Starting phenix.real_space_refine on Mon Mar 18 22:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sky_10231/03_2024/6sky_10231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sky_10231/03_2024/6sky_10231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sky_10231/03_2024/6sky_10231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sky_10231/03_2024/6sky_10231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sky_10231/03_2024/6sky_10231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sky_10231/03_2024/6sky_10231_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 14064 2.51 5 N 3942 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1461": "NH1" <-> "NH2" Residue "A ARG 1468": "NH1" <-> "NH2" Residue "A PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1694": "OE1" <-> "OE2" Residue "A TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A PHE 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1857": "OE1" <-> "OE2" Residue "A ASP 1862": "OD1" <-> "OD2" Residue "A ARG 1863": "NH1" <-> "NH2" Residue "A ARG 1880": "NH1" <-> "NH2" Residue "A TYR 1931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1945": "NH1" <-> "NH2" Residue "A TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1959": "NH1" <-> "NH2" Residue "A TYR 1963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2019": "NH1" <-> "NH2" Residue "A ARG 2056": "NH1" <-> "NH2" Residue "A ARG 2068": "NH1" <-> "NH2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "A GLU 2113": "OE1" <-> "OE2" Residue "A ARG 2115": "NH1" <-> "NH2" Residue "A ARG 2123": "NH1" <-> "NH2" Residue "A ARG 2134": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2173": "NH1" <-> "NH2" Residue "A ARG 2176": "NH1" <-> "NH2" Residue "A ARG 2178": "NH1" <-> "NH2" Residue "A ASP 2216": "OD1" <-> "OD2" Residue "A GLU 2219": "OE1" <-> "OE2" Residue "A ARG 2225": "NH1" <-> "NH2" Residue "A ARG 2245": "NH1" <-> "NH2" Residue "A TYR 2254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2260": "NH1" <-> "NH2" Residue "A ARG 2286": "NH1" <-> "NH2" Residue "A ARG 2314": "NH1" <-> "NH2" Residue "A ARG 2364": "NH1" <-> "NH2" Residue "A ARG 2365": "NH1" <-> "NH2" Residue "A ARG 2370": "NH1" <-> "NH2" Residue "A ASP 2394": "OD1" <-> "OD2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2425": "NH1" <-> "NH2" Residue "A PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2455": "NH1" <-> "NH2" Residue "A ARG 2473": "NH1" <-> "NH2" Residue "A ARG 2515": "NH1" <-> "NH2" Residue "A PHE 2579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2603": "NH1" <-> "NH2" Residue "A ARG 2617": "NH1" <-> "NH2" Residue "A ARG 2637": "NH1" <-> "NH2" Residue "A ARG 2640": "NH1" <-> "NH2" Residue "A ARG 2642": "NH1" <-> "NH2" Residue "A ARG 2647": "NH1" <-> "NH2" Residue "A TYR 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2662": "OE1" <-> "OE2" Residue "A ARG 2680": "NH1" <-> "NH2" Residue "A ARG 2706": "NH1" <-> "NH2" Residue "A TYR 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2711": "NH1" <-> "NH2" Residue "A ARG 2712": "NH1" <-> "NH2" Residue "A ARG 2716": "NH1" <-> "NH2" Residue "A ARG 2722": "NH1" <-> "NH2" Residue "A TYR 2723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2739": "NH1" <-> "NH2" Residue "A TYR 2742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2744": "NH1" <-> "NH2" Residue "A ARG 2761": "NH1" <-> "NH2" Residue "A ARG 2788": "NH1" <-> "NH2" Residue "A PHE 2798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2799": "NH1" <-> "NH2" Residue "A ASP 2803": "OD1" <-> "OD2" Residue "A ARG 2818": "NH1" <-> "NH2" Residue "A ARG 2819": "NH1" <-> "NH2" Residue "A ARG 2829": "NH1" <-> "NH2" Residue "A ARG 2843": "NH1" <-> "NH2" Residue "A ARG 2901": "NH1" <-> "NH2" Residue "A TYR 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1461": "NH1" <-> "NH2" Residue "B ARG 1468": "NH1" <-> "NH2" Residue "B PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1694": "OE1" <-> "OE2" Residue "B TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1769": "NH1" <-> "NH2" Residue "B PHE 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1857": "OE1" <-> "OE2" Residue "B ASP 1862": "OD1" <-> "OD2" Residue "B ARG 1863": "NH1" <-> "NH2" Residue "B ARG 1880": "NH1" <-> "NH2" Residue "B TYR 1931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1945": "NH1" <-> "NH2" Residue "B TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1959": "NH1" <-> "NH2" Residue "B TYR 1963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2019": "NH1" <-> "NH2" Residue "B ARG 2056": "NH1" <-> "NH2" Residue "B ARG 2068": "NH1" <-> "NH2" Residue "B ARG 2081": "NH1" <-> "NH2" Residue "B ARG 2100": "NH1" <-> "NH2" Residue "B GLU 2113": "OE1" <-> "OE2" Residue "B ARG 2115": "NH1" <-> "NH2" Residue "B ARG 2123": "NH1" <-> "NH2" Residue "B ARG 2134": "NH1" <-> "NH2" Residue "B ARG 2158": "NH1" <-> "NH2" Residue "B ARG 2163": "NH1" <-> "NH2" Residue "B ARG 2173": "NH1" <-> "NH2" Residue "B ARG 2176": "NH1" <-> "NH2" Residue "B ARG 2178": "NH1" <-> "NH2" Residue "B ASP 2216": "OD1" <-> "OD2" Residue "B GLU 2219": "OE1" <-> "OE2" Residue "B ARG 2225": "NH1" <-> "NH2" Residue "B ARG 2245": "NH1" <-> "NH2" Residue "B TYR 2254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2260": "NH1" <-> "NH2" Residue "B ARG 2286": "NH1" <-> "NH2" Residue "B ARG 2314": "NH1" <-> "NH2" Residue "B ARG 2364": "NH1" <-> "NH2" Residue "B ARG 2365": "NH1" <-> "NH2" Residue "B ARG 2370": "NH1" <-> "NH2" Residue "B ASP 2394": "OD1" <-> "OD2" Residue "B ARG 2397": "NH1" <-> "NH2" Residue "B ARG 2425": "NH1" <-> "NH2" Residue "B PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2455": "NH1" <-> "NH2" Residue "B ARG 2473": "NH1" <-> "NH2" Residue "B ARG 2515": "NH1" <-> "NH2" Residue "B PHE 2579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2603": "NH1" <-> "NH2" Residue "B ARG 2617": "NH1" <-> "NH2" Residue "B ARG 2637": "NH1" <-> "NH2" Residue "B ARG 2640": "NH1" <-> "NH2" Residue "B ARG 2642": "NH1" <-> "NH2" Residue "B ARG 2647": "NH1" <-> "NH2" Residue "B TYR 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2662": "OE1" <-> "OE2" Residue "B ARG 2680": "NH1" <-> "NH2" Residue "B ARG 2706": "NH1" <-> "NH2" Residue "B TYR 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2711": "NH1" <-> "NH2" Residue "B ARG 2712": "NH1" <-> "NH2" Residue "B ARG 2716": "NH1" <-> "NH2" Residue "B ARG 2722": "NH1" <-> "NH2" Residue "B TYR 2723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2739": "NH1" <-> "NH2" Residue "B TYR 2742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2744": "NH1" <-> "NH2" Residue "B ARG 2761": "NH1" <-> "NH2" Residue "B ARG 2788": "NH1" <-> "NH2" Residue "B PHE 2798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2799": "NH1" <-> "NH2" Residue "B ASP 2803": "OD1" <-> "OD2" Residue "B ARG 2818": "NH1" <-> "NH2" Residue "B ARG 2819": "NH1" <-> "NH2" Residue "B ARG 2829": "NH1" <-> "NH2" Residue "B ARG 2843": "NH1" <-> "NH2" Residue "B ARG 2901": "NH1" <-> "NH2" Residue "B TYR 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22348 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11142 Classifications: {'peptide': 1412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1359} Chain breaks: 7 Chain: "B" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11142 Classifications: {'peptide': 1412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1359} Chain breaks: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.83, per 1000 atoms: 0.53 Number of scatterers: 22348 At special positions: 0 Unit cell: (189.561, 104.841, 115.431, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 6 15.00 Mg 2 11.99 O 4242 8.00 N 3942 7.00 C 14064 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: 8.17 Conformation dependent library (CDL) restraints added in 3.8 seconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 6 sheets defined 65.3% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.38 Creating SS restraints... Processing helix chain 