Starting phenix.real_space_refine on Sat Feb 17 13:06:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zma_14793/02_2024/7zma_14793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zma_14793/02_2024/7zma_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zma_14793/02_2024/7zma_14793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zma_14793/02_2024/7zma_14793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zma_14793/02_2024/7zma_14793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zma_14793/02_2024/7zma_14793.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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 Residue "A ASP 1629": "OD1" <-> "OD2" Residue "A TYR 1897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 2076": "OD1" <-> "OD2" Residue "A PHE 2097": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 2172": "OD1" <-> "OD2" Residue "B ASP 1629": "OD1" <-> "OD2" Residue "B TYR 1897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2076": "OD1" <-> "OD2" Residue "B PHE 2097": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2172": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 8.51, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 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: 15.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.42 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: 7.03 Time building geometry restraints manager: 16.05 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: 71.04 - 84.31: 281 84.31 - 97.59: 4 97.59 - 110.86: 19575 110.86 - 124.14: 13156 124.14 - 137.41: 1324 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 1.850 nonbonded pdb=" OD1 ASN B2174 " pdb=" HZ1 LYS B2181 " model vdw 1.560 1.850 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 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: 2.160 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: 0.260 Extract box with map and model: 7.970 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 60.780 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.050 ------------------------------------------------------------------------------- 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= 0.231 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (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 TRP 0.004 0.001 TRP A2173 HIS 0.009 0.001 HIS A1774 PHE 0.012 0.001 PHE A2139 TYR 0.009 0.001 TYR A1648 ARG 0.007 0.001 ARG A1671 *********************** 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 fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.349 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: 2.7916 time to fit residues: 408.0694 Evaluate side-chains 91 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9696 Z= 0.281 Angle : 0.913 28.362 13116 Z= 0.478 Chirality : 0.176 1.611 1408 Planarity : 0.004 0.036 1714 Dihedral : 4.684 26.905 1336 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.21 % Allowed : 8.05 % Favored : 89.74 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1210 helix: 1.22 (0.25), residues: 430 sheet: -0.25 (0.42), residues: 156 loop : -1.22 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2198 HIS 0.010 0.002 HIS B1862 PHE 0.015 0.002 PHE A2139 TYR 0.012 0.002 TYR B1648 ARG 0.011 0.001 ARG B2183 *********************** 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 118 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.509 Fit side-chains REVERT: A 1762 VAL cc_start: 0.8937 (m) cc_final: 0.8718 (t) REVERT: A 1765 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.4316 (mmt) REVERT: A 1778 HIS cc_start: 0.7864 (m-70) cc_final: 0.7646 (m-70) REVERT: A 2072 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6891 (mt0) REVERT: A 2136 MET cc_start: 0.1974 (OUTLIER) cc_final: 0.1694 (mpp) REVERT: B 1762 VAL cc_start: 0.8904 (m) cc_final: 0.8704 (t) REVERT: B 1765 MET cc_start: 0.5352 (OUTLIER) cc_final: 0.4322 (mmt) REVERT: B 1778 HIS cc_start: 0.7867 (m-70) cc_final: 0.7601 (m-70) outliers start: 22 outliers final: 8 residues processed: 106 average time/residue: 2.6105 time to fit residues: 298.0840 Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 1765 MET Chi-restraints excluded: chain A residue 1786 GLU Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2136 MET 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 1786 GLU 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 60 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2153 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= 0.236 Angle : 0.870 25.135 13116 Z= 0.457 Chirality : 0.177 1.611 1408 Planarity : 0.004 0.035 1714 Dihedral : 4.526 26.339 1332 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.41 % Allowed : 9.96 % Favored : 87.63 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1210 helix: 1.41 (0.25), residues: 430 sheet: -0.12 (0.42), residues: 156 loop : -1.18 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2198 HIS 0.007 0.001 HIS A1862 PHE 0.014 0.002 PHE B2139 TYR 