 'A' and resid 33 through 40 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 33 through 40 current: chain 'A' and resid 119 through 125 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.957A pdb=" N LEU A 62 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N CYS A 165 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 64 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.915A pdb=" N LYS A 181 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS A 228 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 183 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU A 230 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 185 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N MET A 232 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 187 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 269 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 371 removed outlier: 4.217A pdb=" N PHE A 325 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP A 322 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 406 " --> pdb=" O TRP A 322 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 324 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS A 408 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 326 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 561 removed outlier: 3.954A pdb=" N ASP A 578 " --> pdb=" O MET A 627 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 572 through 575 removed outlier: 3.893A pdb=" N VAL A 654 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AB1, first strand: chain 'A' and resid 1586 through 1594 removed outlier: 6.328A pdb=" N ARG A1552 " --> pdb=" O GLN A1629 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG A1631 " --> pdb=" O ARG A1552 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR A1554 " --> pdb=" O ARG A1631 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LYS A1633 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A1556 " --> pdb=" O LYS A1633 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU A1635 " --> pdb=" O ILE A1556 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA A1558 " --> pdb=" O LEU A1635 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1620 through 1623 Processing sheet with id=AB3, first strand: chain 'A' and resid 1776 through 1780 removed outlier: 6.774A pdb=" N ARG A1739 " --> pdb=" O ARG A1799 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS A1801 " --> pdb=" O ARG A1739 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A1741 " --> pdb=" O HIS A1801 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU A1803 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A1743 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1791 through 1793 removed outlier: 6.918A pdb=" N MET A1792 " --> pdb=" O MET A1875 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1881 through 1882 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1881 through 1882 current: chain 'A' and resid 1977 through 1978 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1953 through 1955 Processing sheet with id=AB7, first strand: chain 'A' and resid 2054 through 2056 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2054 through 2056 current: chain 'A' and resid 2119 through 2130 Processing sheet with id=AB8, first strand: chain 'A' and resid 2061 through 2062 removed outlier: 4.341A pdb=" N ASP A2066 " --> pdb=" O SER A2062 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 516 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: 2.09 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3186 1.35 - 1.48: 2808 1.48 - 1.61: 4255 1.61 - 1.74: 3 1.74 - 1.87: 80 Bond restraints: 10332 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" CB CYS A 498 " pdb=" SG CYS A 498 " ideal model delta sigma weight residual 1.808 1.871 -0.063 3.30e-02 9.18e+02 3.60e+00 bond pdb=" N ALA A 1 " pdb=" CA ALA A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 13794 2.37 - 4.74: 173 4.74 - 7.11: 27 7.11 - 9.47: 0 9.47 - 11.84: 1 Bond angle restraints: 13995 Sorted by residual: angle pdb=" CA CYS A 472 " pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 114.40 126.24 -11.84 2.30e+00 1.89e-01 2.65e+01 angle pdb=" N MET A 232 " pdb=" CA MET A 232 " pdb=" C MET A 232 " ideal model delta