Starting phenix.real_space_refine on Fri Jul 19 18:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/07_2024/8tyq_41728.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/07_2024/8tyq_41728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/07_2024/8tyq_41728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/07_2024/8tyq_41728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/07_2024/8tyq_41728.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/07_2024/8tyq_41728.cif" } resolution = 2.99 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= 0.007 sd= 0.028 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 49 5.16 5 C 5484 2.51 5 N 1449 2.21 5 O 1544 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 ASP 1394": "OD1" <-> "OD2" Residue "A GLU 1399": "OE1" <-> "OE2" Residue "A GLU 1689": "OE1" <-> "OE2" Residue "A TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1745": "OE1" <-> "OE2" Residue "A TYR 1747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1753": "OE1" <-> "OE2" Residue "A PHE 1792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1818": "OD1" <-> "OD2" Residue "A ASP 1838": "OD1" <-> "OD2" Residue "A ASP 1863": "OD1" <-> "OD2" Residue "A TYR 1894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1962": "OD1" <-> "OD2" Residue "A TYR 2006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2094": "OD1" <-> "OD2" Residue "A GLU 2108": "OE1" <-> "OE2" Residue "A GLU 2153": "OE1" <-> "OE2" Residue "A ASP 2175": "OD1" <-> "OD2" Residue "A ASP 2183": "OD1" <-> "OD2" Residue "A TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2192": "OE1" <-> "OE2" Residue "A GLU 2193": "OE1" <-> "OE2" Residue "A ASP 2231": "OD1" <-> "OD2" Residue "A GLU 2239": "OE1" <-> "OE2" Residue "A GLU 2337": "OE1" <-> "OE2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A GLU 2503": "OE1" <-> "OE2" Residue "A GLU 2512": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7645 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 957, 7635 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 913} Chain breaks: 24 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 957, 7635 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 913} Chain breaks: 24 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 7756 Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 845 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1998 " occ=0.84 ... (18 atoms not shown) pdb=" NE2BHIS A1998 " occ=0.16 Time building chain proxies: 8.32, per 1000 atoms: 0.98 Number of scatterers: 8529 At special positions: 0 Unit cell: (82.28, 93.5, 144.925, 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 49 16.00 F 3 9.00 O 1544 8.00 N 1449 7.00 C 5484 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: 3.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 33.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 1346 through 1354 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.940A pdb=" N LEU A1435 " --> pdb=" O MET A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1457 Processing helix chain 'A' and resid 1458 through 1469 Processing helix chain 'A' and resid 1499 through 1508 Processing helix chain 'A' and resid 1563 through 1568 Processing helix chain 'A' and resid 1569 through 1579 Processing helix chain 'A' and resid 1631 through 1636 Processing helix chain 'A' and resid 1642 through 1646 Processing helix chain 'A' and resid 1651 through 1656 Processing helix chain 'A' and resid 1686 through 1688 No H-bonds generated for 'chain 'A' and resid 1686 through 1688' Processing helix chain 'A' and resid 1703 through 1712 removed outlier: 3.696A pdb=" N ARG A1707 " --> pdb=" O GLY A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1791 Processing helix chain 'A' and resid 1792 through 1796 Processing helix chain 'A' and resid 1830 through 1837 Processing helix chain 'A' and resid 1851 through 1855 Processing helix chain 'A' and resid 1871 through 1873 No H-bonds generated for 'chain 'A' and resid 1871 through 1873' Processing helix chain 'A' and resid 1884 through 1889 removed outlier: 3.713A pdb=" N ASP A1887 " --> pdb=" O LEU A1884 " (cutoff:3.500A) Processing helix chain 'A' and resid 1914 through 1925 Processing helix chain 'A' and resid 1954 through 1961 Processing helix chain 'A' and resid 1967 through 1988 removed outlier: 4.312A pdb=" N GLY A1981 " --> pdb=" O HIS A1977 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR A1984 " --> pdb=" O ASP