Starting phenix.real_space_refine on Fri Dec 8 00:53:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tze_41756/12_2023/8tze_41756_updated.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= 0.036 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 40 5.16 5 C 4018 2.51 5 N 1061 2.21 5 O 1133 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1745": "OE1" <-> "OE2" Residue "A GLU 1790": "OE1" <-> "OE2" Residue "A PHE 1792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1828": "OD1" <-> "OD2" Residue "A ASP 1873": "OD1" <-> "OD2" Residue "A GLU 1878": "OE1" <-> "OE2" Residue "A GLU 1882": "OE1" <-> "OE2" Residue "A PHE 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1902": "OE1" <-> "OE2" Residue "A TYR 1992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1994": "OD1" <-> "OD2" Residue "A TYR 2057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2098": "OE1" <-> "OE2" Residue "A ASP 2175": "OD1" <-> "OD2" Residue "A TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2212": "OE1" <-> "OE2" Residue "A GLU 2230": "OE1" <-> "OE2" Residue "A GLU 2239": "OE1" <-> "OE2" Residue "A PHE 2324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A ASP 2377": "OD1" <-> "OD2" Residue "A TYR 2475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2512": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6255 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6216 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 35, 'TRANS': 751} Chain breaks: 13 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.81, per 1000 atoms: 0.61 Number of scatterers: 6255 At special positions: 0 Unit cell: (90.695, 136.51, 86.02, 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 40 16.00 F 3 9.00 O 1133 8.00 N 1061 7.00 C 4018 6.00 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 26.6% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 1628 through 1631 No H-bonds generated for 'chain 'A' and resid 1628 through 1631' Processing helix chain 'A' and resid 1650 through 1655 Processing helix chain 'A' and resid 1687 through 1689 No H-bonds generated for 'chain 'A' and resid 1687 through 1689' Processing helix chain 'A' and resid 1704 through 1714 removed outlier: 4.734A pdb=" N GLU A1714 " --> pdb=" O ASN A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1790 Processing helix chain 'A' and resid 1827 through 1836 Processing helix chain 'A' and resid 1857 through 1860 removed outlier: 3.645A pdb=" N ILE A1860 " --> pdb=" O PRO A1857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1872 through 1874 No H-bonds generated for 'chain 'A' and resid 1872 through 1874' Processing helix chain 'A' and resid 1881 through 1883 No H-bonds generated for 'chain 'A' and resid 1881 through 1883' Processing helix chain 'A' and resid 1885 through 1888 removed outlier: 4.234A pdb=" N GLY A1888 " --> pdb=" O LEU A1885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1885 through 1888' Processing helix chain 'A' and resid 1916 through 1925 Processing helix chain 'A' and resid 1955 through 1961 removed outlier: 3.660A pdb=" N GLN A1960 " --> pdb=" O ASP A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1965 No H-bonds generated for 'chain 'A' and resid 1963 through 1965' Processing helix chain 'A' and resid 1968 through 1988 removed outlier: 3.571A pdb=" N ALA A1988 " --> pdb=" O TYR A1984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 1999 No H-bonds generated for 'chain 'A' and resid 1997 through 1999' Processing helix chain 'A' and resid 2041 through 2045 Processing helix chain 'A' and resid 2052 through 2067 Processing helix chain 'A' and resid 2071 through 2073 No H-bonds generated for 'chain 'A' and resid 2071 through 2073' Processing helix chain 'A' and resid 2095 through 2099 Processing helix chain 'A' and resid 2105 through 2114 removed outlier: 3.534A pdb=" N LYS A2109 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2119 through 2121 No H-bonds generated for 'chain 'A' and resid 2119 through 2121' Processing helix chain 'A' and resid 2125 through 2132 Processing helix chain 'A' and resid 2135 through 2139 Processing helix chain 'A' and resid 2279 through 2281 No H-bonds generated for 'chain 'A' and resid 2279 through 2281' Processing helix chain 'A' and resid 2338 through 2343 Processing helix chain 'A' and resid 2347 through 2350 No H-bonds generated for 'chain 'A' and resid 2347 through 2350' Processing helix chain 'A' and resid 2389 through 2395 removed outlier: 3.554A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2521 Processing sheet with id= A, first strand: chain 'A' and resid 1823 through 1826 removed outlier: 4.614A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A1750 " --> pdb=" O TYR A1739 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR A1739 " --> pdb=" O VAL A1750 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N SER A1752 " --> pdb=" O GLY A1737 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A1737 " --> pdb=" O SER A1752 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1839 through 1841 Processing sheet with id= C, first strand: chain 'A' and resid 1893 through 1898 removed outlier: 6.543A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id= E, first strand: chain 'A' and resid 2188 through 2193 removed outlier: 3.899A pdb=" N GLN A2178 " --> pdb=" O CYS A2171 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2233 through 2237 Processing sheet with id= G, first strand: chain 'A' and resid 2289 through 2292 removed outlier: 3.976A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2300 through 2306 removed outlier: 6.588A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A2303 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TRP A2316 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A2305 " --> pdb=" O VAL A2314 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A2314 " --> pdb=" O GLU A2305 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 7.034A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A2359 " --> pdb=" O ALA A2362 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A2362 " --> pdb=" O VAL A2359 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP A2377 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A2383 " --> pdb=" O ASP A2377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2414 through 2420 removed outlier: 6.700A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU A2419 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA A2424 " --> pdb=" O LEU A2419 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.622A pdb=" N VAL A2495 " --> pdb=" O THR A2141 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG A2143 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A2493 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A2145 " --> pdb=" O SER A2491 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N SER A2491 " --> pdb=" O LEU A2145 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1029 1.31 - 1.43: 1573 1.43 - 1.56: 3711 1.56 - 1.68: 2 1.68 - 1.81: 60 Bond restraints: 6375 Sorted by residual: bond pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.453 1.302 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.453 1.303 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.453 1.312 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.453 1.317 0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C20 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.452 1.323 0.129 2.00e-02 2.50e+03 4.17e+01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 96.32 - 112.96: 3682 112.96 - 129.59: 4903 129.59 - 146.22: 49 146.22 - 162.86: 0 162.86 - 179.49: 2 Bond angle restraints: 8636 Sorted by residual: angle pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " ideal model delta sigma weight residual 120.77 113.37 7.40 9.70e-01 1.06e+00 5.82e+01 angle pdb=" N TRP A1734 " pdb=" CA TRP A1734 " pdb=" C TRP A1734 " ideal model delta sigma weight residual 108.34 98.62 9.72 1.31e+00 5.83e-01 5.51e+01 angle pdb=" O ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " ideal model delta sigma weight residual 120.48 126.96 -6.48 8.90e-01 1.26e+00 5.30e+01 angle pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta sigma weight residual 119.84 111.83 8.01 1.25e+00 6.40e-01 4.11e+01 angle pdb=" N PRO A1942 " pdb=" CA PRO A1942 " pdb=" C PRO A1942 " ideal model delta sigma weight residual 112.47 99.99 12.48 2.06e+00 2.36e-01 3.67e+01 ... (remaining 8631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.82: 3565 20.82 - 41.63: 194 41.63 - 62.45: 63 62.45 - 83.27: 4 83.27 - 104.08: 8 Dihedral angle restraints: 3834 sinusoidal: 1555 harmonic: 2279 Sorted by residual: dihedral pdb=" CD ARG A2522 " pdb=" NE ARG A2522 " pdb=" CZ ARG A2522 " pdb=" NH1 ARG A2522 " ideal model delta sinusoidal sigma weight residual 0.00 -56.21 56.21 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLY A2100 " pdb=" C GLY A2100 " pdb=" N CYS A2101 " pdb=" CA CYS A2101 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 639 0.035 - 0.071: 249 0.071 - 0.106: 68 0.106 - 0.142: 41 0.142 - 0.177: 5 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CA PRO A1942 " pdb=" N PRO A1942 " pdb=" C PRO A1942 " pdb=" CB PRO A1942 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA GLN A1960 " pdb=" N GLN A1960 " pdb=" C GLN A1960 " pdb=" CB GLN A1960 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE A2323 " pdb=" N ILE A2323 " pdb=" C ILE A2323 " pdb=" CB ILE A2323 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 999 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2522 " 0.892 9.50e-02 1.11e+02 4.00e-01 9.71e+01 pdb=" NE ARG A2522 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A2522 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A2522 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2522 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " 0.092 5.00e-02 4.00e+02 1.49e-01 3.57e+01 pdb=" N PRO A1942 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2456 " 0.408 9.50e-02 1.11e+02 1.83e-01 2.06e+01 pdb=" NE ARG A2456 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A2456 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A2456 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2456 " 0.016 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 150 2.69 - 3.24: 5700 3.24 - 3.80: 9391 3.80 - 4.35: 13290 4.35 - 4.90: 22004 Nonbonded interactions: 50535 Sorted by model distance: nonbonded pdb=" O ASP A2269 " pdb=" OD1 