sigma weight residual 108.75 112.99 -4.24 1.71e+00 3.42e-01 6.15e+00 angle pdb=" N CYS A 472 " pdb=" CA CYS A 472 " pdb=" C CYS A 472 " ideal model delta sigma weight residual 108.79 112.53 -3.74 1.53e+00 4.27e-01 5.97e+00 angle pdb=" CA LYS A 46 " pdb=" CB LYS A 46 " pdb=" CG LYS A 46 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.67e+00 angle pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sigma weight residual 107.29 114.39 -7.10 3.00e+00 1.11e-01 5.60e+00 ... (remaining 13990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 5732 22.53 - 45.07: 432 45.07 - 67.60: 80 67.60 - 90.14: 23 90.14 - 112.67: 8 Dihedral angle restraints: 6275 sinusoidal: 2697 harmonic: 3578 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 161.70 -68.70 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 498 " pdb=" CB CYS A 498 " ideal model delta sinusoidal sigma weight residual 93.00 39.08 53.92 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CA CYS A 472 " pdb=" C CYS A 472 " pdb=" N LEU A 473 " pdb=" CA LEU A 473 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1275 0.065 - 0.130: 204 0.130 - 0.195: 25 0.195 - 0.260: 2 0.260 - 0.325: 1 Chirality restraints: 1507 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A1982 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1504 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2072 " 0.207 9.50e-02 1.11e+02 9.31e-02 5.90e+00 pdb=" NE ARG A2072 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A2072 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A2072 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A2072 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1880 " -0.154 9.50e-02 1.11e+02 6.94e-02 3.37e+00 pdb=" NE ARG A1880 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A1880 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A1880 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1880 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 269 " -0.015 2.00e-02 2.50e+03 1.43e-02 2.54e+00 pdb=" CG ASN A 269 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 269 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 269 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.016 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 339 2.69 - 3.24: 9056 3.24 - 3.80: 15412 3.80 - 4.35: 22520 4.35 - 4.90: 37998 Nonbonded interactions: 85325 Sorted by model distance: nonbonded pdb=" OD2 ASP A2005 " pdb=" O6 NAG C 1 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU A 329 " pdb=" OG1 THR A 369 " model vdw 2.144 3.040 nonbonded pdb=" O PHE A1592 " pdb=" NH1 ARG A1593 " model vdw 2.181 3.120 nonbonded pdb=" OE2 GLU A1559 " pdb=" OH TYR A1595 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU A1740 " pdb=" NH1 ARG A1799 " model vdw 2.218 3.120 ... (remaining 85320 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 'B' selection = chain 'C' } 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: 1.380 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.005 0.073 10349 Z= 0.208 Angle : 0.730 11.843 14039 Z= 0.358 Chirality : 0.051 0.325 1507 Planarity : 0.005 0.093 1770 Dihedral : 16.957 112.675 3954 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 18.11 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1205 helix: -1.31 (0.52), residues: 93 sheet: -0.36 (0.26), residues: 399 loop : -0.97 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A2072 TYR 0.013 0.001 TYR A 144 PHE 0.022 0.001 PHE A1900 TRP 0.016 0.001 TRP A2180 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (10332) covalent geometry : angle 0.70487 / 0.35 (13995) SS BOND : bond 0.00676 / 0.22 ( 7) SS BOND : angle 1.94847 / 1.15 ( 14) hydrogen bonds : bond 0.14545 / 8.72 ( 217) hydrogen bonds : angle 6.92878 / 4.57 ( 516) link_ALPHA1-3 : bond 0.00008 / 0.00 ( 1) link_ALPHA1-3 : angle 2.55682 / 1.27 ( 3) link_ALPHA1-6 : bond 0.00701 / 0.37 ( 1) link_ALPHA1-6 : angle 1.42058 / 0.94 ( 3) link_BETA1-4 : bond 0.00819 / 0.40 ( 4) link_BETA1-4 : angle 3.84017 / 2.37 ( 12) link_NAG-ASN : bond 0.00390 / 0.18 ( 4) link_NAG-ASN : angle 4.70570 / 2.