Starting phenix.real_space_refine on Fri Oct 23 08:35:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36jk_77610/10_2026/36jk_77610.cif Found real_map, /net/cci-nas-00/data/ceres_data/36jk_77610/10_2026/36jk_77610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36jk_77610/10_2026/36jk_77610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36jk_77610/10_2026/36jk_77610.map" model { file = "/net/cci-nas-00/data/ceres_data/36jk_77610/10_2026/36jk_77610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36jk_77610/10_2026/36jk_77610.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Ca 1 9.91 5 Cu 2 5.60 5 S 53 5.16 5 C 5831 2.51 5 N 1515 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 9039 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8966 Classifications: {'peptide': 1106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1051} Chain breaks: 16 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 73 Unusual residues: {' CA': 1, 'CPS': 1, 'CU1': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7277 SG CYS A2000 40.427 55.252 56.231 1.00 9.48 S ATOM 2142 SG CYS A 310 39.315 69.671 70.307 1.00 15.59 S Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 9039 At special positions: 0 Unit cell: (73.603, 100.894, 120.742, 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) Cu 2 28.99 Ca 1 19.99 S 53 16.00 O 1637 8.00 N 1515 7.00 C 5831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.01 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " 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 NAG-ASN " NAG A2401 " - " ASN A2118 " " NAG A2402 " - " ASN A 239 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 295.6 milliseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 19 sheets defined 8.1% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.817A pdb=" N GLY A 70 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 removed outlier: 3.810A pdb=" N GLU A 110 " --> pdb=" O LYS A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.634A pdb=" N ASN A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.509A pdb=" N SER A 446 " --> pdb=" O GLN A 443 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 447 " --> pdb=" O HIS A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 443 through 447' Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.685A pdb=" N LEU A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 1752 through 1757 removed outlier: 4.165A pdb=" N HIS A1755 " --> pdb=" O LEU A1752 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A1757 " --> pdb=" O GLU A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1890 through 1899 removed outlier: 3.874A pdb=" N ARG A1897 " --> pdb=" O GLU A1893 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A1898 " --> pdb=" O ASN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2009 removed outlier: 3.604A pdb=" N ALA A2008 " --> pdb=" O GLU A2004 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53 removed outlier: 3.661A pdb=" N VAL A 52 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG A 3 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR A 87 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 5 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS A 89 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 7 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 84 " --> pdb=" O TRP A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.015A pdb=" N ILE A 76 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N CYS A 179 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 78 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 234 removed outlier: 6.676A pdb=" N PHE A 195 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 258 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 197 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET A 260 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 199 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 removed outlier: 5.796A pdb=" N GLY A 247 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 384 removed outlier: 3.637A pdb=" N ILE A 463 " --> pdb=" O TYR A 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394 removed outlier: 3.598A pdb=" N ARG A 427 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 391 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 425 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.709A pdb=" N THR A 438 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 477 Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.772A pdb=" N SER A 616 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 572 " --> pdb=" O TYR A 636 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 639 " --> pdb=" O GLU A 676 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 626 through 629 Processing sheet with id=AB2, first strand: chain 'A' and resid 1730 