'A' and resid 1429 through 1443 removed outlier: 4.670A pdb=" N VAL A1440 " --> pdb=" O HIS A1436 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A1443 " --> pdb=" O ARG A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1466 removed outlier: 3.729A pdb=" N ASP A1463 " --> pdb=" O ILE A1459 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR A1465 " --> pdb=" O ARG A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1487 removed outlier: 3.645A pdb=" N GLY A1475 " --> pdb=" O SER A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1521 Processing helix chain 'A' and resid 1530 through 1545 removed outlier: 3.753A pdb=" N HIS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1569 Processing helix chain 'A' and resid 1578 through 1588 Processing helix chain 'A' and resid 1606 through 1619 removed outlier: 5.111A pdb=" N ALA A1614 " --> pdb=" O ILE A1610 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A1615 " --> pdb=" O LYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1644 Processing helix chain 'A' and resid 1649 through 1651 No H-bonds generated for 'chain 'A' and resid 1649 through 1651' Processing helix chain 'A' and resid 1657 through 1663 Processing helix chain 'A' and resid 1670 through 1681 removed outlier: 3.753A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1706 Processing helix chain 'A' and resid 1710 through 1719 removed outlier: 3.595A pdb=" N GLU A1718 " --> pdb=" O SER A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1726 Processing helix chain 'A' and resid 1756 through 1758 No H-bonds generated for 'chain 'A' and resid 1756 through 1758' Processing helix chain 'A' and resid 1762 through 1773 removed outlier: 3.803A pdb=" N SER A1773 " --> pdb=" O ARG A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1781 No H-bonds generated for 'chain 'A' and resid 1778 through 1781' Processing helix chain 'A' and resid 1783 through 1789 Processing helix chain 'A' and resid 1793 through 1810 Proline residue: A1799 - end of helix removed outlier: 3.651A pdb=" N LEU A1810 " --> pdb=" O LEU A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1827 removed outlier: 4.041A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1851 removed outlier: 3.774A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A1851 " --> pdb=" O LEU A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1865 removed outlier: 3.992A pdb=" N ALA A1864 " --> pdb=" O ALA A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1880 Processing helix chain 'A' and resid 1884 through 1898 Processing helix chain 'A' and resid 1916 through 1923 removed outlier: 3.727A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1932 Processing helix chain 'A' and resid 1939 through 1948 Processing helix chain 'A' and resid 1953 through 1968 removed outlier: 3.805A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1988 removed outlier: 3.792A pdb=" N ARG A1975 " --> pdb=" O LEU A1972 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A1988 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 1999 Processing helix chain 'A' and resid 2011 through 2021 Processing helix chain 'A' and resid 2035 through 2047 Processing helix chain 'A' and resid 2052 through 2072 Processing helix chain 'A' and resid 2077 through 2098 Processing helix chain 'A' and resid 2102 through 2121 removed outlier: 4.935A pdb=" N SER A2121 " --> pdb=" O LYS A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2143 Processing helix chain 'A' and resid 2154 through 2174 Processing helix chain 'A' and resid 2178 through 2191 removed outlier: 3.734A pdb=" N LEU A2191 " --> pdb=" O ALA A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2193 through 2196 No H-bonds generated for 'chain 'A' and resid 2193 through 2196' Processing helix chain 'A' and resid 2203 through 2217 Processing helix chain 'A' and resid 2220 through 2232 Processing helix chain 'A' and resid 2245 through 2258 Processing helix chain 'A' and resid 2264 through 2270 removed