ASP A2269 " model vdw 2.140 3.040 nonbonded pdb=" OE1 GLN A1845 " pdb=" NE ARG A1847 " model vdw 2.195 2.520 nonbonded pdb=" O GLU A1797 " pdb=" OG1 THR A1806 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A2213 " pdb=" OG1 THR A2229 " model vdw 2.206 2.440 nonbonded pdb=" OG SER A1954 " pdb=" OD1 ASP A1956 " model vdw 2.210 2.440 ... (remaining 50530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.270 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.006 0.151 6375 Z= 0.414 Angle : 0.770 14.042 8636 Z= 0.439 Chirality : 0.045 0.177 1002 Planarity : 0.015 0.400 1080 Dihedral : 15.058 104.082 2352 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 13.91 % Favored : 84.78 % Cbeta Deviations : 0.00 % 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: 0.15 (0.31), residues: 759 helix: 1.34 (0.40), residues: 191 sheet: 0.33 (0.35), residues: 206 loop : -0.68 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1734 HIS 0.005 0.001 HIS A2391 PHE 0.028 0.002 PHE A2326 TYR 0.014 0.001 TYR A1984 ARG 0.005 0.000 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 1.2487 time to fit residues: 124.7029 Evaluate side-chains 83 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1736 time to fit residues: 1.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2236 HIS A2468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6375 Z= 0.252 Angle : 0.555 5.410 8636 Z= 0.286 Chirality : 0.045 0.157 1002 Planarity : 0.005 0.069 1080 Dihedral : 7.985 97.891 846 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 3.19 % Allowed : 14.93 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.04 (0.31), residues: 759 helix: 1.11 (0.39), residues: 201 sheet: 0.34 (0.35), residues: 206 loop : -0.76 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1734 HIS 0.005 0.001 HIS A2510 PHE 0.023 0.002 PHE A2326 TYR 0.011 0.002 TYR A2346 ARG 0.005 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 91 average time/residue: 1.1727 time to fit residues: 112.5640 Evaluate side-chains 86 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.1360 time to fit residues: 1.9316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2261 ASN A2476 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6375 Z= 0.176 Angle : 0.509 5.311 8636 Z= 0.265 Chirality : 0.044 0.151 1002 Planarity : 0.004 0.063 1080 Dihedral : 7.926 99.394 846 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 3.04 % Allowed : 14.20 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.16 (0.31), residues: 759 helix: 1.24 (0.39), residues: 203 sheet: 0.40 (0.34), residues: 216 loop : -0.74 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.023 0.001 PHE A2326 TYR 0.009 0.001 TYR A2346 ARG 0.006 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 1.1387 time to fit residues: 116.5682 Evaluate side-chains 88 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.3576 time to fit residues: 3.0422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7304 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6375 Z= 0.211 Angle : 0.524 5.336 8636 Z= 0.270 Chirality : 0.044 0.151 1002 Planarity : 0.004 0.055 1080 Dihedral : 7.907 98.532 846 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 2.75 % Allowed : 15.65 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.18 (0.31), residues: 759 helix: 1.33 (0.40), residues: 198 sheet: 0.31 (0.34), residues: 219 loop : -0.68 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.010 0.001 PHE A1700 TYR 0.015 0.001 TYR A2006 ARG 0.007 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 1.2197 time to fit residues: 113.2948 Evaluate side-chains 88 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.1529 time to fit residues: 1.9387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.0170 chunk 14 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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: 0.7289 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6375 Z= 0.176 Angle : 0.503 5.248 8636 Z= 0.262 Chirality : 0.044 0.159 1002 Planarity : 0.004 0.054 1080 Dihedral : 7.844 99.836 846 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 3.04 % Allowed : 15.80 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.27 (0.31), residues: 759 helix: 1.45 (0.40), residues: 198 sheet: 0.38 (0.34), residues: 218 loop : -0.67 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.024 0.001 PHE A2326 TYR 0.009 0.001 TYR A2006 ARG 0.007 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 94 average time/residue: 1.1673 time to fit residues: 115.9007 Evaluate side-chains 86 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1755 time to fit residues: 1.9949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.0270 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 42 optimal weight: 0.3980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6375 Z= 0.143 Angle : 0.481 5.260 8636 Z= 0.250 Chirality : 0.043 0.147 1002 Planarity : 0.004 0.050 1080 Dihedral : 7.721 99.917 846 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 2.75 % Allowed : 16.23 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.32 (0.31), residues: 759 helix: 1.56 (0.40), residues: 198 sheet: 0.40 (0.35), residues: 210 loop : -0.65 