through 1738 removed outlier: 4.572A pdb=" N PHE A1699 " --> pdb=" O PHE A1738 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG A1696 " --> pdb=" O MET A1772 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A1774 " --> pdb=" O ARG A1696 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A1698 " --> pdb=" O THR A1774 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG A1776 " --> pdb=" O TYR A1698 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A1700 " --> pdb=" O ARG A1776 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A1811 " --> pdb=" O ASN A1777 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1832 through 1838 Processing sheet with id=AB4, first strand: chain 'A' and resid 1917 through 1921 removed outlier: 6.155A pdb=" N GLN A1874 " --> pdb=" O ARG A1941 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR A1943 " --> pdb=" O GLN A1874 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A1876 " --> pdb=" O TYR A1943 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU A1945 " --> pdb=" O PHE A1876 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A1878 " --> pdb=" O LEU A1945 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1933 through 1935 Processing sheet with id=AB6, first strand: chain 'A' and resid 1963 through 1966 Processing sheet with id=AB7, first strand: chain 'A' and resid 2023 through 2024 removed outlier: 6.797A pdb=" N GLU A2165 " --> pdb=" O ILE A2084 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE A2084 " --> pdb=" O GLU A2165 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET A2167 " --> pdb=" O HIS A2082 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A2080 " --> pdb=" O CYS A2169 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ILE A2080 " --> pdb=" O PRO A2142 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS A2082 " --> pdb=" O PHE A2140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A2140 " --> pdb=" O HIS A2082 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2037 through 2039 removed outlier: 6.649A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2037 through 2039 removed outlier: 6.649A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2238 through 2240 211 hydrogen bonds defined for protein. 528 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: 1.75 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1415 1.31 - 1.44: 2725 1.44 - 1.56: 5058 1.56 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 9286 Sorted by residual: bond pdb=" CA MET A2010 " pdb=" C MET A2010 " ideal model delta sigma weight residual 1.530 1.418 0.111 1.10e-02 8.26e+03 1.02e+02 bond pdb=" C MET A2010 " pdb=" O MET A2010 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.09e-02 8.42e+03 1.60e+01 bond pdb=" C MET A2010 " pdb=" N SER A2011 " ideal model delta sigma weight residual 1.331 1.284 0.047 1.22e-02 6.72e+03 1.47e+01 bond pdb=" C HIS A 267 " pdb=" O HIS A 267 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.22e-02 6.72e+03 1.29e+01 bond pdb=" CA HIS A 267 " pdb=" C HIS A 267 " ideal model delta sigma weight residual 1.521 1.480 0.041 1.20e-02 6.94e+03 1.15e+01 ... (remaining 9281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12113 1.76 - 3.52: 384 3.52 - 5.28: 73 5.28 - 7.05: 10 7.05 - 8.81: 3 Bond angle restraints: 12583 Sorted by residual: angle pdb=" C MET A2010 " pdb=" CA MET A2010 " pdb=" CB MET A2010 " ideal model delta sigma weight residual 112.00 103.98 8.02 1.61e+00 3.86e-01 2.48e+01 angle pdb=" N GLY A2168 " pdb=" CA GLY A2168 " pdb=" C GLY A2168 " ideal model delta sigma weight residual 111.42 118.53 -7.11 1.51e+00 4.39e-01 2.21e+01 angle pdb=" CA LYS A2239 " pdb=" CB LYS A2239 " pdb=" CG LYS A2239 " ideal model delta sigma weight residual 114.10 122.91 -8.81 2.00e+00 2.50e-01 1.94e+01 angle pdb=" C MET A2176 " pdb=" CA MET A2176 " pdb=" CB MET A2176 " ideal model delta sigma weight residual 110.33 113.93 -3.60 1.02e+00 9.61e-01 1.24e+01 angle pdb=" CA MET A2176 " pdb=" CB MET A2176 " pdb=" CG MET A2176 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 12578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.90: 5132 25.90 - 51.79: 365 51.79 - 77.69: 38 77.69 - 103.59: 5 103.59 - 129.49: 1 Dihedral angle restraints: 5541 sinusoidal: 2325 harmonic: 3216 Sorted by residual: dihedral pdb=" CB CYS A 630 " pdb=" SG CYS A 630 " pdb=" SG CYS A 711 " pdb=" CB CYS A 711 " ideal model delta sinusoidal sigma weight residual 93.00 154.