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 1826 ASN cc_start: 0.7955 (m-40) cc_final: 0.7641 (p0) REVERT: A 2069 GLU cc_start: 0.7540 (mp0) cc_final: 0.6316 (mp0) REVERT: A 2092 LYS cc_start: 0.8087 (mttm) cc_final: 0.7692 (mtpt) REVERT: A 2156 THR cc_start: 0.8186 (p) cc_final: 0.7796 (m) outliers start: 20 outliers final: 17 residues processed: 144 average time/residue: 0.4857 time to fit residues: 75.9766 Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 1660 ASP Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1786 SER Chi-restraints excluded: chain A residue 1840 SER Chi-restraints excluded: chain A residue 1869 GLN Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2146 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 GLN A 293 GLN A 517 GLN A 639 ASN A1829 HIS A2085 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.096253 restraints weight = 11567.582| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.08 r_work: 0.2948 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10349 Z= 0.133 Angle : 0.570 9.522 14039 Z= 0.283 Chirality : 0.047 0.209 1507 Planarity : 0.004 0.035 1770 Dihedral : 11.153 96.988 1567 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.30 % Allowed : 16.54 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1205 helix: -1.29 (0.52), residues: 94 sheet: -0.34 (0.27), residues: 400 loop : -0.92 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1880 TYR 0.013 0.001 TYR A 144 PHE 0.010 0.001 PHE A2071 TRP 0.012 0.001 TRP A1665 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10332) covalent geometry : angle 0.55293 / 0.28 (13995) SS BOND : bond 0.00628 / 0.21 ( 7) SS BOND : angle 1.32464 / 0.74 ( 14) hydrogen bonds : bond 0.03506 / 2.20 ( 217) hydrogen bonds : angle 5.95159 / 3.89 ( 516) link_ALPHA1-3 : bond 0.01075 / 0.57 ( 1) link_ALPHA1-3 : angle 1.37861 / 0.82 ( 3) link_ALPHA1-6 : bond 0.01571 / 0.83 ( 1) link_ALPHA1-6 : angle 2.03090 / 1.35 ( 3) link_BETA1-4 : bond 0.00749 / 0.39 ( 4) link_BETA1-4 : angle 3.11331 / 2.16 ( 12) link_NAG-ASN : bond 0.00280 / 0.13 ( 4) link_NAG-ASN : angle 3.21705 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7760 (tt0) cc_final: 0.7183 (tt0) REVERT: A 1826 ASN cc_start: 0.8142 (m-40) cc_final: 0.7661 (p0) REVERT: A 1869 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: A 2069 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7228 (mp0) REVERT: A 2092 LYS cc_start: 0.8040 (mttm) cc_final: 0.7694 (mtpt) REVERT: A 2156 THR cc_start: 0.8148 (p) cc_final: 0.7883 (m) outliers start: 25 outliers final: 8 residues processed: 147 average time/residue: 0.4970 time to fit residues: 79.4244 Evaluate side-chains 135 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 1660 ASP Chi-restraints excluded: chain A residue 1869 GLN Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [100, 80, 74, 115, 82, 31, 76, 0, 55, 69, 43] chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.096493 restraints weight = 11686.449| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.09 r_work: 0.2956 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10349 Z= 0.125 Angle : 0.543 8.970 14039 Z= 0.268 Chirality : 0.046 0.187 1507 Planarity : 0.004 0.044 1770 Dihedral : 9.777 81.325 1552 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.39 % Allowed : 16.91 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1205 helix: -1.30 (0.51), residues: 94 sheet: -0.26 (0.27), residues: 400 loop : -0.88 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1880 TYR 0.012 0.001 TYR A 144 PHE 0.015 0.001 PHE A1900 TRP 0.011 0.001 TRP A2180 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (10332) covalent geometry : angle 0.52565 / 0.26 (13995) SS BOND : bond 0.00613 / 0.20 ( 7) SS BOND : angle 1.28800 / 0.70 ( 14) hydrogen bonds : bond 0.03183 / 2.00 ( 217) hydrogen bonds : angle 5.76980 / 3.76 ( 516) link_ALPHA1-3 : bond 0.01026 / 0.54 ( 1) link_ALPHA1-3 : angle 1.11206 / 0.56 ( 3) link_ALPHA1-6 : bond 0.01276 / 0.67 ( 1) link_ALPHA1-6 : angle 2.67347 / 1.68 ( 3) link_BETA1-4 : bond 0.00565 / 0.29 ( 4) link_BETA1-4 : angle 2.95106 / 2.10 ( 12) link_NAG-ASN : bond 0.00210 / 0.10 ( 4) link_NAG-ASN : angle 3.16448 / 1.