Starting phenix.real_space_refine on Fri Dec 8 14:05:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyq_41728/12_2023/8tyq_41728_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 8.52, per 1000 atoms: 1.00 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: 3.11 Conformation dependent library (CDL) restraints added in 2.8 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... running ksdssp... Secondary structure from input PDB file: 41 helices and 12 sheets defined 28.1% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 1347 through 1353 Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 7.236A pdb=" N GLN A1425 " --> pdb=" O SER A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1436 Processing helix chain 'A' and resid 1454 through 1456 No H-bonds generated for 'chain 'A' and resid 1454 through 1456' Processing helix chain 'A' and resid 1459 through 1468 Processing helix chain 'A' and resid 1499 through 1507 Processing helix chain 'A' and resid 1564 through 1568 Processing helix chain 'A' and resid 1570 through 1578 Processing helix chain 'A' and resid 1632 through 1635 No H-bonds generated for 'chain 'A' and resid 1632 through 1635' Processing helix chain 'A' and resid 1643 through 1645 No H-bonds generated for 'chain 'A' and resid 1643 through 1645' Processing helix chain 'A' and resid 1652 through 1655 No H-bonds generated for 'chain 'A' and resid 1652 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 1711 Processing helix chain 'A' and resid 1771 through 1790 Processing helix chain 'A' and resid 1793 through 1795 No H-bonds generated for 'chain 'A' and resid 1793 through 1795' Processing helix chain 'A' and resid 1831 through 1836 Processing helix chain 'A' and resid 1852 through 1854 No H-bonds generated for 'chain 'A' and resid 1852 through 1854' 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 1885 through 1888 Processing helix chain 'A' and resid 1914 through 1926 removed outlier: 4.030A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1960 Processing helix chain 'A' and resid 1968 through 1987 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 1997 through 1999 No H-bonds generated for 'chain 'A' and resid 1997 through 1999' Processing helix chain 'A' and resid 2052 through 2067 Processing helix chain 'A' and resid 2095 through 2099 Processing helix chain 'A' and resid 2108 through 2114 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 2138 No H-bonds generated for 'chain 'A' and resid 2135 through 2138' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' 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 2394 Processing helix chain 'A' and resid 2500 through 2524 Processing helix chain 'B' and resid 52 through 59 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing sheet with id= A, first strand: chain 'A' and resid 1481 through 1486 removed outlier: 7.574A pdb=" N LEU A1449 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A1485 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLY A1451 " --> pdb=" O TYR A1485 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A1452 " --> pdb=" O ALA A1417 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR A1419 " --> pdb=" O THR A1452 " (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: 3.553A pdb=" N ASP A1372 " --> pdb=" O ASP A1394 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1761 through 1768 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= C, 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= D, 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= E, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id= F, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id= G, first strand: chain 'A' and resid 2235 through 2237 Processing sheet with id= H, first strand: chain 'A' and resid 2289 through 2292 removed outlier: 4.269A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2300 through 2304 removed outlier: 6.753A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A2303 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP A2316 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.906A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (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= K, 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) Processing sheet with id= L, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.741A pdb=" N VAL A2495 " --> pdb=" O THR A2141 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG A2143 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A2493 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A2145 " --> pdb=" O SER A2491 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER A2491 " --> pdb=" O LEU A2145 " (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) 276 hydrogen bonds defined for protein. 756 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: 3.22 Time building geometry restraints manager: 3.43 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 1.453 1.277 0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.453 1.289 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.453 1.296 0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.453 1.301 0.152 2.00e-02 2.50e+03 5.78e+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 - 26.13: 4981 26.13 - 52.25: 227 52.25 - 78.37: 19 78.37 - 104.50: 4 104.50 - 130.62: 1 Dihedral angle restraints: 5232 sinusoidal: 2135 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 5229 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: 589 2.74 - 3.28: 8329 3.28 - 3.82: 13675 3.82 - 4.36: 16984 4.36 - 4.90: 28338 Nonbonded interactions: 67915 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 67910 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: 1.380 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: 7.200 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 32.110 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:15.