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CA SER A1787 " pdb=" C SER A1787 " pdb=" N SER A1788 " pdb=" CA SER A1788 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE A 608 " pdb=" C PHE A 608 " pdb=" N GLN A 609 " pdb=" CA GLN A 609 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 5538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1050 0.051 - 0.101: 234 0.101 - 0.152: 70 0.152 - 0.203: 1 0.203 - 0.253: 2 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CB ILE A 617 " pdb=" CA ILE A 617 " pdb=" CG1 ILE A 617 " pdb=" CG2 ILE A 617 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1 NAG A2401 " pdb=" ND2 ASN A2118 " pdb=" C2 NAG A2401 " pdb=" O5 NAG A2401 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.65e-01 ... (remaining 1354 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A2141 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO A2142 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A2142 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A2142 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 597 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 598 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A2176 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A2177 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A2177 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2177 " 0.029 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 124 2.61 - 3.18: 7602 3.18 - 3.75: 13385 3.75 - 4.33: 20377 4.33 - 4.90: 33998 Nonbonded interactions: 75486 Sorted by model distance: nonbonded pdb=" O SER A2265 " pdb=" OG1 THR A2303 " model vdw 2.036 3.040 nonbonded pdb=" OG SER A1839 " pdb=" OD2 ASP A1846 " model vdw 2.059 3.040 nonbonded pdb=" OE2 GLU A 11 " pdb=" OG SER A 93 " model vdw 2.119 3.040 nonbonded pdb=" OG1 THR A 55 " pdb=" O ILE A 61 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP A 433 " pdb=" OG1 THR A 435 " model vdw 2.206 3.040 ... (remaining 75481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.060 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 0.111 9294 Z= 0.245 Angle : 0.764 8.808 12601 Z= 0.404 Chirality : 0.048 0.253 1357 Planarity : 0.006 0.062 1577 Dihedral : 16.759 129.487 3455 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.30 % Allowed : 21.34 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.35 (0.24), residues: 1072 helix: -2.83 (0.53), residues: 76 sheet: -2.20 (0.26), residues: 342 loop : -2.20 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2033 TYR 0.017 0.002 TYR A1786 PHE 0.014 0.002 PHE A2035 TRP 0.012 0.001 TRP A1817 HIS 0.018 0.001 HIS A2007 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.24 ( 9286) covalent geometry : angle 0.76229 / 0.40 (12583) SS BOND : bond 0.00701 / 0.52 ( 6) SS BOND : angle 1.14880 / 0.63 ( 12) hydrogen bonds : bond 0.17045 / 10.89 ( 198) hydrogen bonds : angle 8.40152 / 5.60 ( 528) link_NAG-ASN : bond 0.00448 / 0.23 ( 2) link_NAG-ASN : angle 1.81876 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.311 Fit side-chains REVERT: A 380 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7118 (tptp) REVERT: A 1721 ARG cc_start: 0.4915 (mmp80) cc_final: 0.4671 (mmm-85) REVERT: A 1792 TYR cc_start: 0.8273 (m-80) cc_final: 0.7732 (m-80) REVERT: A 2176 MET cc_start: 0.3686 (ptm) cc_final: 0.3468 (ptm) outliers start: 3 outliers final: 1 residues processed: 137 average time/residue: 0.0909 time to fit residues: 17.7092 Evaluate side-chains 133 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0270 chunk 106 optimal weight: 10.0000 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN A1919 HIS A1954 HIS A2082 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138123 restraints weight = 10543.349| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.75 r_work: 0.3443 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9294 Z= 0.112 Angle : 0.579 6.472 12601 Z= 0.301 Chirality : 0.045 0.204 1357 Planarity : 0.005 0.053 1577 Dihedral : 6.989 124.791 1325 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.03 % Allowed : 19.51 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.04 (0.24), residues: 1072 helix: -2.29 (0.54), residues: 77 sheet: -1.91 (0.27), residues: 353 loop : -2.07 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2304 TYR 0.013 0.001 TYR A1837 PHE 0.016 0.001 PHE A1983 TRP 0.011 0.001 TRP A 688 HIS 0.008 0.001 HIS A2007 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9286) covalent geometry : angle 0.57646 / 0.30 (12583) SS BOND : bond 0.00279 / 0.21 ( 6) SS BOND : angle 0.55039 / 0.31 ( 12) hydrogen bonds : bond 0.03178 / 2.12 ( 198) hydrogen bonds : angle 6.36056 / 4.32 ( 528) link_NAG-ASN : bond 0.00803 / 0.41 ( 2) link_NAG-ASN : angle 2.31401 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.278 Fit side-chains REVERT: A 65 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6907 (mtp-110) REVERT: A 263 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 380 LYS cc_start: 0.7524 (mmmt) cc_final: 0.7022 (tptp) REVERT: A 501 PHE cc_start: 0.8438 (t80) cc_final: 0.8195 (t80) REVERT: A 620 TYR cc_start: 0.8429 (m-80) cc_final: 0.8189 (m-80) REVERT: A 636 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 696 ASP cc_start: 0.7272 (p0) cc_final: 0.7051 (m-30) REVERT: A 1714 SER cc_start: 0.7390 (OUTLIER) cc_final: 0.7132 (m) REVERT: A 1748 TYR cc_start: 0.7317 (m-80) cc_final: 0.7088 (m-80) REVERT: A 1792 TYR cc_start: 0.8473 (m-80) cc_final: 0.7815 (m-80) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 0.0801 time to fit residues: 17.4510 Evaluate side-chains 140 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1936 GLN Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [69, 22, 18, 98, 101, 84, 52, 107, 71, 87, 42] chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 18 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 249 HIS A 632 HIS A1745 GLN ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124040 restraints weight = 10905.068| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.77 r_work: 0.3191 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9294 Z= 0.245 Angle : 0.670 7.777 12601 Z= 0.348 Chirality : 0.048 0.205 1357 Planarity : 0.005 0.048 1577 Dihedral : 7.311 114.324 1325 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.76 % Allowed : 19.31 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.12 (0.24), residues: 1072 helix: -2.31 (0.53), residues: 81 sheet: -1.93 (0.27), residues: 350 loop : -2.16 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 279 TYR 0.016 0.002 TYR A1837 PHE 0.019 0.002 PHE A1983 TRP 0.012 0.002 TRP A1817 HIS 0.006 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 ( 9286) covalent geometry : angle 0.66873 / 0.35 (12583) SS BOND : bond 0.00421 / 0.31 ( 6) SS BOND : angle 0.73633 / 0.43 ( 12) hydrogen bonds : bond 0.03549 / 2.38 ( 198) hydrogen bonds : angle 6.42148 / 4.33 ( 528) link_NAG-ASN : bond 0.00642 / 0.33 ( 2) link_NAG-ASN : angle 2.08513 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 209 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8738 (m90) REVERT: A 316 GLN cc_start: 0.7067 (tt0) cc_final: 0.6825 (tp40) REVERT: A 380 LYS cc_start: 0.7342 (mmmt) cc_final: 0.6921 (tptp) REVERT: A 620 TYR cc_start: 0.8479 (m-80) cc_final: 0.8230 (m-80) REVERT: A 636 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 1792 TYR cc_start: 0.8589 (m-80) cc_final: 0.7900 (m-80) REVERT: A 1970 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7033 (pt0) outliers start: 37 outliers final: 19 residues processed: 162 average time/residue: 0.0935 time to fit residues: 21.4951 Evaluate side-chains 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1745 GLN Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 2012 THR Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [26, 11, 50, 3, 18, 47, 87, 37, 31, 4, 15] chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.0270 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 161 HIS A 169 ASN A 602 GLN A 684 ASN ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136308 restraints weight = 10596.151| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.73 r_work: 0.3282 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9294 Z= 0.109 Angle : 0.573 9.192 12601 Z= 0.295 Chirality : 0.045 0.190 1357 Planarity : 0.005 0.052 1577 Dihedral : 6.849 111.828 1325 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.85 % Allowed : 21.04 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.92 (0.24), residues: 1072 helix: -1.96 (0.57), residues: 78 sheet: -1.88 (0.27), residues: 346 loop : -1.99 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2033 TYR 0.022 0.001 TYR A1786 PHE 0.019 0.001 PHE A1983 TRP 0.011 0.001 TRP A 255 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9286) covalent geometry : angle 0.57057 / 0.29 (12583) SS BOND : bond 0.00399 / 0.24 ( 6) SS BOND : angle 0.59242 / 0.33 ( 12) hydrogen bonds : bond 0.02910 / 1.97 ( 198) hydrogen bonds : angle 5.92185 / 4.02 ( 528) link_NAG-ASN : bond 0.00647 / 0.34 ( 2) link_NAG-ASN : angle 2.25604 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.284 Fit side-chains REVERT: A 65 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6871 (mtp-110) REVERT: A 380 LYS cc_start: 0.7349 (mmmt) cc_final: 0.6948 (tptp) REVERT: A 527 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7540 (tmt170) REVERT: A 539 MET cc_start: 0.7762 (ttp) cc_final: 0.7406 (ttp) REVERT: A 636 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 1714 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7161 (m) REVERT: A 1792 TYR cc_start: 0.8544 (m-80) cc_final: 0.7895 (m-80) REVERT: A 1970 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: A 2027 MET cc_start: 0.8643 (mmt) cc_final: 0.8275 (tpt) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 0.0857 time to fit residues: 18.7481 Evaluate side-chains 142 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2020 LYS Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2326 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [98, 43, 11, 3, 100, 96, 62, 15, 19, 6, 107] chunk 98 