A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2052 through 2068 Processing helix chain 'A' and resid 2094 through 2100 Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.762A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2280 No H-bonds generated for 'chain 'A' and resid 2278 through 2280' Processing helix chain 'A' and resid 2339 through 2344 Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2396 removed outlier: 3.618A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2525 Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.633A pdb=" N TYR B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.599A pdb=" N LEU B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 155' Processing sheet with id=AA1, first strand: chain 'A' and resid 1372 through 1376 removed outlier: 3.553A pdb=" N ASP A1372 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1337 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A1393 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1752 through 1753 removed outlier: 3.546A pdb=" N PHE A1762 " --> pdb=" O GLU A1753 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1763 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1730 through 1734 removed outlier: 3.836A pdb=" N GLY A1737 " --> pdb=" O TRP A1734 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AA5, first strand: chain 'A' and resid 1875 through 1877 removed outlier: 7.076A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AA7, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.882A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2152 through 2157 removed outlier: 4.233A pdb=" N CYS A2154 " --> pdb=" O GLY A2170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2199 through 2207 Processing sheet with id=AB1, first strand: chain 'A' and resid 2245 through 2249 removed outlier: 4.269A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2300 through 2304 removed outlier: 3.576A pdb=" N CYS A2302 " --> pdb=" O GLY A2318 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A2323 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A2335 " --> pdb=" O ILE A2323 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A2325 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 3.688A pdb=" N THR A2356 " --> pdb=" O ALA A2366 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP A2377 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A2383 " --> pdb=" O ASP A2377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2414 through 2420 removed outlier: 6.831A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A2419 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A2424 " --> pdb=" O LEU A2419 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 927 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: 3.24 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1407 1.29 - 1.42: 2110 1.42 - 1.55: 5088 1.55 - 1.68: 8 1.68 - 1.81: 76 Bond restraints: 8689 Sorted by residual: bond pdb=" N PRO A2208 " pdb=" CD PRO A2208 " ideal model delta sigma weight residual 1.473 1.257 0.216 1.40e-02 5.10e+03 2.39e+02 bond pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.456 1.277 0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.467 1.289 0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.466 1.301 0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.451 1.296 0.155 2.00e-02 2.50e+03 6.00e+01 ... (remaining 8684 not shown) Histogram of bond angle deviations from ideal: 79.48 - 99.43: 15 99.43 - 119.38: 7541 119.38 - 139.33: 4192 139.33 - 159.29: 0 159.29 - 179.24: 2 Bond angle restraints: 11750 Sorted by residual: angle pdb=" C TYR A1699 " pdb=" CA TYR A1699 " pdb=" CB TYR A1699 " ideal model delta sigma weight residual 109.66 79.48 30.18 1.94e+00 2.66e-01 2.42e+02 angle pdb=" C PHE A1700 " pdb=" N PRO A1701 " pdb=" CA PRO A1701 " ideal model delta sigma weight residual 119.84 132.02 -12.18 1.25e+00 6.40e-01 9.50e+01 angle pdb=" CA TYR A1695 " pdb=" C TYR A1695 " pdb=" N GLU A1696 " ideal model delta sigma weight residual 116.20 128.33 -12.13 1.25e+00 6.40e-01 9.41e+01 angle pdb=" CA TYR A1699 " pdb=" C TYR A1699 " pdb=" O TYR A1699 " ideal model delta sigma weight residual 121.46 110.80 10.66 1.17e+00 7.31e-01 8.29e+01 angle pdb=" N PRO A2208 " pdb=" CD PRO A2208 " pdb=" CG PRO A2208 " ideal model delta sigma weight residual 103.20 113.77 -10.57 1.50e+00 4.44e-01 4.97e+01 ... (remaining 11745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 4949 24.21 - 48.43: 252 48.43 - 72.64: 37 72.64 - 96.85: 6 