Starting phenix.real_space_refine on Thu Mar 5 04:03:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zma_14793/03_2026/7zma_14793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zma_14793/03_2026/7zma_14793.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 { model { file = "/net/cci-nas-00/data/ceres_data/7zma_14793/03_2026/7zma_14793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zma_14793/03_2026/7zma_14793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zma_14793/03_2026/7zma_14793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zma_14793/03_2026/7zma_14793.map" } 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= -0.000 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 6006 2.51 5 N 1652 2.21 5 O 1794 1.98 5 H 9332 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18816 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 9408 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 25, 'TRANS': 581} Chain: "B" Number of atoms: 9408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 9408 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 25, 'TRANS': 581} Time building chain proxies: 3.22, per 1000 atoms: 0.17 Number of scatterers: 18816 At special positions: 0 Unit cell: (106.858, 115.322, 80.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 1794 8.00 N 1652 7.00 C 6006 6.00 H 9332 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 570.4 milliseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 39.5% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 1608 through 1619 Processing helix chain 'A' and resid 1662 through 1667 Processing helix chain 'A' and resid 1669 through 1674 Processing helix chain 'A' and resid 1677 through 1694 Processing helix chain 'A' and resid 1722 through 1733 removed outlier: 4.091A pdb=" N ALA A1726 " --> pdb=" O TYR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1754 removed outlier: 4.159A pdb=" N VAL A1749 " --> pdb=" O ILE A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1783 Processing helix chain 'A' and resid 1799 through 1808 Processing helix chain 'A' and resid 1841 through 1848 Processing helix chain 'A' and resid 1873 through 1889 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 1908 through 1922 removed outlier: 3.734A pdb=" N GLU A1922 " --> pdb=" O LYS A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1940 Processing helix chain 'A' and resid 1945 through 1961 Processing helix chain 'A' and resid 2054 through 2072 removed outlier: 3.519A pdb=" N LEU A2058 " --> pdb=" O ASN A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2089 Processing helix chain 'A' and resid 2103 through 2116 Processing helix chain 'A' and resid 2135 through 2141 Processing helix chain 'A' and resid 2143 through 2156 Processing helix chain 'A' and resid 2157 through 2166 removed outlier: 4.291A pdb=" N ILE A2161 " --> pdb=" O LYS A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2177 Processing helix chain 'B' and resid 1608 through 1619 Processing helix chain 'B' and resid 1662 through 1667 Processing helix chain 'B' and resid 1669 through 1674 Processing helix chain 'B' and resid 1677 through 1694 Processing helix chain 'B' and resid 1722 through 1733 removed outlier: 4.091A pdb=" N ALA B1726 " --> pdb=" O TYR B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1743 through 1754 removed outlier: 4.159A pdb=" N VAL B1749 " --> pdb=" O ILE B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1767 through 1783 Processing helix chain 'B' and resid 1799 through 1808 Processing helix chain 'B' and resid 1841 through 1848 Processing helix chain 'B' and resid 1873 through 1889 Processing helix chain 'B' and resid 1891 through 1893 No H-bonds generated for 'chain 'B' and resid 1891 through 1893' Processing helix chain 'B' and resid 1908 through 1922 removed outlier: 3.734A pdb=" N GLU B1922 " --> pdb=" O LYS B1918 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1940 Processing helix chain 'B' and resid 1945 through 1961 Processing helix chain 'B' and resid 2054 through 2072 removed outlier: 3.518A pdb=" N LEU B2058 " --> pdb=" O ASN B2054 " (cutoff:3.500A) Processing helix chain 'B' and resid 2078 through 2089 Processing helix chain 'B' and resid 2103 through 2116 Processing helix chain 'B' and