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 451 GLU cc_start: 0.8037 (tt0) cc_final: 0.7813 (tt0) REVERT: A 464 GLU cc_start: 0.7753 (tt0) cc_final: 0.7148 (tt0) REVERT: A 484 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7007 (mtp) REVERT: A 581 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7601 (mm-40) REVERT: A 1826 ASN cc_start: 0.8161 (m-40) cc_final: 0.7641 (p0) REVERT: A 1883 MET cc_start: 0.8871 (mmp) cc_final: 0.8377 (mmm) REVERT: A 2069 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7176 (mp0) REVERT: A 2092 LYS cc_start: 0.7998 (mttm) cc_final: 0.7643 (mtpt) REVERT: A 2156 THR cc_start: 0.8109 (p) cc_final: 0.7868 (m) REVERT: A 2178 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7631 (mptt) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 0.4850 time to fit residues: 76.3213 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 1660 ASP Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2040 THR Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2178 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [63, 58, 57, 49, 8, 10, 17, 70, 99, 104, 14] chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1775 HIS A2153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097204 restraints weight = 11691.238| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.09 r_work: 0.2968 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10349 Z= 0.117 Angle : 0.531 8.338 14039 Z= 0.261 Chirality : 0.046 0.188 1507 Planarity : 0.004 0.046 1770 Dihedral : 8.677 80.555 1549 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.84 % Allowed : 18.75 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1205 helix: -1.27 (0.51), residues: 95 sheet: -0.12 (0.27), residues: 396 loop : -0.84 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2072 TYR 0.012 0.001 TYR A 144 PHE 0.015 0.001 PHE A1900 TRP 0.012 0.001 TRP A2180 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10332) covalent geometry : angle 0.51430 / 0.26 (13995) SS BOND : bond 0.00596 / 0.22 ( 7) SS BOND : angle 1.17177 / 0.63 ( 14) hydrogen bonds : bond 0.02901 / 1.83 ( 217) hydrogen bonds : angle 5.60833 / 3.64 ( 516) link_ALPHA1-3 : bond 0.01193 / 0.63 ( 1) link_ALPHA1-3 : angle 1.00936 / 0.51 ( 3) link_ALPHA1-6 : bond 0.01357 / 0.71 ( 1) link_ALPHA1-6 : angle 2.93492 / 1.73 ( 3) link_BETA1-4 : bond 0.00488 / 0.25 ( 4) link_BETA1-4 : angle 2.88429 / 2.06 ( 12) link_NAG-ASN : bond 0.00185 / 0.09 ( 4) link_NAG-ASN : angle 2.98129 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7444 (ptmm) REVERT: A 384 ASN cc_start: 0.6628 (m110) cc_final: 0.6337 (m110) REVERT: A 451 GLU cc_start: 0.7956 (tt0) cc_final: 0.7689 (tt0) REVERT: A 464 GLU cc_start: 0.7849 (tt0) cc_final: 0.7230 (tt0) REVERT: A 536 ASN cc_start: 0.7843 (m-40) cc_final: 0.7557 (m110) REVERT: A 581 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7577 (mm110) REVERT: A 1602 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7676 (mttm) REVERT: A 1679 THR cc_start: 0.8268 (t) cc_final: 0.7998 (m) REVERT: A 1826 ASN cc_start: 0.8198 (m-40) cc_final: 0.7638 (p0) REVERT: A 1883 MET cc_start: 0.8778 (mmp) cc_final: 0.8333 (mmm) REVERT: A 2069 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7162 (mp0) REVERT: A 2092 LYS cc_start: 0.7967 (mttm) cc_final: 0.7604 (mtpt) REVERT: A 2156 THR cc_start: 0.8056 (p) cc_final: 0.7800 (m) REVERT: A 2178 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7765 (mptt) outliers start: 20 outliers final: 8 residues processed: 143 average time/residue: 0.5129 time to fit residues: 79.5570 Evaluate side-chains 135 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 1602 LYS Chi-restraints excluded: chain A residue 1660 ASP Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2040 THR Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2178 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [5, 75, 107, 105, 14, 52, 57, 66, 27, 17, 61] chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093257 restraints weight = 11721.531| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.07 r_work: 0.2905 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10349 Z= 0.247 Angle : 0.622 9.420 14039 Z= 0.305 Chirality : 0.049 0.186 1507 Planarity : 0.004 0.043 1770 Dihedral : 8.357 82.961 1548 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.58 % Allowed : 17.19 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1205 helix: -1.22 (0.52), residues: 94 sheet: -0.20 (0.27), residues: 399 loop : -0.97 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1880 TYR 0.013 0.002 TYR A 144 