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.230 ------------------------------------------------------------------------------- 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= 0.469 Angle : 0.984 30.180 11750 Z= 0.550 Chirality : 0.052 0.516 1360 Planarity : 0.007 0.123 1461 Dihedral : 14.103 130.623 3210 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 : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 236 average time/residue: 1.0395 time to fit residues: 263.5750 Evaluate side-chains 139 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 0.9980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6582 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8689 Z= 0.239 Angle : 0.698 9.610 11750 Z= 0.346 Chirality : 0.047 0.171 1360 Planarity : 0.006 0.096 1461 Dihedral : 6.543 135.179 1133 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.14 % Allowed : 17.73 % Favored : 78.13 % 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: -0.05 (0.27), residues: 1018 helix: 0.42 (0.30), residues: 307 sheet: 0.20 (0.34), residues: 232 loop : -0.33 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1791 HIS 0.010 0.002 HIS B 113 PHE 0.023 0.002 PHE A1877 TYR 0.023 0.002 TYR A1419 ARG 0.006 0.001 ARG A1895 *********************** 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 196 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 158 time to evaluate : 1.126 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 9 residues processed: 180 average time/residue: 1.0753 time to fit residues: 208.0580 Evaluate side-chains 136 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.1069 time to fit residues: 1.9238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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** ** A2422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2433 HIS A2505 GLN B 43 ASN B 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8689 Z= 0.262 Angle : 0.680 10.149 11750 Z= 0.337 Chirality : 0.046 0.148 1360 Planarity : 0.005 0.078 1461 Dihedral : 6.379 131.520 1133 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.18 % Allowed : 19.75 % Favored : 77.07 % 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: -0.05 (0.27), residues: 1018 helix: 0.41 (0.31), residues: 301 sheet: 0.15 (0.34), residues: 235 loop : -0.29 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1811 HIS 0.006 0.001 HIS B 113 PHE 0.020 0.002 PHE A2326 TYR 0.021 0.002 TYR A1419 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 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.989 Fit side-chains outliers start: 29 outliers final: 8 residues processed: 154 average time/residue: 0.9665 time to fit residues: 161.3266 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0915 time to fit residues: 1.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1657 GLN ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8689 Z= 0.240 Angle : 0.670 9.139 11750 Z= 0.329 Chirality : 0.046 0.232 1360 Planarity : 0.005 0.070 1461 Dihedral : 6.363 132.950 1133 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.40 % Allowed : 19.85 % 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: -0.10 (0.27), residues: 1018 helix: 0.38 (0.31), residues: 302 sheet: 0.10 (0.34), residues: 234 loop : -0.32 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2214 HIS 0.004 0.001 HIS B 113 PHE 0.015 0.002 PHE A1890 TYR 0.021 0.002 TYR A2189 ARG 0.006 0.001 ARG A2176 *********************** 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 155 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.032 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 144 average time/residue: 0.9351 time to fit residues: 146.6047 Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.4768 time to fit residues: 3.0944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8689 Z= 0.259 Angle : 0.661 9.047 11750 Z= 0.323 Chirality : 0.046 0.193 1360 Planarity : 0.005 0.070 1461 Dihedral : 6.290 130.974 1133 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.40 % Allowed : 19.96 % Favored : 76.65 % 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: -0.17 (0.27), residues: 1018 helix: 0.25 (0.30), residues: 308 sheet: 0.07 (0.34), residues: 236 loop : -0.31 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1811 HIS 0.004 0.001 HIS B 80 PHE 0.016 0.002 PHE A1890 TYR 0.020 0.002 TYR A2189 ARG 0.006 0.001 ARG A2176 *********************** 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 155 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 0.930 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 146 average time/residue: 0.9098 time to fit residues: 144.7856 Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.3695 time to fit residues: 3.1251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.5492 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= 0.257 Angle : 0.671 11.518 11750 Z= 0.328 Chirality : 0.045 0.167 1360 Planarity : 0.005 0.067 1461 Dihedral : 6.275 131.003 1133 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.97 % Allowed : 21.97 % Favored : 75.05 % 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: -0.21 (0.27), residues: 1018 helix: 0.22 (0.30), residues: 308 sheet: -0.03 (0.34), residues: 235 loop : -0.30 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2214 HIS 0.004 0.001 HIS A1929 PHE 0.017 0.002 PHE A2326 TYR 0.021 0.002 TYR A2189 ARG 0.008 0.001 ARG A1728 *********************** 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 145 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 0.954 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 136 average time/residue: 1.0277 time to fit residues: 151.3099 Evaluate side-chains 119 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 4 average time/residue: 0.1452 time to fit residues: 2.