resid 2135 through 2141 Processing helix chain 'B' and resid 2143 through 2156 Processing helix chain 'B' and resid 2157 through 2166 removed outlier: 4.291A pdb=" N ILE B2161 " --> pdb=" O LYS B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2173 through 2177 Processing sheet with id=AA1, first strand: chain 'A' and resid 1759 through 1762 removed outlier: 8.611A pdb=" N MET A1760 " --> pdb=" O VAL A1711 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A1713 " --> pdb=" O MET A1760 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A1762 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A1715 " --> pdb=" O VAL A1762 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A1598 " --> pdb=" O LEU A1837 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A1839 " --> pdb=" O ILE A1596 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A1596 " --> pdb=" O LYS A1839 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A1594 " --> pdb=" O ILE A1855 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A1855 " --> pdb=" O GLU A2027 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU A2027 " --> pdb=" O ILE A1855 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A1857 " --> pdb=" O VAL A2025 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A2009 " --> pdb=" O VAL A1895 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A1897 " --> pdb=" O ILE A2009 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A1896 " --> pdb=" O ALA A1931 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY A1933 " --> pdb=" O SER A1896 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A1898 " --> pdb=" O GLY A1933 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS A1930 " --> pdb=" O VAL A1984 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1660 through 1661 Processing sheet with id=AA3, first strand: chain 'A' and resid 1962 through 1963 Processing sheet with id=AA4, first strand: chain 'A' and resid 1996 through 1999 Processing sheet with id=AA5, first strand: chain 'A' and resid 2046 through 2052 Processing sheet with id=AA6, first strand: chain 'B' and resid 1759 through 1762 removed outlier: 8.611A pdb=" N MET B1760 " --> pdb=" O VAL B1711 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B1713 " --> pdb=" O MET B1760 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL B1762 " --> pdb=" O VAL B1713 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B1715 " --> pdb=" O VAL B1762 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B1598 " --> pdb=" O LEU B1837 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS B1839 " --> pdb=" O ILE B1596 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B1596 " --> pdb=" O LYS B1839 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B1594 " --> pdb=" O ILE B1855 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B1855 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU B2027 " --> pdb=" O ILE B1855 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY B1857 " --> pdb=" O VAL B2025 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B2009 " --> pdb=" O VAL B1895 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B1897 " --> pdb=" O ILE B2009 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B1896 " --> pdb=" O ALA B1931 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY B1933 " --> pdb=" O SER B1896 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B1898 " --> pdb=" O GLY B1933 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS B1930 " --> pdb=" O VAL B1984 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1660 through 1661 Processing sheet with id=AA8, first strand: chain 'B' and resid 1962 through 1963 Processing sheet with id=AA9, first strand: chain 'B' and resid 1996 through 1999 Processing sheet with id=AB1, first strand: chain 'B' and resid 2046 through 2052 416 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9316 1.03 - 1.23: 20 1.23 - 1.42: 4136 1.42 - 1.61: 5508 1.61 - 1.81: 48 Bond restraints: 19028 Sorted by residual: bond pdb=" CB PRO A2045 " pdb=" CG PRO A2045 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CB PRO B2045 " pdb=" CG PRO B2045 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CB ASP A2144 " pdb=" CG ASP A2144 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.44e+00 