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1734 HIS 0.003 0.000 HIS A2510 PHE 0.023 0.001 PHE A2326 TYR 0.008 0.001 TYR A2006 ARG 0.006 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.680 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 1.1456 time to fit residues: 112.7670 Evaluate side-chains 86 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1537 time to fit residues: 1.3931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.0060 chunk 75 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.0050 chunk 22 optimal weight: 0.5980 overall best weight: 0.4010 ------------------------------------------------------------------------------- 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: 0.7273 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6375 Z= 0.147 Angle : 0.494 9.215 8636 Z= 0.253 Chirality : 0.043 0.147 1002 Planarity : 0.004 0.051 1080 Dihedral : 7.708 99.726 846 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 2.32 % Allowed : 16.96 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.36 (0.31), residues: 759 helix: 1.59 (0.40), residues: 198 sheet: 0.41 (0.35), residues: 202 loop : -0.59 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1734 HIS 0.003 0.000 HIS A2510 PHE 0.010 0.001 PHE A1700 TYR 0.008 0.001 TYR A1699 ARG 0.006 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.709 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 1.1463 time to fit residues: 118.8064 Evaluate side-chains 92 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1778 time to fit residues: 1.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1758 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6375 Z= 0.159 Angle : 0.499 8.036 8636 Z= 0.256 Chirality : 0.043 0.146 1002 Planarity : 0.004 0.049 1080 Dihedral : 7.710 99.107 846 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 1.88 % Allowed : 17.83 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.42 (0.31), residues: 759 helix: 1.58 (0.40), residues: 198 sheet: 0.49 (0.34), residues: 212 loop : -0.57 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1734 HIS 0.003 0.001 HIS A2510 PHE 0.025 0.001 PHE A2326 TYR 0.007 0.001 TYR A2006 ARG 0.007 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.658 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 1.1469 time to fit residues: 112.7330 Evaluate side-chains 92 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.2284 time to fit residues: 1.5290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.7295 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6375 Z= 0.200 Angle : 0.518 8.308 8636 Z= 0.265 Chirality : 0.044 0.145 1002 Planarity : 0.004 0.051 1080 Dihedral : 7.797 99.243 846 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 2.03 % Allowed : 17.39 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.37 (0.31), residues: 759 helix: 1.48 (0.39), residues: 198 sheet: 0.50 (0.34), residues: 211 loop : -0.60 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.010 0.001 PHE A1700 TYR 0.009 0.001 TYR A2449 ARG 0.008 0.000 ARG A2394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 93 average time/residue: 1.0043 time to fit residues: 98.6861 Evaluate side-chains 93 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.3253 time to fit residues: 1.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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: 0.7298 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6375 Z= 0.200 Angle : 0.520 8.141 8636 Z= 0.266 Chirality : 0.044 0.146 1002 Planarity : 0.004 0.049 1080 Dihedral : 7.818 99.342 846 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.74 % Allowed : 18.12 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.28 (0.31), residues: 759 helix: 1.44 (0.39), residues: 198 sheet: 0.35 (0.34), residues: 220 loop : -0.62 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1734 HIS 0.004 0.001 HIS A2510 PHE 0.025 0.001 PHE A2326 TYR 0.010 0.001 TYR A1733 ARG 0.007 0.000 ARG A2394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 1.1049 time to fit residues: 105.6505 Evaluate side-chains 89 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2283 time to fit residues: 1.0123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.0570 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.0570 chunk 54 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.184466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145278 restraints weight = 7094.630| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.53 r_work: 0.3557 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6375 Z= 0.141 Angle : 0.493 8.305 8636 Z= 0.254 Chirality : 0.043 0.147 1002 Planarity : 0.004 0.048 1080 Dihedral : 7.733 100.265 846 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 17.68 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.38 (0.31), residues: 759 helix: 1.64 (0.40), residues: 197 sheet: 0.42 (0.35), residues: 207 loop : -0.60 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1734 HIS 0.003 0.000 HIS A2510 PHE 0.011 0.001 PHE A1700 TYR 0.011 0.001 TYR A1733 ARG 0.007 0.000 ARG A2394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.11 seconds wall clock time: 50 minutes 35.92 seconds (3035.92 seconds total)