0.011 0.001 TYR B1648 ARG 0.008 0.001 ARG A2183 *********************** 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 121 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1765 MET cc_start: 0.5198 (OUTLIER) cc_final: 0.4384 (mmt) REVERT: A 1778 HIS cc_start: 0.7894 (m-70) cc_final: 0.7673 (m-70) REVERT: A 2136 MET cc_start: 0.1921 (OUTLIER) cc_final: 0.1333 (mmt) REVERT: B 1675 LEU cc_start: 0.8035 (mt) cc_final: 0.7834 (mp) REVERT: B 1765 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4333 (mmt) REVERT: B 1778 HIS cc_start: 0.7856 (m-70) cc_final: 0.7628 (m-70) REVERT: B 2072 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: B 2136 MET cc_start: 0.1517 (mpp) cc_final: 0.0955 (mmt) outliers start: 24 outliers final: 7 residues processed: 108 average time/residue: 2.6310 time to fit residues: 305.7750 Evaluate side-chains 103 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 1765 MET 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 1765 MET Chi-restraints excluded: chain B residue 1867 ASN Chi-restraints excluded: chain B residue 2072 GLN Chi-restraints excluded: chain B residue 2169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9696 Z= 0.356 Angle : 0.918 26.379 13116 Z= 0.484 Chirality : 0.177 1.656 1408 Planarity : 0.005 0.060 1714 Dihedral : 4.833 27.805 1332 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.21 % Allowed : 12.78 % Favored : 85.01 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1210 helix: 1.18 (0.25), residues: 430 sheet: -0.04 (0.42), residues: 152 loop : -1.32 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2198 HIS 0.009 0.002 HIS B1862 PHE 0.016 0.002 PHE A2139 TYR 0.013 0.002 TYR B1648 ARG 0.010 0.001 ARG A2183 *********************** 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 120 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1778 HIS cc_start: 0.7987 (m-70) cc_final: 0.7748 (m-70) REVERT: A 2072 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: A 2136 MET cc_start: 0.1927 (OUTLIER) cc_final: 0.1445 (mmt) REVERT: B 1765 MET cc_start: 0.5426 (OUTLIER) cc_final: 0.4694 (mmt) REVERT: B 1778 HIS cc_start: 0.7982 (m-70) cc_final: 0.7741 (m-70) REVERT: B 2072 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: B 2136 MET cc_start: 0.1689 (mpp) cc_final: 0.1471 (mpp) outliers start: 22 outliers final: 10 residues processed: 109 average time/residue: 2.6260 time to fit residues: 307.8267 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 1988 GLU Chi-restraints excluded: chain A residue 2072 GLN 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 1765 MET Chi-restraints excluded: chain B residue 1786 GLU Chi-restraints excluded: chain B residue 2072 GLN 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 96 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- 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 ** B1867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2890 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= 0.228 Angle : 0.872 25.910 13116 Z= 0.459 Chirality : 0.177 1.604 1408 Planarity : 0.004 0.040 1714 Dihedral : 4.603 28.123 1332 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.11 % Allowed : 12.98 % Favored : 84.91 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1210 helix: 1.37 (0.25), residues: 430 sheet: 0.03 (0.42), residues: 152 loop : -1.32 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2198 HIS 0.006 0.001 HIS B1862 PHE 0.014 0.002 PHE A2139 TYR 0.010 0.001 TYR B1648 ARG 0.009 0.001 ARG A2183 *********************** 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 fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 1765 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.4633 (mmt) REVERT: A 1778 HIS cc_start: 0.7878 (m-70) cc_final: 0.7660 (m-70) REVERT: A 1976 ILE cc_start: 0.6857 (pt) cc_final: 0.6513 (tt) REVERT: B 1765 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4461 (mmt) REVERT: B 1778 HIS cc_start: 0.7900 (m-70) cc_final: 0.7682 (m-70) REVERT: B 1958 MET cc_start: 0.8786 (mtp) cc_final: 0.8585 (mtm) REVERT: B 1976 ILE cc_start: 0.6875 (pt) cc_final: 0.6526 (tt) REVERT: B 2169 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.6550 (mp) outliers start: 21 outliers final: 8 residues processed: 113 average time/residue: 2.4327 time to fit residues: 296.9549 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 2164 MET 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 39 optimal weight: 0.7980 chunk 104 optimal weight: 0.0770 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 B1867 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2985 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= 0.215 Angle : 0.863 26.130 13116 Z= 0.454 Chirality : 0.177 1.608 1408 Planarity : 0.004 0.044 1714 Dihedral : 4.488 28.488 1332 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.21 % Allowed : 13.48 % Favored : 84.31 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1210 helix: 1.50 (0.25), residues: 