bond pdb=" CB ASP B2144 " pdb=" CG ASP B2144 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CA GLU A1639 " pdb=" HA GLU A1639 " ideal model delta sigma weight residual 0.970 0.951 0.019 2.00e-02 2.50e+03 9.37e-01 ... (remaining 19023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.59: 33984 7.59 - 15.18: 36 15.18 - 22.78: 28 22.78 - 30.37: 128 30.37 - 37.96: 164 Bond angle restraints: 34340 Sorted by residual: angle pdb=" C ASP B1825 " pdb=" CA ASP B1825 " pdb=" HA ASP B1825 " ideal model delta sigma weight residual 109.00 71.04 37.96 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C ASP A1825 " pdb=" CA ASP A1825 " pdb=" HA ASP A1825 " ideal model delta sigma weight residual 109.00 71.08 37.92 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C ASP A1638 " pdb=" CA ASP A1638 " pdb=" HA ASP A1638 " ideal model delta sigma weight residual 109.00 71.58 37.42 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C ASP B1638 " pdb=" CA ASP B1638 " pdb=" HA ASP B1638 " ideal model delta sigma weight residual 109.00 71.62 37.38 3.00e+00 1.11e-01 1.55e+02 angle pdb=" CB ILE B2100 " pdb=" CA ILE B2100 " pdb=" HA ILE B2100 " ideal model delta sigma weight residual 109.00 72.01 36.99 3.00e+00 1.11e-01 1.52e+02 ... (remaining 34335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8245 17.92 - 35.84: 503 35.84 - 53.76: 148 53.76 - 71.68: 46 71.68 - 89.60: 6 Dihedral angle restraints: 8948 sinusoidal: 4844 harmonic: 4104 Sorted by residual: dihedral pdb=" C LYS A1646 " pdb=" N LYS A1646 " pdb=" CA LYS A1646 " pdb=" CB LYS A1646 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C LYS B1646 " pdb=" N LYS B1646 " pdb=" CA LYS B1646 " pdb=" CB LYS B1646 " ideal model delta harmonic sigma weight residual -122.60 -136.29 13.69 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA ASP A1642 " pdb=" C ASP A1642 " pdb=" N LYS A1643 " pdb=" CA LYS A1643 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 8945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.325: 1340 0.325 - 0.651: 52 0.651 - 0.976: 0 0.976 - 1.302: 2 1.302 - 1.627: 14 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB ILE A1898 " pdb=" CA ILE A1898 " pdb=" CG1 ILE A1898 " pdb=" CG2 ILE A1898 " both_signs ideal model delta sigma weight residual False 2.64 1.02 1.63 2.00e-01 2.50e+01 6.62e+01 chirality pdb=" CB ILE B1898 " pdb=" CA ILE B1898 " pdb=" CG1 ILE B1898 " pdb=" CG2 ILE B1898 " both_signs ideal model delta sigma weight residual False 2.64 1.02 1.63 2.00e-01 2.50e+01 6.60e+01 chirality pdb=" CB ILE B1913 " pdb=" CA ILE B1913 " pdb=" CG1 ILE B1913 " pdb=" CG2 ILE B1913 " both_signs ideal model delta sigma weight residual False 2.64 1.04 1.60 2.00e-01 2.50e+01 6.44e+01 ... (remaining 1405 not shown) Planarity restraints: 2876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1839 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1840 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1840 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1840 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B1839 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B1840 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B1840 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B1840 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B2044 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B2045 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B2045 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B2045 " -0.022 5.00e-02 4.00e+02 ... (remaining 2873 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 867 2.13 - 2.75: 34406 2.75 - 3.37: 51829 3.37 - 3.98: 67748 3.98 - 4.60: 109472 Nonbonded interactions: 264322 Sorted by model distance: nonbonded pdb=" HE3 LYS A1703 " pdb=" HZ2 LYS A1703 " model vdw 1.517 1.816 nonbonded pdb=" H ILE B2100 " pdb=" HA ILE B2100 " model vdw 1.539 1.816 nonbonded pdb=" OD1 ASN A2174 " pdb=" HZ1 LYS A2181 " model vdw 1.554 2.450 nonbonded pdb=" OD1 ASN B2174 " pdb=" HZ1 LYS B2181 " model vdw 1.560 2.450 nonbonded pdb=" HE3 LYS A1703 " pdb=" HZ3 LYS A1703 " model vdw 1.564 1.816 ... (remaining 264317 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.090 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.660 Find NCS groups from input model: 0.110 