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 74 optimal weight: 0.0020 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8689 Z= 0.184 Angle : 0.632 9.735 11750 Z= 0.310 Chirality : 0.044 0.169 1360 Planarity : 0.005 0.068 1461 Dihedral : 6.282 134.091 1133 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.44 % Allowed : 22.08 % 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: -0.07 (0.28), residues: 1018 helix: 0.42 (0.31), residues: 306 sheet: 0.02 (0.35), residues: 234 loop : -0.25 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1811 HIS 0.003 0.001 HIS B 80 PHE 0.018 0.001 PHE A2326 TYR 0.022 0.002 TYR A2189 ARG 0.007 0.001 ARG A2176 *********************** 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 138 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.999 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.9020 time to fit residues: 132.0811 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 4 average time/residue: 0.1169 time to fit residues: 2.1273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1437 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: 0.6846 moved from start: 0.5881 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= 0.251 Angle : 0.687 10.759 11750 Z= 0.333 Chirality : 0.046 0.222 1360 Planarity : 0.005 0.066 1461 Dihedral : 6.239 129.734 1133 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.12 % Allowed : 23.35 % Favored : 74.52 % 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: -0.07 (0.28), residues: 1018 helix: 0.41 (0.31), residues: 300 sheet: -0.03 (0.35), residues: 236 loop : -0.21 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2496 HIS 0.007 0.001 HIS A1929 PHE 0.016 0.002 PHE A1890 TYR 0.021 0.002 TYR A2189 ARG 0.009 0.001 ARG A1728 *********************** 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 132 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.012 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.9662 time to fit residues: 134.4709 Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.6684 time to fit residues: 4.3542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8689 Z= 0.307 Angle : 0.726 9.926 11750 Z= 0.352 Chirality : 0.047 0.238 1360 Planarity : 0.005 0.067 1461 Dihedral : 6.305 125.676 1133 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.02 % Allowed : 23.46 % Favored : 74.52 % 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: -0.27 (0.28), residues: 1018 helix: 0.28 (0.31), residues: 298 sheet: -0.17 (0.35), residues: 234 loop : -0.33 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2496 HIS 0.007 0.001 HIS A1929 PHE 0.019 0.002 PHE A1890 TYR 0.022 0.002 TYR A2189 ARG 0.008 0.001 ARG A1735 *********************** 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 128 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.045 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 1.0480 time to fit residues: 141.4292 Evaluate side-chains 117 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 3 average time/residue: 0.1301 time to fit residues: 2.0419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 84 optimal weight: 0.0770 chunk 8 optimal weight: 0.0870 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8689 Z= 0.198 Angle : 0.684 10.113 11750 Z= 0.333 Chirality : 0.045 0.243 1360 Planarity : 0.005 0.067 1461 Dihedral : 6.349 130.773 1133 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.70 % Allowed : 24.52 % Favored : 73.78 % 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: -0.23 (0.28), residues: 1018 helix: 0.36 (0.31), residues: 304 sheet: -0.21 (0.35), residues: 235 loop : -0.31 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 78 HIS 0.006 0.001 HIS A1929 PHE 0.014 0.001 PHE A2262 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 122 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.997 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 120 average time/residue: 0.9742 time to fit residues: 127.8411 Evaluate side-chains 118 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 2 average time/residue: 0.1531 time to fit residues: 1.8390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0170 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ** 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 = 0.4259 r_free = 0.4259 target = 0.149169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116931 restraints weight = 30359.606| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 4.34 r_work: 0.3613 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8689 Z= 0.210 Angle : 0.683 10.532 11750 Z= 0.332 Chirality : 0.045 0.161 1360 Planarity : 0.005 0.071 1461 Dihedral : 6.288 129.763 1133 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.70 % Allowed : 24.63 % Favored : 73.67 % 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: -0.20 (0.28), residues: 1018 helix: 0.43 (0.31), residues: 297 sheet: -0.22 (0.35), residues: 235 loop : -0.31 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 78 HIS 0.006 0.001 HIS A1929 PHE 0.014 0.001 PHE A2262 TYR 0.022 0.002 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: 3451.28 seconds wall clock time: 62 minutes 14.71 seconds (3734.71 seconds total)