PHE 0.016 0.002 PHE A1900 TRP 0.011 0.002 TRP A1665 HIS 0.005 0.001 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (10332) covalent geometry : angle 0.60485 / 0.30 (13995) SS BOND : bond 0.00716 / 0.24 ( 7) SS BOND : angle 1.48646 / 0.81 ( 14) hydrogen bonds : bond 0.03714 / 2.38 ( 217) hydrogen bonds : angle 5.85533 / 3.79 ( 516) link_ALPHA1-3 : bond 0.01188 / 0.63 ( 1) link_ALPHA1-3 : angle 1.04882 / 0.42 ( 3) link_ALPHA1-6 : bond 0.01350 / 0.71 ( 1) link_ALPHA1-6 : angle 3.05264 / 1.75 ( 3) link_BETA1-4 : bond 0.00474 / 0.24 ( 4) link_BETA1-4 : angle 3.22447 / 2.25 ( 12) link_NAG-ASN : bond 0.00417 / 0.20 ( 4) link_NAG-ASN : angle 3.14047 / 1.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 367 MET cc_start: 0.7942 (ttm) cc_final: 0.7319 (ttt) REVERT: A 464 GLU cc_start: 0.7873 (tt0) cc_final: 0.7259 (tt0) REVERT: A 484 MET cc_start: 0.7489 (mmp) cc_final: 0.7060 (mtp) REVERT: A 581 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7703 (mm-40) REVERT: A 653 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: A 1883 MET cc_start: 0.8907 (mmp) cc_final: 0.8462 (mmm) REVERT: A 1939 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7077 (mmm) REVERT: A 2069 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7382 (mp0) REVERT: A 2092 LYS cc_start: 0.8026 (mttm) cc_final: 0.7663 (mtmt) REVERT: A 2156 THR cc_start: 0.8176 (p) cc_final: 0.7859 (m) REVERT: A 2178 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7737 (mptt) outliers start: 39 outliers final: 16 residues processed: 150 average time/residue: 0.4808 time to fit residues: 78.6257 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 1660 ASP Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2124 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2178 LYS Chi-restraints excluded: chain A residue 2186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [63, 93, 103, 82, 115, 101, 81, 55, 92, 30, 70] chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2078 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096132 restraints weight = 11690.211| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.10 r_work: 0.2949 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10349 Z= 0.120 Angle : 0.536 8.140 14039 Z= 0.263 Chirality : 0.046 0.173 1507 Planarity : 0.004 0.050 1770 Dihedral : 7.503 83.932 1546 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.67 % Allowed : 18.57 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1205 helix: -1.18 (0.52), residues: 95 sheet: -0.23 (0.27), residues: 399 loop : -0.85 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1880 TYR 0.012 0.001 TYR A 144 PHE 0.016 0.001 PHE A1900 TRP 0.014 0.001 TRP A2180 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10332) covalent geometry : angle 0.51903 / 0.26 (13995) SS BOND : bond 0.00586 / 0.19 ( 7) SS BOND : angle 1.15838 / 0.62 ( 14) hydrogen bonds : bond 0.02909 / 1.83 ( 217) hydrogen bonds : angle 5.64839 / 3.68 ( 516) link_ALPHA1-3 : bond 0.01272 / 0.67 ( 1) link_ALPHA1-3 : angle 1.02078 / 0.42 ( 3) link_ALPHA1-6 : bond 0.01492 / 0.79 ( 1) link_ALPHA1-6 : angle 3.03593 / 1.69 ( 3) link_BETA1-4 : bond 0.00462 / 0.23 ( 4) link_BETA1-4 : angle 2.86567 / 2.02 ( 12) link_NAG-ASN : bond 0.00197 / 0.10 ( 4) link_NAG-ASN : angle 2.99724 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 384 ASN cc_start: 0.6565 (m110) cc_final: 0.6292 (m110) REVERT: A 451 GLU cc_start: 0.7989 (tt0) cc_final: 0.7740 (tt0) REVERT: A 464 GLU cc_start: 0.7841 (tt0) cc_final: 0.7210 (tt0) REVERT: A 484 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6986 (mtp) REVERT: A 536 ASN cc_start: 0.7787 (m-40) cc_final: 0.7546 (m110) REVERT: A 581 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7744 (mm-40) REVERT: A 1679 THR cc_start: 0.8175 (t) cc_final: 0.7884 (m) REVERT: A 1826 ASN cc_start: 0.8180 (m-40) cc_final: 0.7649 (p0) REVERT: A 1883 MET cc_start: 0.8756 (mmp) cc_final: 0.8455 (mmm) REVERT: A 2069 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7228 (mp0) REVERT: A 2092 LYS cc_start: 0.8027 (mttm) cc_final: 0.7628 (mtpt) REVERT: A 2110 THR cc_start: 0.8345 (m) cc_final: 0.7916 (p) REVERT: A 2145 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7231 (pp-130) REVERT: A 2156 THR cc_start: 0.8095 (p) cc_final: 0.7783 (m) REVERT: A 2178 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7720 (mptt) outliers start: 29 outliers final: 14 residues processed: 146 average time/residue: 0.4607 time to fit residues: 73.4839 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2042 LEU Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2124 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2178 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [111, 81, 98, 120, 27, 31, 33, 116, 6, 78, 52] chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091867 restraints weight = 11785.762| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.08 r_work: 0.2883 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 10349 Z= 0.320 Angle : 0.686 11.420 14039 Z= 0.338 Chirality : 0.051 0.207 1507 Planarity : 0.005 0.051 1770 Dihedral : 7.490 83.844 1544 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.03 % Allowed : 18.57 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1205 helix: -1.13 (0.52), residues: 94 sheet: -0.39 (0.26), residues: 400 loop : -1.07 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1880 TYR 0.014 0.002 TYR A 144 PHE 0.015 0.002 PHE A1900 TRP 0.013 0.002 TRP A1834 HIS 0.006 0.001 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.32 (10332) covalent geometry : angle 0.66764 / 0.33 (13995) SS BOND : bond 0.00782 / 0.26 ( 7) SS BOND : angle 2.58624 / 1.28 ( 14) hydrogen bonds : bond 0.04009 / 2.61 ( 217) hydrogen bonds : angle 5.97464 / 3.86 ( 516) link_ALPHA1-3 : bond 0.01266 / 0.67 ( 1) link_ALPHA1-3 : angle 1.20000 / 0.51 ( 3) link_ALPHA1-6 : bond 0.01477 / 0.78 ( 1) link_ALPHA1-6 : angle 2.87908 / 1.61 ( 3) link_BETA1-4 : bond 0.00447 / 0.22 ( 4) link_BETA1-4 : angle 3.29018 / 2.23 ( 12) link_NAG-ASN : bond 0.00529 / 0.25 ( 4) link_NAG-ASN : angle 3.17274 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.400 Fit side-chains REVERT: A 47 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7782 (ptmm) REVERT: A 384 ASN cc_start: 0.6583 (m110) cc_final: 0.6349 (m110) REVERT: A 464 GLU cc_start: 0.7859 (tt0) cc_final: 0.7241 (tt0) REVERT: A 536 ASN cc_start: 0.7747 (m-40) cc_final: 0.7463 (m110) REVERT: A 581 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7687 (mm-40) REVERT: A 653 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: A 1883 MET cc_start: 0.8861 (mmp) cc_final: 0.8410 (mmm) REVERT: A 1939 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7147 (mmm) REVERT: A 2069 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7294 (mp0) REVERT: A 2092 LYS cc_start: 0.7989 (mttm) cc_final: 0.7647 (mtmt) REVERT: A 2110 THR cc_start: 0.8396 (m) cc_final: 0.8038 (p) REVERT: A 2145 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7452 (pp-130) REVERT: A 2156 THR cc_start: 0.8222 (p) cc_final: 0.7877 (m) REVERT: A 2178 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7715 (mptt) outliers start: 33 outliers final: 16 residues processed: 144 average time/residue: 0.4562 time to fit residues: 71.7921 Evaluate side-chains 137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2013 ILE Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2124 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2178 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [59, 15, 56, 10, 54, 100, 3, 25, 106, 26, 74] chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1733 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095801 restraints weight = 11613.196| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.09 r_work: 0.2950 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10349 Z= 0.117 Angle : 0.542 8.190 14039 Z= 0.267 Chirality : 0.045 0.168 1507 Planarity : 0.004 0.052 1770 Dihedral : 6.837 85.607 1544 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.02 % Allowed : 19.30 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1205 helix: -1.13 (0.52), residues: 95 sheet: -0.40 (0.26), residues: 401 loop : -0.87 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1880 TYR 0.011 0.001 TYR A 144 PHE 0.015 0.001 PHE A1900 TRP 0.014 0.001 TRP A2180 HIS 0.002 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10332) covalent geometry : angle 0.52653 / 0.26 (13995) SS BOND : bond 0.00643 / 0.23 ( 7) SS BOND : angle 1.38046 / 0.69 ( 14) hydrogen bonds : bond 0.02882 / 1.82 ( 217) hydrogen