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:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.071 9696 Z= 0.148 Angle : 0.894 15.800 13116 Z= 0.484 Chirality : 0.175 1.627 1408 Planarity : 0.004 0.040 1714 Dihedral : 12.201 89.597 3572 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 1.00 % 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: -0.24 (0.25), residues: 1210 helix: 1.31 (0.26), residues: 430 sheet: 0.06 (0.45), residues: 146 loop : -1.29 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1671 TYR 0.009 0.001 TYR A1648 PHE 0.012 0.001 PHE A2139 TRP 0.004 0.001 TRP A2173 HIS 0.009 0.001 HIS A1774 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9696) covalent geometry : angle 0.89405 (13116) hydrogen bonds : bond 0.04685 ( 416) hydrogen bonds : angle 4.67242 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 137 average time/residue: 1.3386 time to fit residues: 194.9479 Evaluate side-chains 91 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain B residue 1599 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.192831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156802 restraints weight = 28672.700| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.96 r_work: 0.3743 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9696 Z= 0.171 Angle : 0.900 25.939 13116 Z= 0.472 Chirality : 0.176 1.624 1408 Planarity : 0.004 0.036 1714 Dihedral : 4.611 27.507 1336 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.91 % Allowed : 7.75 % Favored : 90.34 % Cbeta Deviations : 1.09 % 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: -0.35 (0.24), residues: 1210 helix: 1.20 (0.25), residues: 430 sheet: -0.37 (0.42), residues: 156 loop : -1.25 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B2183 TYR 0.010 0.001 TYR A1648 PHE 0.014 0.002 PHE A2139 TRP 0.005 0.001 TRP B2198 HIS 0.009 0.002 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9696) covalent geometry : angle 0.90021 (13116) hydrogen bonds : bond 0.04091 ( 416) hydrogen bonds : angle 4.60052 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.478 Fit side-chains REVERT: A 1675 LEU cc_start: 0.8099 (pp) cc_final: 0.7856 (mt) REVERT: A 1778 HIS cc_start: 0.8088 (m-70) cc_final: 0.7803 (m-70) REVERT: A 2072 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6690 (mt0) REVERT: B 1675 LEU cc_start: 0.8166 (pp) cc_final: 0.7936 (mt) REVERT: B 1762 VAL cc_start: 0.8915 (m) cc_final: 0.8688 (t) REVERT: B 1778 HIS cc_start: 0.8051 (m-70) cc_final: 0.7741 (m-70) REVERT: B 1998 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7201 (tm-30) outliers start: 19 outliers final: 3 residues processed: 104 average time/residue: 1.2718 time to fit residues: 140.9976 Evaluate side-chains 91 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1867 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.191885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155714 restraints weight = 28877.924| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.95 r_work: 0.3721 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9696 Z= 0.143 Angle : 0.872 25.058 13116 Z= 0.458 Chirality : 0.176 1.639 1408 Planarity : 0.004 0.036 1714 Dihedral : 4.467 27.157 1332 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.71 % Allowed : 9.76 % Favored : 88.53 % Cbeta Deviations : 1.09 % 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: -0.23 (0.24), residues: 1210 helix: 1.37 (0.25), residues: 430 sheet: -0.24 (0.42), residues: 156 loop : -1.26 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2183 TYR 0.009 0.001 TYR A1648 PHE 0.015 0.001 PHE A2139 TRP 0.005 0.001 TRP A2198 HIS 0.009 0.001 HIS B1862 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9696) covalent geometry : angle 0.87212 (13116) hydrogen bonds : bond 0.03772 ( 416) hydrogen bonds : angle 4.48826 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.400 Fit side-chains REVERT: A 1762 VAL cc_start: 0.8951 (m) cc_final: 0.8738 (t) REVERT: A 1765 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.4864 (mmt) REVERT: A 1778 HIS cc_start: 0.8034 (m-70) cc_final: 0.7803 (m-70) REVERT: B 1778 HIS cc_start: 0.8112 (m-70) cc_final: 0.7839 (m-70) REVERT: B 1998 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 2136 MET cc_start: 0.1988 (OUTLIER) cc_final: 0.1003 (mmt) outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 1.3080 time to fit residues: 142.3231 Evaluate side-chains 95 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1765 MET Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1867 ASN Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2164 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 104 optimal weight: 0.0980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1781 GLN A1867 ASN B1781 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.188971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152918 restraints weight = 29094.162| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.94 r_work: 0.3685 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9696 Z= 0.161 Angle : 0.883 25.939 13116 Z= 0.463 Chirality : 0.176 1.610 1408 Planarity : 0.004 0.067 1714 Dihedral : 4.513 26.732 1332 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.01 % Allowed : 11.07 % Favored : 86.92 % Cbeta Deviations : 1.27 % 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: -0.23 (0.24), residues: 1210 helix: 1.38 (0.25), residues: 430 sheet: -0.17 (0.43), residues: 156 loop : -1.29 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B2183 TYR 0.010 0.001 TYR A1648 PHE 0.016 0.002 PHE A2139 TRP 0.006 0.001 TRP A2198 HIS 0.008 0.001 HIS A1862 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9696) covalent geometry : angle 0.88276 (13116) hydrogen bonds : bond 0.03977 ( 416) hydrogen bonds : angle 4.54778 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1765 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.4952 (mmt) REVERT: A 1778 HIS cc_start: 0.8136 (m-70) cc_final: 0.7895 (m-70) REVERT: A 2072 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6796 (mt0) REVERT: B 1765 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5032 (mmt) REVERT: B 1778 HIS cc_start: 0.8101 (m-70) cc_final: 0.7861 (m-70) REVERT: B 2072 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6879 (mt0) REVERT: B 2136 MET cc_start: 0.1892 (OUTLIER) cc_final: 0.1063 (mmt) outliers start: 20 outliers final: 7 residues processed: 102 average time/residue: 1.3170 time to fit residues: 143.2634 Evaluate side-chains 100 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1765 MET Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1622 CYS Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1765 MET Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2072 GLN Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1781 GLN A1867 ASN B1781 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.184392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147943 restraints weight = 29350.577| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.94 r_work: 0.3640 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9696 Z= 0.222 Angle : 0.928 26.113 13116 Z= 0.489 Chirality : 0.177 1.611 1408 Planarity : 0.005 0.035 1714 Dihedral : 4.901 28.941 1332 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.41 % Allowed : 12.47 % Favored : 85.11 % Cbeta Deviations : 1.45 % 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: -0.45 (0.24), residues: 1210 helix: 1.13 (0.25), residues: 430 sheet: -0.06 (0.42), residues: 152 loop : -1.42 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2183 TYR 0.014 0.002 TYR B1960 PHE 0.018 0.002 PHE A2139 TRP 0.009 0.001 TRP A2198 HIS 0.007 0.002 HIS A1862 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 9696) covalent geometry : angle 0.92789 (13116) hydrogen bonds : bond 0.04767 ( 416) hydrogen bonds : angle 4.83694 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1778 HIS cc_start: 0.8181 (m-70) cc_final: 0.7900 (m-70) REVERT: A 1976 ILE cc_start: 0.7180 (pt) cc_final: 0.6434 (tt) REVERT: B 1765 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5660 (mmt) REVERT: B 1778 HIS cc_start: 0.8181 (m-70) cc_final: 0.7908 (m-70) REVERT: B 1882 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8000 (ttt90) REVERT: B 1976 ILE cc_start: 0.7179 (pt) cc_final: 0.6457 (tt) REVERT: B 2072 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6823 (mp10) outliers start: 24 outliers final: 12 residues processed: 112 average time/residue: 1.2782 time to fit residues: 152.8810 Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1765 MET Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1622 CYS Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1717 VAL Chi-restraints excluded: chain B residue 1765 MET Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 1988 GLU Chi-restraints excluded: chain B residue 2072 GLN Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1608 ASN A1781 GLN A1867 ASN B1608 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.188170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152011 restraints weight = 29076.125| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.94 r_work: 0.3682 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9696 Z= 0.127 Angle : 0.870 25.937 13116 Z= 0.456 Chirality : 0.176 1.599 1408 Planarity : 0.005 0.057 1714 Dihedral : 4.596 29.857 1332 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.51 % Allowed : 13.88 % Favored : 84.61 % Cbeta Deviations : 1.27 % 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: -0.39 (0.24), residues: 1210 helix: 1.40 (0.25), residues: 430 sheet: -0.50 (0.38), residues: 194 loop : -1.48 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1782 TYR 0.011 0.001 TYR B1923 PHE 0.014 0.001 PHE B2139 TRP 0.006 0.001 TRP B2152 HIS 0.005 0.001 HIS A1774 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9696) covalent geometry : angle 0.86958 (13116) hydrogen bonds : bond 0.03603 ( 416) hydrogen bonds : angle 4.48614 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 1778 HIS cc_start: 0.8131 (m-70) cc_final: 0.7873 (m-70) REVERT: A 1976 ILE cc_start: 0.7206 (pt) cc_final: 0.6434 (tt) REVERT: A 2136 MET cc_start: 0.1508 (OUTLIER) cc_final: 0.0645 (mmt) REVERT: A 2169 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.6378 (mp) REVERT: B 1778 HIS cc_start: 0.8117 (m-70) cc_final: 0.7848 (m-70) REVERT: B 1976 ILE cc_start: 0.7174 (pt) cc_final: 0.6414 (tt) REVERT: B 2136 MET cc_start: 0.1563 (OUTLIER) cc_final: 0.0805 (mmt) REVERT: B 2169 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.6397 (mp) outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 1.2165 time to fit residues: 131.3696 Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2136 MET Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1781 GLN A1867 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.186801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150549 restraints weight = 29285.548| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.95 r_work: 0.3667 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9696 Z= 0.150 Angle : 0.874 26.133 13116 Z= 0.459 Chirality : 0.176 1.610 1408 Planarity : 0.004 0.048 1714 Dihedral : 4.556 29.041 1332 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.41 % Allowed : 14.39 % Favored : 84.21 % Cbeta Deviations : 1.45 % 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: -0.23 (0.24), residues: 1210 helix: 1.40 (0.25), residues: 430 sheet: 0.10 (0.42), residues: 152 loop : -1.38 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2183 TYR 0.011 0.001 TYR B1648 PHE 0.014 0.001 PHE B2139 TRP 0.007 0.001 TRP B2152 HIS 0.006 0.001 HIS A1778 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9696) covalent geometry : angle 0.87418 (13116) hydrogen bonds : bond 0.03850 ( 416) hydrogen bonds : angle 4.50663 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.518 Fit side-chains REVERT: A 1778 HIS cc_start: 0.8231 (m-70) cc_final: 0.7967 (m-70) REVERT: A 1882 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8084 (ttt90) REVERT: A 1976 ILE cc_start: 0.7229 (pt) cc_final: 0.6532 (tt) REVERT: A 2136 MET cc_start: 0.1236 (OUTLIER) cc_final: 0.0459 (mmt) REVERT: A 2169 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.6411 (mp) REVERT: B 1778 HIS cc_start: 0.8196 (m-70) cc_final: 0.7891 (m-70) REVERT: B 1976 ILE cc_start: 0.7224 (pt) cc_final: 0.6534 (tt) REVERT: B 2136 MET cc_start: 0.1356 (OUTLIER) cc_final: 0.0580 (mmt) REVERT: B 2169 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.6427 (mp) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 1.1135 time to fit residues: 116.3969 Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2136 MET Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1622 CYS Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1717 