96.85 - 121.07: 3 Dihedral angle restraints: 5247 sinusoidal: 2150 harmonic: 3097 Sorted by residual: dihedral pdb=" C TYR A1699 " pdb=" N TYR A1699 " pdb=" CA TYR A1699 " pdb=" CB TYR A1699 " ideal model delta harmonic sigma weight residual -122.60 -83.37 -39.23 0 2.50e+00 1.60e-01 2.46e+02 dihedral pdb=" N TYR A1699 " pdb=" C TYR A1699 " pdb=" CA TYR A1699 " pdb=" CB TYR A1699 " ideal model delta harmonic sigma weight residual 122.80 104.66 18.14 0 2.50e+00 1.60e-01 5.27e+01 dihedral pdb=" N GLU A1696 " pdb=" C GLU A1696 " pdb=" CA GLU A1696 " pdb=" CB GLU A1696 " ideal model delta harmonic sigma weight residual 122.80 105.23 17.57 0 2.50e+00 1.60e-01 4.94e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1296 0.103 - 0.206: 58 0.206 - 0.309: 3 0.309 - 0.413: 1 0.413 - 0.516: 2 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA TYR A1699 " pdb=" N TYR A1699 " pdb=" C TYR A1699 " pdb=" CB TYR A1699 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA GLU A1696 " pdb=" N GLU A1696 " pdb=" C GLU A1696 " pdb=" CB GLU A1696 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CB VAL A1946 " pdb=" CA VAL A1946 " pdb=" CG1 VAL A1946 " pdb=" CG2 VAL A1946 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1357 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO A1942 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1700 " 0.060 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO A1701 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A1701 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A1701 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1695 " 0.031 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A1695 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A1695 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A1695 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1695 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A1695 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A1695 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1695 " -0.014 2.00e-02 2.50e+03 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 581 2.74 - 3.28: 8281 3.28 - 3.82: 13609 3.82 - 4.36: 16855 4.36 - 4.90: 28325 Nonbonded interactions: 67651 Sorted by model distance: nonbonded pdb=" OG1 THR A2267 " pdb=" OD1 ASP A2269 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASP A2243 " pdb=" N SER A2244 " model vdw 2.205 2.520 nonbonded pdb=" O VAL A2152 " pdb=" OH TYR A2475 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A1419 " pdb=" OH TYR A1485 " model vdw 2.220 2.440 nonbonded pdb=" OD2 ASP A1962 " pdb=" OG SER A1965 " model vdw 2.244 2.440 ... (remaining 67646 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=0.16 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 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 : 0.007 0.216 8689 Z= 0.462 Angle : 0.977 30.180 11750 Z= 0.549 Chirality : 0.052 0.516 1360 Planarity : 0.007 0.123 1461 Dihedral : 14.458 121.065 3225 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Rotamer: Outliers : 0.53 % Allowed : 11.15 % Favored : 88.32 % Cbeta Deviations : 0.30 % 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: -0.16 (0.27), residues: 1018 helix: 0.28 (0.30), residues: 312 sheet: 0.28 (0.35), residues: 211 loop : -0.42 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A2214 HIS 0.006 0.001 HIS B 54 PHE 0.028 0.002 PHE A1700 TYR 0.059 0.003 TYR A1695 ARG 0.005 0.000 ARG A1895 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2214 TRP cc_start: 0.7542 (m100) cc_final: 0.7310 (m100) REVERT: B 43 ASN cc_start: 0.7276 (m-40) cc_final: 0.7042 (p0) outliers start: 5 outliers final: 2 residues processed: 236 average time/residue: 1.0092 time to fit residues: 255.6559 Evaluate side-chains 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2295 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 42 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1342 ASN ** A1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1919 GLN A2295 ASN A2328 ASN B 113 HIS B 137 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8689 Z= 0.220 Angle : 0.711 10.175 11750 Z= 0.348 Chirality : 0.046 0.198 1360 Planarity : 0.006 0.096 1461 Dihedral : 8.070 129.436 1151 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.72 % Allowed : 18.05 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.03 (0.27), residues: 1018 helix: 0.70 (0.30), residues: 306 sheet: 0.08 (0.34), residues: 234 loop : -0.35 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1791 