bonds : angle 5.65772 / 3.68 ( 516) link_ALPHA1-3 : bond 0.01264 / 0.67 ( 1) link_ALPHA1-3 : angle 1.21968 / 0.51 ( 3) link_ALPHA1-6 : bond 0.01591 / 0.84 ( 1) link_ALPHA1-6 : angle 2.34437 / 1.31 ( 3) link_BETA1-4 : bond 0.00415 / 0.21 ( 4) link_BETA1-4 : angle 2.76917 / 1.93 ( 12) link_NAG-ASN : bond 0.00217 / 0.11 ( 4) link_NAG-ASN : angle 2.99362 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7411 (ptmm) REVERT: A 384 ASN cc_start: 0.6616 (m110) cc_final: 0.6387 (m110) REVERT: A 464 GLU cc_start: 0.7833 (tt0) cc_final: 0.7191 (tt0) REVERT: A 484 MET cc_start: 0.7294 (mmp) cc_final: 0.6890 (mtp) REVERT: A 536 ASN cc_start: 0.7802 (m-40) cc_final: 0.7522 (m110) REVERT: A 581 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7740 (mm-40) REVERT: A 1602 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7730 (mttm) REVERT: A 1679 THR cc_start: 0.8118 (t) cc_final: 0.7815 (m) REVERT: A 1826 ASN cc_start: 0.8175 (m-40) cc_final: 0.7651 (p0) REVERT: A 1883 MET cc_start: 0.8764 (mmp) cc_final: 0.8452 (mmm) REVERT: A 2069 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7229 (mp0) REVERT: A 2110 THR cc_start: 0.8326 (m) cc_final: 0.7937 (p) REVERT: A 2145 MET cc_start: 0.8028 (mtm) cc_final: 0.7455 (pp-130) REVERT: A 2156 THR cc_start: 0.8068 (p) cc_final: 0.7750 (m) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 0.4817 time to fit residues: 72.6270 Evaluate side-chains 132 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2042 LEU Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [50, 120, 43, 16, 89, 88, 82, 18, 26, 111, 23] chunk 50 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN A 581 GLN A1733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.095789 restraints weight = 11589.212| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.09 r_work: 0.2948 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10349 Z= 0.130 Angle : 0.533 7.877 14039 Z= 0.264 Chirality : 0.046 0.165 1507 Planarity : 0.004 0.056 1770 Dihedral : 6.360 83.719 1544 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.02 % Allowed : 19.76 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1205 helix: -1.07 (0.52), residues: 95 sheet: -0.32 (0.27), residues: 402 loop : -0.83 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1880 TYR 0.013 0.001 TYR A 144 PHE 0.015 0.001 PHE A1900 TRP 0.016 0.001 TRP A2180 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10332) covalent geometry : angle 0.51834 / 0.26 (13995) SS BOND : bond 0.00609 / 0.21 ( 7) SS BOND : angle 1.34662 / 0.68 ( 14) hydrogen bonds : bond 0.02928 / 1.86 ( 217) hydrogen bonds : angle 5.58353 / 3.64 ( 516) link_ALPHA1-3 : bond 0.01220 / 0.64 ( 1) link_ALPHA1-3 : angle 1.22306 / 0.51 ( 3) link_ALPHA1-6 : bond 0.01350 / 0.71 ( 1) link_ALPHA1-6 : angle 1.52053 / 0.88 ( 3) link_BETA1-4 : bond 0.00360 / 0.18 ( 4) link_BETA1-4 : angle 2.70939 / 1.84 ( 12) link_NAG-ASN : bond 0.00201 / 0.10 ( 4) link_NAG-ASN : angle 2.97233 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7450 (ptmm) REVERT: A 464 GLU cc_start: 0.7859 (tt0) cc_final: 0.7226 (tt0) REVERT: A 484 MET cc_start: 0.7026 (mmp) cc_final: 0.6619 (mtp) REVERT: A 1602 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7720 (mttm) REVERT: A 1679 THR cc_start: 0.8205 (t) cc_final: 0.7914 (m) REVERT: A 1826 ASN cc_start: 0.8218 (m-40) cc_final: 0.7640 (p0) REVERT: A 1883 MET cc_start: 0.8684 (mmp) cc_final: 0.8418 (mmm) REVERT: A 1959 SER cc_start: 0.7254 (m) cc_final: 0.6941 (p) REVERT: A 2069 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7266 (mp0) REVERT: A 2110 THR cc_start: 0.8309 (m) cc_final: 0.7898 (p) REVERT: A 2145 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7458 (pp-130) REVERT: A 2156 THR cc_start: 0.8067 (p) cc_final: 0.7719 (m) outliers start: 22 outliers final: 16 residues processed: 133 average time/residue: 0.4778 time to fit residues: 69.4142 Evaluate side-chains 135 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2040 THR Chi-restraints excluded: chain A residue 2042 LEU Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2124 SER Chi-restraints excluded: chain A residue 2145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [103, 80, 77, 63, 25, 29, 108, 89, 4, 87, 51] chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 