optimal weight: 10.0000 chunk 43 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121928 restraints weight = 10985.043| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.91 r_work: 0.3366 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9294 Z= 0.187 Angle : 0.613 7.862 12601 Z= 0.316 Chirality : 0.046 0.200 1357 Planarity : 0.005 0.049 1577 Dihedral : 6.939 110.960 1325 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.56 % Allowed : 21.34 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.87 (0.24), residues: 1072 helix: -1.93 (0.57), residues: 79 sheet: -1.84 (0.27), residues: 335 loop : -1.97 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.025 0.002 TYR A 81 PHE 0.014 0.002 PHE A2014 TRP 0.020 0.001 TRP A 688 HIS 0.007 0.001 HIS A2007 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 9286) covalent geometry : angle 0.61171 / 0.32 (12583) SS BOND : bond 0.00508 / 0.38 ( 6) SS BOND : angle 0.74258 / 0.43 ( 12) hydrogen bonds : bond 0.03081 / 2.08 ( 198) hydrogen bonds : angle 5.92745 / 4.01 ( 528) link_NAG-ASN : bond 0.00588 / 0.31 ( 2) link_NAG-ASN : angle 2.06376 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6991 (tptp) REVERT: A 539 MET cc_start: 0.7784 (ttp) cc_final: 0.7559 (tmm) REVERT: A 636 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7556 (t80) REVERT: A 1714 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.7225 (m) REVERT: A 1792 TYR cc_start: 0.8600 (m-80) cc_final: 0.8019 (m-80) REVERT: A 1970 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7075 (pt0) outliers start: 35 outliers final: 20 residues processed: 157 average time/residue: 0.0936 time to fit residues: 20.5769 Evaluate side-chains 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1697 HIS Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 2012 THR Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [22, 83, 109, 104, 84, 89, 31, 25, 94, 17, 42] chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 GLN ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1822 HIS A2007 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139777 restraints weight = 10601.690| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.75 r_work: 0.3261 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9294 Z= 0.153 Angle : 0.591 7.765 12601 Z= 0.305 Chirality : 0.045 0.196 1357 Planarity : 0.004 0.051 1577 Dihedral : 6.836 110.412 1325 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.46 % Allowed : 21.85 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.80 (0.24), residues: 1072 helix: -1.77 (0.58), residues: 78 sheet: -1.80 (0.27), residues: 335 loop : -1.94 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2033 TYR 0.021 0.001 TYR A 81 PHE 0.014 0.001 PHE A2014 TRP 0.016 0.001 TRP A 688 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9286) covalent geometry : angle 0.58922 / 0.30 (12583) SS BOND : bond 0.00314 / 0.23 ( 6) SS BOND : angle 0.69480 / 0.39 ( 12) hydrogen bonds : bond 0.02950 / 2.00 ( 198) hydrogen bonds : angle 5.76564 / 3.90 ( 528) link_NAG-ASN : bond 0.00592 / 0.31 ( 2) link_NAG-ASN : angle 2.08198 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.7371 (mmmt) cc_final: 0.6963 (tptp) REVERT: A 539 MET cc_start: 0.7727 (ttp) cc_final: 0.7458 (ttp) REVERT: A 636 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 1714 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.7186 (m) REVERT: A 1776 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8008 (tpt-90) REVERT: A 1792 TYR cc_start: 0.8575 (m-80) cc_final: 0.7967 (m-80) REVERT: A 1970 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6905 (pt0) REVERT: A 2027 MET cc_start: 0.8615 (mmt) cc_final: 0.8378 (tpt) outliers start: 34 outliers final: 19 residues processed: 155 average time/residue: 0.0946 time to fit residues: 20.6057 Evaluate side-chains 154 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 2012 THR Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [85, 33, 26, 59, 87, 67, 27, 89, 78, 64, 6] chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 HIS A 615 HIS A 660 HIS A 684 ASN ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124972 restraints weight = 10972.455| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.83 r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9294 Z= 0.188 Angle : 0.620 8.199 12601 Z= 0.321 Chirality : 0.046 0.201 1357 Planarity : 0.005 0.049 1577 Dihedral : 6.919 110.212 1325 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.35 % Allowed : 22.05 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.85 (0.24), residues: 1072 helix: -1.79 (0.58), residues: 80 sheet: -1.79 (0.27), residues: 338 loop : -2.00 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 279 TYR 0.019 0.002 TYR A 81 PHE 0.014 0.002 PHE A2014 TRP 0.016 0.001 TRP A 688 HIS 0.008 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 