HIS 0.013 0.002 HIS B 113 PHE 0.030 0.002 PHE A1700 TYR 0.027 0.002 TYR A1419 ARG 0.005 0.001 ARG A2176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 1.132 Fit side-chains REVERT: A 1646 MET cc_start: 0.3790 (OUTLIER) cc_final: 0.3509 (mtt) REVERT: A 2214 TRP cc_start: 0.7671 (m100) cc_final: 0.7357 (m100) REVERT: A 2235 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6980 (mtp85) REVERT: A 2459 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.6651 (pmm) REVERT: B 43 ASN cc_start: 0.7636 (m-40) cc_final: 0.7171 (p0) outliers start: 34 outliers final: 9 residues processed: 176 average time/residue: 1.1093 time to fit residues: 210.5815 Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1646 MET Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2440 SER Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 0.0010 chunk 77 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2118 ASN A2295 ASN ** A2422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8689 Z= 0.252 Angle : 0.695 9.843 11750 Z= 0.344 Chirality : 0.046 0.213 1360 Planarity : 0.005 0.079 1461 Dihedral : 7.154 105.476 1148 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.14 % Allowed : 19.11 % Favored : 76.75 % 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: -0.02 (0.27), residues: 1018 helix: 0.66 (0.30), residues: 302 sheet: -0.04 (0.34), residues: 230 loop : -0.31 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2214 HIS 0.008 0.001 HIS B 113 PHE 0.018 0.002 PHE A1890 TYR 0.021 0.002 TYR A2189 ARG 0.007 0.001 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 0.878 Fit side-chains REVERT: A 1646 MET cc_start: 0.3902 (OUTLIER) cc_final: 0.3591 (mtt) REVERT: A 1690 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7484 (mt) REVERT: A 2151 ILE cc_start: 0.6760 (mm) cc_final: 0.6301 (tp) REVERT: A 2459 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.6771 (pmm) REVERT: B 43 ASN cc_start: 0.7644 (m-40) cc_final: 0.7151 (p0) outliers start: 38 outliers final: 13 residues processed: 166 average time/residue: 0.9761 time to fit residues: 174.6467 Evaluate side-chains 138 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1646 MET Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1699 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1657 GLN A1960 GLN ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2433 HIS ** A2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN B 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8689 Z= 0.264 Angle : 0.682 10.151 11750 Z= 0.340 Chirality : 0.046 0.238 1360 Planarity : 0.005 0.070 1461 Dihedral : 7.278 110.372 1148 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.72 % Allowed : 20.06 % Favored : 76.22 % 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: -0.13 (0.27), residues: 1018 helix: 0.52 (0.30), residues: 308 sheet: -0.09 (0.35), residues: 226 loop : -0.35 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1811 HIS 0.004 0.001 HIS B 113 PHE 0.019 0.002 PHE A1877 TYR 0.020 0.002 TYR A2189 ARG 0.008 0.001 ARG A1866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.992 Fit side-chains REVERT: A 1690 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 1829 ASP cc_start: 0.6554 (m-30) cc_final: 0.6323 (m-30) REVERT: A 1869 MET cc_start: 0.6567 (mpt) cc_final: 0.6114 (mpp) REVERT: A 2235 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: A 2444 LEU cc_start: 0.7691 (tm) cc_final: 0.7483 (tp) REVERT: A 2459 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.6938 (pmm) REVERT: B 43 ASN cc_start: 0.7663 (m-40) cc_final: 0.7179 (p0) outliers start: 34 outliers final: 12 residues processed: 144 average time/residue: 0.9850 time to fit residues: 153.2011 Evaluate side-chains 132 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2183 ASP Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1960 GLN ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN ** A2422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8689 Z= 0.269 Angle : 0.693 10.496 11750 Z= 0.339 Chirality : 0.047 0.238 1360 Planarity : 0.005 0.067 1461 Dihedral : 7.277 109.711 1148 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.18 % Allowed : 20.91 % Favored : 75.90 % 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: -0.14 (0.27), residues: 1018 helix: 0.51 (0.30), residues: 308 sheet: -0.09 (0.35), residues: 230 loop : -0.37 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1811 HIS 0.004 0.001 HIS B 94 PHE 0.018 