HIS A 601 HIS A 609 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098242 restraints weight = 11477.089| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.08 r_work: 0.2989 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10349 Z= 0.092 Angle : 0.500 6.838 14039 Z= 0.249 Chirality : 0.044 0.158 1507 Planarity : 0.004 0.055 1770 Dihedral : 5.991 83.283 1544 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.75 % Allowed : 20.13 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1205 helix: -1.07 (0.52), residues: 95 sheet: -0.27 (0.27), residues: 402 loop : -0.72 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1880 TYR 0.011 0.001 TYR A 477 PHE 0.016 0.001 PHE A1900 TRP 0.017 0.001 TRP A2180 HIS 0.002 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 (10332) covalent geometry : angle 0.48653 / 0.25 (13995) SS BOND : bond 0.00526 / 0.17 ( 7) SS BOND : angle 1.10849 / 0.56 ( 14) hydrogen bonds : bond 0.02587 / 1.62 ( 217) hydrogen bonds : angle 5.41414 / 3.54 ( 516) link_ALPHA1-3 : bond 0.01188 / 0.63 ( 1) link_ALPHA1-3 : angle 1.22073 / 0.51 ( 3) link_ALPHA1-6 : bond 0.00973 / 0.51 ( 1) link_ALPHA1-6 : angle 1.14827 / 0.70 ( 3) link_BETA1-4 : bond 0.00357 / 0.17 ( 4) link_BETA1-4 : angle 2.47018 / 1.66 ( 12) link_NAG-ASN : bond 0.00153 / 0.08 ( 4) link_NAG-ASN : angle 2.82532 / 1.70 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7493 (ptmm) REVERT: A 118 ARG cc_start: 0.8317 (mmt90) cc_final: 0.7934 (mmp80) REVERT: A 451 GLU cc_start: 0.8001 (tt0) cc_final: 0.7763 (tt0) REVERT: A 464 GLU cc_start: 0.7797 (tt0) cc_final: 0.7185 (tt0) REVERT: A 653 ASP cc_start: 0.7027 (m-30) cc_final: 0.6726 (m-30) REVERT: A 1602 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7726 (mttm) REVERT: A 1679 THR cc_start: 0.8112 (t) cc_final: 0.7833 (m) REVERT: A 1826 ASN cc_start: 0.8260 (m-40) cc_final: 0.7685 (OUTLIER) REVERT: A 1883 MET cc_start: 0.8671 (mmp) cc_final: 0.8416 (mmm) REVERT: A 2042 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7162 (mp) REVERT: A 2069 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7241 (mp0) REVERT: A 2110 THR cc_start: 0.8373 (m) cc_final: 0.7942 (p) REVERT: A 2145 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7470 (pp-130) REVERT: A 2156 THR cc_start: 0.7981 (p) cc_final: 0.7664 (m) outliers start: 19 outliers final: 9 residues processed: 132 average time/residue: 0.4812 time to fit residues: 69.0145 Evaluate side-chains 126 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 1885 LEU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2042 LEU Chi-restraints excluded: chain A residue 2124 SER Chi-restraints excluded: chain A residue 2145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: [65, 15, 48, 119, 49, 5, 81, 25, 36, 23, 13] chunk 65 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN A1713 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098328 restraints weight = 11562.861| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.09 r_work: 0.2987 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10349 Z= 0.095 Angle : 0.493 6.757 14039 Z= 0.246 Chirality : 0.044 0.146 1507 Planarity : 0.004 0.058 1770 Dihedral : 5.754 81.393 1543 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.47 % Allowed : 20.50 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1205 helix: -1.05 (0.51), residues: 96 sheet: -0.17 (0.27), residues: 407 loop : -0.66 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1880 TYR 0.012 0.001 TYR A 477 PHE 0.016 0.001 PHE A1900 TRP 0.016 0.001 TRP A2180 HIS 0.002 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.09 (10332) covalent geometry : angle 0.47999 / 0.24 (13995) SS BOND : bond 0.00535 / 0.17 ( 7) SS BOND : angle 1.16557 / 0.59 ( 14) hydrogen bonds : bond 0.02570 / 1.60 ( 217) hydrogen bonds : angle 5.34041 / 3.49 ( 516) link_ALPHA1-3 : bond 0.01058 / 0.56 ( 1) link_ALPHA1-3 : angle 1.16705 / 0.50 ( 3) link_ALPHA1-6 : bond 0.01097 / 0.58 ( 1) link_ALPHA1-6 : angle 1.16929 / 0.75 ( 3) link_BETA1-4 : bond 0.00374 / 0.18 ( 4) link_BETA1-4 : angle 2.38819 / 1.57 ( 12) link_NAG-ASN : bond 0.00146 / 0.07 ( 4) link_NAG-ASN : angle 2.78893 / 1.68 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.05 seconds wall clock time: 53 minutes 36.00 seconds (3216.00 seconds total)