9286) covalent geometry : angle 0.61849 / 0.32 (12583) SS BOND : bond 0.00354 / 0.26 ( 6) SS BOND : angle 0.80598 / 0.46 ( 12) hydrogen bonds : bond 0.03086 / 2.10 ( 198) hydrogen bonds : angle 5.81069 / 3.91 ( 528) link_NAG-ASN : bond 0.00593 / 0.31 ( 2) link_NAG-ASN : angle 2.04339 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.7347 (mmmt) cc_final: 0.6940 (tptp) REVERT: A 539 MET cc_start: 0.7736 (ttp) cc_final: 0.7441 (ttp) REVERT: A 636 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 1714 SER cc_start: 0.7510 (OUTLIER) cc_final: 0.7248 (m) REVERT: A 1776 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8079 (tpt-90) REVERT: A 1792 TYR cc_start: 0.8585 (m-80) cc_final: 0.7989 (m-80) REVERT: A 1970 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7032 (pt0) REVERT: A 2027 MET cc_start: 0.8531 (mmt) cc_final: 0.8307 (tpt) outliers start: 33 outliers final: 24 residues processed: 152 average time/residue: 0.0979 time to fit residues: 20.7888 Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1697 HIS Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 2012 THR Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2149 ILE Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [48, 82, 38, 63, 84, 44, 72, 7, 43, 93, 53] chunk 48 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 ASN ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124920 restraints weight = 10966.254| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.81 r_work: 0.3237 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9294 Z= 0.159 Angle : 0.598 8.377 12601 Z= 0.309 Chirality : 0.045 0.198 1357 Planarity : 0.005 0.050 1577 Dihedral : 6.857 110.211 1325 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.66 % Allowed : 22.15 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.76 (0.24), residues: 1072 helix: -1.68 (0.59), residues: 79 sheet: -1.68 (0.27), residues: 327 loop : -1.98 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.026 0.001 TYR A1786 PHE 0.014 0.001 PHE A2014 TRP 0.016 0.001 TRP A 688 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9286) covalent geometry : angle 0.59668 / 0.31 (12583) SS BOND : bond 0.00357 / 0.27 ( 6) SS BOND : angle 0.75660 / 0.42 ( 12) hydrogen bonds : bond 0.02983 / 2.03 ( 198) hydrogen bonds : angle 5.72476 / 3.86 ( 528) link_NAG-ASN : bond 0.00593 / 0.31 ( 2) link_NAG-ASN : angle 2.04912 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.7345 (mmmt) cc_final: 0.6939 (tptp) REVERT: A 539 MET cc_start: 0.7714 (ttp) cc_final: 0.7429 (ttp) REVERT: A 553 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 636 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7521 (t80) REVERT: A 1714 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.7250 (m) REVERT: A 1745 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7864 (tp40) REVERT: A 1776 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8066 (tpt-90) REVERT: A 1792 TYR cc_start: 0.8586 (m-80) cc_final: 0.8028 (m-80) REVERT: A 1970 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: A 2027 MET cc_start: 0.8468 (mmt) cc_final: 0.8242 (tpt) REVERT: A 2087 GLN cc_start: 0.5183 (pm20) cc_final: 0.4266 (pm20) outliers start: 36 outliers final: 25 residues processed: 155 average time/residue: 0.0929 time to fit residues: 20.3287 Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1697 HIS Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2012 THR Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2149 ILE Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [98, 3, 58, 92, 90, 33, 105, 55, 82, 22, 0] chunk 98 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 ASN ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.151057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121210 restraints weight = 10952.280| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.90 r_work: 0.3194 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9294 Z= 0.198 Angle : 0.631 9.218 12601 Z= 0.325 Chirality : 0.046 0.203 1357 Planarity : 0.005 0.050 1577 Dihedral : 6.927 110.097 1325 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.96 % Allowed : 21.85 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.82 (0.24), residues: 1072 helix: -1.69 (0.59), residues: 80 sheet: -1.71 (0.27), residues: 334 loop : -2.04 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.022 0.002 TYR A1786 PHE 0.015 0.002 PHE A2014 TRP 0.017 0.001 TRP A 688 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 9286) covalent geometry : angle 0.62922 / 0.33 (12583) SS BOND : bond 0.00432 / 0.32 ( 6) SS BOND : angle 0.88227 / 0.50 ( 12) hydrogen bonds : bond 0.03126 / 2.12 ( 198) hydrogen bonds : angle 5.80076 / 3.91 ( 528) link_NAG-ASN : bond 0.00569 / 0.30 ( 2) link_NAG-ASN : angle 2.03370 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6921 (tptp) REVERT: A 539 MET