VAL Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1781 GLN A1867 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.186860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150645 restraints weight = 29153.350| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.94 r_work: 0.3670 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9696 Z= 0.144 Angle : 0.872 26.118 13116 Z= 0.458 Chirality : 0.176 1.608 1408 Planarity : 0.005 0.070 1714 Dihedral : 4.522 28.745 1332 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.71 % Allowed : 14.69 % Favored : 83.60 % Cbeta Deviations : 1.27 % 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: -0.20 (0.24), residues: 1210 helix: 1.42 (0.25), residues: 430 sheet: 0.10 (0.42), residues: 152 loop : -1.35 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1883 TYR 0.012 0.001 TYR B1648 PHE 0.013 0.001 PHE B2139 TRP 0.008 0.001 TRP A2152 HIS 0.004 0.001 HIS A1862 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9696) covalent geometry : angle 0.87178 (13116) hydrogen bonds : bond 0.03730 ( 416) hydrogen bonds : angle 4.48153 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.354 Fit side-chains REVERT: A 1778 HIS cc_start: 0.8151 (m-70) cc_final: 0.7875 (m-70) REVERT: A 1976 ILE cc_start: 0.7152 (pt) cc_final: 0.6546 (tt) REVERT: A 2136 MET cc_start: 0.1422 (OUTLIER) cc_final: 0.0613 (mmt) REVERT: A 2144 ASP cc_start: 0.4119 (OUTLIER) cc_final: 0.3052 (t0) REVERT: A 2169 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6396 (mp) REVERT: B 1778 HIS cc_start: 0.8155 (m-70) cc_final: 0.7901 (m-70) REVERT: B 1976 ILE cc_start: 0.7124 (pt) cc_final: 0.6523 (tt) REVERT: B 2136 MET cc_start: 0.1345 (OUTLIER) cc_final: 0.0557 (mmt) REVERT: B 2144 ASP cc_start: 0.4020 (OUTLIER) cc_final: 0.3113 (t0) REVERT: B 2169 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.6408 (mp) outliers start: 17 outliers final: 10 residues processed: 95 average time/residue: 1.1081 time to fit residues: 113.1879 Evaluate side-chains 100 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2136 MET Chi-restraints excluded: chain A residue 2144 ASP Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1622 CYS Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1717 VAL Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2144 ASP Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 ASN B1781 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.186466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150319 restraints weight = 29199.019| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.93 r_work: 0.3663 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9696 Z= 0.148 Angle : 0.872 26.151 13116 Z= 0.458 Chirality : 0.176 1.611 1408 Planarity : 0.005 0.073 1714 Dihedral : 4.511 28.475 1332 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.81 % Allowed : 14.39 % Favored : 83.80 % Cbeta Deviations : 1.27 % 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: -0.20 (0.24), residues: 1210 helix: 1.40 (0.25), residues: 430 sheet: 0.09 (0.43), residues: 152 loop : -1.33 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1883 TYR 0.012 0.001 TYR B1648 PHE 0.013 0.001 PHE A2139 TRP 0.009 0.001 TRP A2152 HIS 0.006 0.001 HIS A1778 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9696) covalent geometry : angle 0.87213 (13116) hydrogen bonds : bond 0.03769 ( 416) hydrogen bonds : angle 4.49664 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.464 Fit side-chains REVERT: A 1778 HIS cc_start: 0.8234 (m-70) cc_final: 0.7978 (m-70) REVERT: A 1976 ILE cc_start: 0.7047 (pt) cc_final: 0.6620 (tt) REVERT: A 2136 MET cc_start: 0.1392 (OUTLIER) cc_final: 0.0600 (mmt) REVERT: A 2144 ASP cc_start: 0.4151 (OUTLIER) cc_final: 0.3118 (t0) REVERT: A 2169 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.6388 (mp) REVERT: B 1778 HIS cc_start: 0.8244 (m-70) cc_final: 0.8001 (m-70) REVERT: B 1976 ILE cc_start: 0.7041 (pt) cc_final: 0.6627 (tt) REVERT: B 2136 MET cc_start: 0.1312 (OUTLIER) cc_final: 0.0541 (mmt) REVERT: B 2144 ASP cc_start: 0.4067 (OUTLIER) cc_final: 0.2893 (t0) REVERT: B 2169 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.6404 (mp) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 1.0655 time to fit residues: 110.2383 