430 sheet: 0.03 (0.42), residues: 152 loop : -1.29 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2152 HIS 0.005 0.001 HIS B1778 PHE 0.014 0.002 PHE A2139 TYR 0.011 0.001 TYR B1648 ARG 0.011 0.001 ARG A2183 *********************** 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 120 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.607 Fit side-chains REVERT: A 1765 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4603 (mmt) REVERT: A 1778 HIS cc_start: 0.7939 (m-70) cc_final: 0.7712 (m-70) REVERT: A 1976 ILE cc_start: 0.6916 (pt) cc_final: 0.6593 (tt) REVERT: A 2072 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: A 2136 MET cc_start: 0.1409 (OUTLIER) cc_final: 0.1181 (mpp) REVERT: A 2169 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6460 (mp) REVERT: B 1765 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4456 (mmt) REVERT: B 1778 HIS cc_start: 0.7932 (m-70) cc_final: 0.7708 (m-70) REVERT: B 1958 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8576 (mtm) REVERT: B 1976 ILE cc_start: 0.6897 (pt) cc_final: 0.6569 (tt) REVERT: B 2144 ASP cc_start: 0.3254 (OUTLIER) cc_final: 0.2270 (t0) REVERT: B 2169 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.6477 (mp) outliers start: 22 outliers final: 7 residues processed: 110 average time/residue: 2.5383 time to fit residues: 301.0252 Evaluate side-chains 112 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 2072 GLN 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 1765 MET Chi-restraints excluded: chain B residue 1958 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 B1867 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3060 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= 0.186 Angle : 0.853 26.130 13116 Z= 0.448 Chirality : 0.177 1.614 1408 Planarity : 0.004 0.033 1714 Dihedral : 4.340 27.972 1332 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1210 helix: 1.67 (0.25), residues: 430 sheet: 0.02 (0.43), residues: 154 loop : -1.26 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A2152 HIS 0.005 0.001 HIS A1774 PHE 0.014 0.001 PHE B2139 TYR 0.010 0.001 TYR B1648 ARG 0.008 0.000 ARG B1883 *********************** 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 118 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.569 Fit side-chains REVERT: A 1765 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4528 (mmt) REVERT: A 1778 HIS cc_start: 0.7805 (m-70) cc_final: 0.7551 (m-70) REVERT: A 1882 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7423 (ttt90) REVERT: A 1976 ILE cc_start: 0.6915 (pt) cc_final: 0.6602 (tt) REVERT: A 2072 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: A 2136 MET cc_start: 0.1617 (OUTLIER) cc_final: 0.0813 (mmt) REVERT: A 2169 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6327 (mp) REVERT: B 1765 MET cc_start: 0.5181 (OUTLIER) cc_final: 0.4389 (mmt) REVERT: B 1778 HIS cc_start: 0.7804 (m-70) cc_final: 0.7542 (m-70) REVERT: B 1882 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7473 (ttt-90) REVERT: B 1958 MET cc_start: 0.8812 (mtp) cc_final: 0.8588 (mtm) REVERT: B 1976 ILE cc_start: 0.6909 (pt) cc_final: 0.6596 (tt) REVERT: B 2144 ASP cc_start: 0.3267 (OUTLIER) cc_final: 0.2319 (t0) REVERT: B 2169 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6202 (mm) outliers start: 18 outliers final: 6 residues processed: 110 average time/residue: 2.4693 time to fit residues: 293.5139 Evaluate side-chains 107 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 2072 GLN 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 1765 MET Chi-restraints excluded: chain B residue 2144 ASP 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 71 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 B1867 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3332 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= 0.325 Angle : 0.903 26.225 13116 Z= 0.475 Chirality : 0.177 1.599 1408 Planarity : 0.006 0.074 1714 Dihedral : 4.684 29.376 1332 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.01 % Allowed : 14.99 % Favored : 83.00 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1210 helix: 1.35 (0.25), residues: 430 sheet: -0.05 (0.42), residues: 154 loop : -1.31 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2152 HIS 0.007 0.002 HIS A1862 PHE 0.016 0.002 PHE B2139 TYR 0.013 0.002 TYR A1648 ARG 0.013 0.001 ARG B1883 *********************** 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 116 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.494 Fit side-chains REVERT: A 1778 HIS cc_start: 0.7953 (m-70) cc_final: 0.7723 (m-70) REVERT: A 2169 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.6545 (mp) REVERT: B 1765 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4741 (mmt) REVERT: B 1778 HIS cc_start: 0.7949 (m-70) cc_final: 0.7715 (m-70) REVERT: B 1958 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8615 (mtm) REVERT: B 2136 MET cc_start: 0.1582 (OUTLIER) cc_final: 0.0851 (mmt) REVERT: B 2169 