0.002 PHE A1877 TYR 0.020 0.002 TYR A2189 ARG 0.009 0.001 ARG A1866 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 1697 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7772 (mtp) REVERT: A 1929 HIS cc_start: 0.4227 (m-70) cc_final: 0.3399 (m-70) REVERT: A 2235 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7420 (mtp85) REVERT: A 2459 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7003 (pmm) REVERT: B 43 ASN cc_start: 0.7699 (m-40) cc_final: 0.7221 (p0) outliers start: 29 outliers final: 16 residues processed: 141 average time/residue: 0.9232 time to fit residues: 141.1555 Evaluate side-chains 134 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1879 GLN Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2183 ASP Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1960 GLN ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN ** A2422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8689 Z= 0.287 Angle : 0.690 10.641 11750 Z= 0.341 Chirality : 0.047 0.264 1360 Planarity : 0.005 0.065 1461 Dihedral : 7.292 110.294 1148 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.61 % Allowed : 21.13 % Favored : 75.27 % 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: -0.11 (0.27), residues: 1018 helix: 0.70 (0.30), residues: 296 sheet: -0.22 (0.35), residues: 230 loop : -0.38 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2496 HIS 0.004 0.001 HIS B 80 PHE 0.016 0.002 PHE A1890 TYR 0.021 0.002 TYR A2189 ARG 0.007 0.001 ARG A2176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 1929 HIS cc_start: 0.4300 (m-70) cc_final: 0.3295 (m-70) REVERT: A 2235 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7472 (mtp85) REVERT: A 2459 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7035 (pmm) outliers start: 33 outliers final: 17 residues processed: 141 average time/residue: 1.0515 time to fit residues: 160.0063 Evaluate side-chains 128 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1879 GLN Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2183 ASP Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2440 SER Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8689 Z= 0.286 Angle : 0.710 10.755 11750 Z= 0.346 Chirality : 0.047 0.321 1360 Planarity : 0.005 0.067 1461 Dihedral : 7.297 110.312 1148 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.50 % Allowed : 21.13 % Favored : 75.37 % 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: -0.14 (0.27), residues: 1018 helix: 0.69 (0.30), residues: 296 sheet: -0.32 (0.34), residues: 232 loop : -0.34 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2496 HIS 0.005 0.001 HIS B 80 PHE 0.015 0.002 PHE A1890 TYR 0.022 0.002 TYR A2189 ARG 0.008 0.001 ARG A1735 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.936 Fit side-chains REVERT: A 1929 HIS cc_start: 0.4280 (m-70) cc_final: 0.3414 (m-70) REVERT: A 1944 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.4719 (pp-130) REVERT: A 1983 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7733 (ptt180) REVERT: A 2235 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7481 (mtp85) REVERT: A 2459 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7054 (pmm) REVERT: B 87 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6569 (m90) outliers start: 32 outliers final: 19 residues processed: 129 average time/residue: 1.0348 time to fit residues: 143.9662 Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1983 ARG Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2183 ASP Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2391 HIS Chi-restraints excluded: chain A residue 2440 SER Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1342 ASN ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8689 Z= 0.286 Angle : 0.710 10.755 11750 Z= 0.346 Chirality : 0.047 0.321 1360 Planarity : 0.005 0.071 1461 Dihedral : 7.297 110.312 1148 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.65 % Allowed : 21.97 % Favored : 75.37 % 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: -0.14 (0.27), residues: 1018 helix: 0.69 (0.30), residues: 296 sheet: -0.32 (0.34), residues: 232 loop : -0.34 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2496 HIS 0.005 0.001 HIS B 80 PHE 0.015 0.002 PHE A1890 TYR 0.022 0.002 TYR A2189 ARG 0.008 0.001 ARG A1735 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.885 Fit side-chains REVERT: A 1929 HIS cc_start: 0.4273 (m-70) cc_final: 0.3414 (m-70) REVERT: A 1944 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.4720 (pp-130) REVERT: A 1983 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7734 (ptt180) REVERT: A 2235 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7481 (mtp85) REVERT: A 2459 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7058 (pmm) REVERT: B 87 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6568 (m90) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 1.0291 time to fit residues: 138.7680 Evaluate side-chains 131 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1983 ARG Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2183 ASP Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2391 HIS Chi-restraints excluded: chain A residue 2440 SER Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8689 Z= 0.242 Angle : 0.695 12.334 11750 Z= 0.341 Chirality : 0.046 0.288 1360 Planarity : 0.005 0.070 1461 Dihedral : 7.260 110.557 1148 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.08 % Allowed : 21.66 % Favored : 75.27 % 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: -0.13 (0.28), residues: 1018 helix: 0.67 (0.30), residues: 297 sheet: -0.33 (0.35), residues: 229 loop : -0.32 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2214 HIS 0.003 0.001 HIS A2510 PHE 0.014 0.002 PHE A2262 TYR 0.022 0.002 TYR A2189 ARG 0.007 0.001 ARG A2176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.856 Fit side-chains REVERT: A 1929 HIS cc_start: 0.4204 (m-70) cc_final: 0.3191 (m-70) REVERT: A 1944 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.4849 (pp-130) REVERT: A 1983 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7735 (ptt180) REVERT: A 2235 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7443 (mtp85) REVERT: A 2459 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7042 (pmm) REVERT: B 87 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6552 (m90) outliers start: 28 outliers final: 18 residues processed: 130 average time/residue: 0.9819 time to fit residues: 138.0065 Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1983 ARG Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2183 ASP Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2391 HIS Chi-restraints excluded: chain A residue 2440 SER Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.0010 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1342 ASN A1437 ASN ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8689 Z= 0.176 Angle : 0.686 11.996 11750 Z= 0.333 Chirality : 0.046 0.312 1360 Planarity : 0.005 0.071 1461 Dihedral : 7.177 111.142 1148 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.59 % Allowed : 22.93 % Favored : 75.48 % 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: -0.01 (0.28), residues: 1018 helix: 0.79 (0.31), residues: 297 sheet: -0.23 (0.36), residues: 225 loop : -0.26 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 78 HIS 0.003 0.001 HIS B 80 PHE 0.016 0.001 PHE A1877 TYR 0.022 0.002 TYR A2189 ARG 0.008 0.001 ARG A2176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.284 Fit side-chains REVERT: A 1929 HIS cc_start: 0.4179 (m-70) cc_final: 0.3382 (m-70) REVERT: A 2235 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7315 (mtp85) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 1.0184 time to fit residues: 141.7550 Evaluate side-chains 119 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 2196 ASP Chi-restraints excluded: chain A residue 2235 ARG Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 35 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.0770 chunk 73 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.151015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.123502 restraints weight = 30232.619| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 5.62 r_work: 0.3597 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8689 Z= 0.172 Angle : 0.659 11.347 11750 Z= 0.325 Chirality : 0.045 0.282 1360 Planarity : 0.005 0.075 1461 Dihedral : 7.127 110.853 1148 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.27 % Allowed : 24.10 % Favored : 74.63 % 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: 0.03 (0.27), residues: 1018 helix: 0.81 (0.31), residues: 297 sheet: -0.23 (0.36), residues: 225 loop : -0.22 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2214 HIS 0.004 0.001 HIS A2236 PHE 0.014 0.001 PHE A2262 TYR 0.022 0.001 TYR A2189 ARG 0.008 0.001 ARG A2176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.52 seconds wall clock time: 61 minutes 14.88 seconds (3674.88 seconds total)