Evaluate side-chains 100 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2136 MET Chi-restraints excluded: chain A residue 2144 ASP Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1622 CYS Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1717 VAL Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2144 ASP Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1781 GLN A1867 ASN B1781 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.185585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149391 restraints weight = 29403.492| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.94 r_work: 0.3651 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9696 Z= 0.166 Angle : 0.883 26.091 13116 Z= 0.465 Chirality : 0.176 1.601 1408 Planarity : 0.005 0.079 1714 Dihedral : 4.603 27.595 1332 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.81 % Allowed : 14.49 % Favored : 83.70 % Cbeta Deviations : 1.27 % 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: -0.23 (0.24), residues: 1210 helix: 1.34 (0.25), residues: 430 sheet: 0.12 (0.43), residues: 152 loop : -1.34 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1883 TYR 0.012 0.002 TYR B1648 PHE 0.014 0.002 PHE B2139 TRP 0.011 0.001 TRP A2152 HIS 0.005 0.001 HIS B1778 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9696) covalent geometry : angle 0.88350 (13116) hydrogen bonds : bond 0.04020 ( 416) hydrogen bonds : angle 4.61529 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 1778 HIS cc_start: 0.8170 (m-70) cc_final: 0.7909 (m-70) REVERT: A 1825 ASP cc_start: 0.7310 (p0) cc_final: 0.7021 (p0) REVERT: A 2136 MET cc_start: 0.1213 (OUTLIER) cc_final: 0.0470 (mmt) REVERT: A 2144 ASP cc_start: 0.4218 (OUTLIER) cc_final: 0.3166 (t0) REVERT: A 2169 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.6459 (mp) REVERT: B 1765 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5389 (mmt) REVERT: B 1778 HIS cc_start: 0.8260 (m-70) cc_final: 0.7995 (m-70) REVERT: B 1825 ASP cc_start: 0.7307 (p0) cc_final: 0.7005 (p0) REVERT: B 1976 ILE cc_start: 0.7209 (pt) cc_final: 0.6861 (tt) REVERT: B 2136 MET cc_start: 0.1293 (OUTLIER) cc_final: 0.0541 (mmt) REVERT: B 2144 ASP cc_start: 0.4129 (OUTLIER) cc_final: 0.3141 (t0) REVERT: B 2169 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.6455 (mp) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 1.0660 time to fit residues: 110.5917 Evaluate side-chains 98 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1636 TYR Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1971 THR Chi-restraints excluded: chain A residue 2136 MET Chi-restraints excluded: chain A residue 2144 ASP Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain B residue 1622 CYS Chi-restraints excluded: chain B residue 1636 TYR Chi-restraints excluded: chain B residue 1717 VAL Chi-restraints excluded: chain B residue 1765 MET Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2136 MET Chi-restraints excluded: chain B residue 2144 ASP Chi-restraints excluded: chain B residue 2164 MET Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1781 GLN A1867 ASN B1781 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.186564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150293 restraints weight = 29144.651| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.95 r_work: 0.3672 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9696 Z= 0.139 Angle : 0.868 26.236 13116 Z= 0.455 Chirality : 0.176 1.610 1408 Planarity : 0.005 0.079 1714 Dihedral : 4.497 27.754 1332 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.81 % Allowed : 14.39 % Favored : 83.80 % Cbeta Deviations : 1.27 % 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: -0.16 (0.24), residues: 1210 helix: 1.46 (0.25), residues: 430 sheet: 0.14 (0.43), residues: 152 loop : -1.34 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1883 TYR 0.010 0.001 TYR A1648 PHE 0.012 0.001 PHE B2139 TRP 0.022 0.001 TRP A1651 HIS 0.004 0.001 HIS B1778 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9696) covalent geometry : angle 0.86769 (13116) hydrogen bonds : bond 0.03643 ( 416) hydrogen bonds : angle 4.49201 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5606.51 seconds wall clock time: 96 minutes 25.18 seconds (5785.18 seconds total)