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.6537 (mp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 2.4964 time to fit residues: 286.1875 Evaluate side-chains 108 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1765 MET Chi-restraints excluded: chain A residue 2054 ASN 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 1958 MET Chi-restraints excluded: chain B residue 2054 ASN Chi-restraints excluded: chain B residue 2136 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 110 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 B1781 GLN B1867 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9696 Z= 0.282 Angle : 0.880 26.200 13116 Z= 0.467 Chirality : 0.173 1.592 1408 Planarity : 0.005 0.074 1714 Dihedral : 4.683 29.538 1332 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.71 % Allowed : 15.19 % Favored : 83.10 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1210 helix: 1.33 (0.25), residues: 430 sheet: -0.03 (0.42), residues: 154 loop : -1.32 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1651 HIS 0.006 0.001 HIS B1862 PHE 0.015 0.002 PHE A2139 TYR 0.012 0.002 TYR B1719 ARG 0.014 0.001 ARG B1883 *********************** 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 107 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 1778 HIS cc_start: 0.7940 (m-70) cc_final: 0.7696 (m-70) REVERT: A 1882 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7535 (ttt-90) REVERT: A 2169 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.6520 (mp) REVERT: B 1765 MET cc_start: 0.5310 (OUTLIER) cc_final: 0.4710 (mmt) REVERT: B 1778 HIS cc_start: 0.7941 (m-70) cc_final: 0.7701 (m-70) REVERT: B 1825 ASP cc_start: 0.7017 (p0) cc_final: 0.6752 (p0) REVERT: B 1958 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: B 2169 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6526 (mp) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 2.5989 time to fit residues: 282.5875 Evaluate side-chains 102 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1765 MET Chi-restraints excluded: chain A residue 2054 ASN 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 1958 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 54 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 B1781 GLN B1867 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9696 Z= 0.230 Angle : 0.869 26.106 13116 Z= 0.458 Chirality : 0.175 1.604 1408 Planarity : 0.006 0.081 1714 Dihedral : 4.598 29.586 1332 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.51 % Allowed : 15.49 % Favored : 83.00 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1210 helix: 1.48 (0.25), residues: 430 sheet: 0.00 (0.42), residues: 154 loop : -1.29 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1651 HIS 0.005 0.001 HIS A1778 PHE 0.015 0.002 PHE A1637 TYR 0.012 0.001 TYR A1648 ARG 0.014 0.001 ARG A1883 ********************** 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 111 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1676 MET cc_start: 0.8494 (ttm) cc_final: 0.8216 (ttm) REVERT: A 1765 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4641 (mmt) REVERT: A 1778 HIS cc_start: 0.7913 (m-70) cc_final: 0.7686 (m-70) REVERT: A 2169 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6442 (mp) REVERT: B 1765 MET cc_start: 0.5248 (OUTLIER) cc_final: 0.4591 (mmt) REVERT: B 1778 HIS cc_start: 0.7917 (m-70) cc_final: 0.7679 (m-70) REVERT: B 1958 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8621 (mtm) REVERT: B 2169 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6446 (mp) outliers start: 15 outliers final: 6 residues processed: 106 average time/residue: 2.4923 time to fit residues: 285.7132 Evaluate side-chains 104 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1622 CYS Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1765 MET Chi-restraints excluded: chain A residue 2054 ASN 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 1958 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 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1608 ASN A1781 GLN A1867 ASN B1608 ASN B1781 GLN B1867 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136409 restraints weight = 28452.875| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.86 r_work: 0.3485 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9696 Z= 0.288 Angle : 0.889 26.131 13116 Z= 0.468 Chirality : 0.175 1.588 1408 Planarity : 0.006 0.070 1714 Dihedral : 4.702 30.222 1332 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.51 % Allowed : 15.39 % Favored : 83.10 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1210 helix: 1.38 (0.25), residues: 430 sheet: -0.04 (0.42), residues: 154 loop : -1.30 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B1651 HIS 0.006 0.001 HIS A1778 PHE 0.018 0.002 PHE A1637 TYR 0.013 0.002 TYR B1719 ARG 0.015 0.001 ARG B1883 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6657.39 seconds wall clock time: 117 minutes 36.31 seconds (7056.31 seconds total)