cc_start: 0.7652 (ttp) cc_final: 0.7397 (ttp) REVERT: A 553 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 633 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 636 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 1714 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7246 (m) REVERT: A 1776 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8161 (tpt-90) REVERT: A 1792 TYR cc_start: 0.8583 (m-80) cc_final: 0.7948 (m-80) REVERT: A 1895 MET cc_start: 0.7663 (ttm) cc_final: 0.7154 (tpt) REVERT: A 1970 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: A 2027 MET cc_start: 0.8439 (mmt) cc_final: 0.8225 (tpt) REVERT: A 2087 GLN cc_start: 0.5369 (pm20) cc_final: 0.4514 (pm20) outliers start: 39 outliers final: 26 residues processed: 160 average time/residue: 0.0917 time to fit residues: 20.4442 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1697 HIS Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 2012 THR Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2149 ILE Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [42, 104, 56, 97, 6, 74, 106, 98, 12, 63, 39] chunk 42 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 HIS A 684 ASN ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130434 restraints weight = 10778.766| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.80 r_work: 0.3257 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9294 Z= 0.119 Angle : 0.575 8.948 12601 Z= 0.298 Chirality : 0.045 0.192 1357 Planarity : 0.004 0.053 1577 Dihedral : 6.682 109.981 1325 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.85 % Allowed : 23.07 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.24), residues: 1072 helix: -1.42 (0.62), residues: 78 sheet: -1.52 (0.28), residues: 317 loop : -1.95 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2116 TYR 0.021 0.001 TYR A1786 PHE 0.015 0.001 PHE A1983 TRP 0.014 0.001 TRP A 688 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9286) covalent geometry : angle 0.57296 / 0.30 (12583) SS BOND : bond 0.00310 / 0.23 ( 6) SS BOND : angle 0.69061 / 0.37 ( 12) hydrogen bonds : bond 0.02792 / 1.90 ( 198) hydrogen bonds : angle 5.58699 / 3.78 ( 528) link_NAG-ASN : bond 0.00630 / 0.33 ( 2) link_NAG-ASN : angle 2.09359 / 1.22 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.302 Fit side-chains REVERT: A 65 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6952 (mtp-110) REVERT: A 380 LYS cc_start: 0.7340 (mmmt) cc_final: 0.6939 (tptp) REVERT: A 583 ARG cc_start: 0.6510 (ptt-90) cc_final: 0.6257 (ptt-90) REVERT: A 636 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 1714 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7183 (m) REVERT: A 1776 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8203 (tpt-90) REVERT: A 1792 TYR cc_start: 0.8565 (m-80) cc_final: 0.7966 (m-80) REVERT: A 1895 MET cc_start: 0.7588 (ttm) cc_final: 0.7100 (tpt) REVERT: A 1970 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: A 2087 GLN cc_start: 0.5215 (pm20) cc_final: 0.4424 (pm20) REVERT: A 2147 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7517 (tpt-90) outliers start: 28 outliers final: 17 residues processed: 154 average time/residue: 0.0928 time to fit residues: 20.0925 Evaluate side-chains 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1970 GLU Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2139 ILE Chi-restraints excluded: chain A residue 2147 ARG Chi-restraints excluded: chain A residue 2149 ILE Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [13, 100, 106, 32, 58, 80, 70, 65, 42, 69, 63] chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 HIS A 660 HIS ** A1822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126076 restraints weight = 10791.514| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.80 r_work: 0.3248 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9294 Z= 0.194 Angle : 0.631 9.591 12601 Z= 0.325 Chirality : 0.046 0.203 1357 Planarity : 0.005 0.050 1577 Dihedral : 6.647 109.517 1323 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.05 % Allowed : 23.27 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.24), residues: 1072 helix: -1.51 (0.61), residues: 79 sheet: -1.63 (0.27), residues: 335 loop : -1.98 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 279 TYR 0.018 0.002 TYR A1786 PHE 0.015 0.002 PHE A2014 TRP 0.014 0.001 TRP A 688 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 9286) covalent geometry : angle 0.62949 / 0.33 (12583) SS BOND : bond 0.00437 / 0.32 ( 6) SS BOND : angle 0.79785 / 0.46 ( 12) hydrogen bonds : bond 0.03090 / 2.09 ( 198) hydrogen bonds : angle 5.71931 / 3.86 ( 528) link_NAG-ASN : bond 0.00576 / 0.30 ( 2) link_NAG-ASN : angle 2.03837 / 1.20 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.98 seconds wall clock time: 38 minutes 22.65 seconds (2302.65 seconds total)