outlier: 3.829A pdb=" N GLN A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A2269 " --> pdb=" O ASP A2265 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2279 Processing helix chain 'A' and resid 2286 through 2303 Processing helix chain 'A' and resid 2306 through 2328 Processing helix chain 'A' and resid 2348 through 2385 Processing helix chain 'A' and resid 2394 through 2404 Processing helix chain 'A' and resid 2409 through 2421 removed outlier: 5.250A pdb=" N ASN A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS A2421 " --> pdb=" O LYS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2426 No H-bonds generated for 'chain 'A' and resid 2424 through 2426' Processing helix chain 'A' and resid 2431 through 2434 No H-bonds generated for 'chain 'A' and resid 2431 through 2434' Processing helix chain 'A' and resid 2444 through 2459 removed outlier: 3.620A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2472 removed outlier: 5.859A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2499 removed outlier: 3.935A pdb=" N LYS A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2541 through 2552 Processing helix chain 'A' and resid 2616 through 2635 removed outlier: 3.868A pdb=" N LYS A2634 " --> pdb=" O SER A2630 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU A2635 " --> pdb=" O GLU A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'A' and resid 2670 through 2681 Proline residue: A2676 - end of helix removed outlier: 3.897A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2688 through 2699 removed outlier: 3.740A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A2699 " --> pdb=" O ILE A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2716 removed outlier: 3.876A pdb=" N ARG A2716 " --> pdb=" O ARG A2712 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2728 removed outlier: 3.804A pdb=" N PHE A2725 " --> pdb=" O ARG A2722 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A2727 " --> pdb=" O PHE A2724 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A2728 " --> pdb=" O PHE A2725 " (cutoff:3.500A) Processing helix chain 'A' and resid 2732 through 2755 Processing helix chain 'A' and resid 2786 through 2789 removed outlier: 3.678A pdb=" N VAL A2789 " --> pdb=" O MET A2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2786 through 2789' Processing helix chain 'A' and resid 2802 through 2808 removed outlier: 3.501A pdb=" N GLY A2807 " --> pdb=" O ASP A2803 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A2808 " --> pdb=" O ILE A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2829 Processing helix chain 'A' and resid 2832 through 2843 Processing helix chain 'A' and resid 2854 through 2860 Processing helix chain 'A' and resid 2898 through 2909 Processing helix chain 'A' and resid 2916 through 2927 Processing helix chain 'A' and resid 2930 through 2933 No H-bonds generated for 'chain 'A' and resid 2930 through 2933' Processing helix chain 'B' and resid 1429 through 1443 removed outlier: 4.670A pdb=" N VAL B1440 " --> pdb=" O HIS B1436 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B1441 " --> pdb=" O SER B1437 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL B1443 " --> pdb=" O ARG B1439 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1466 removed outlier: 3.729A pdb=" N ASP B1463 " --> pdb=" O ILE B1459 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B1464 " --> pdb=" O LYS B1460 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR B1465 " --> pdb=" O ARG B1461 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1487 removed outlier: 3.645A pdb=" N GLY B1475 " --> pdb=" O SER B1471 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1521 Processing helix chain 'B' and resid 1530 through 1545 removed outlier: 3.753A pdb=" N HIS B1545 " --> pdb=" O GLU B1541 " (cutoff:3.500A) Processing helix chain 'B' and resid 1557 through 1569 Processing helix chain 'B' and resid 1578 through 1588 Processing helix chain 'B' and resid 1606 through 1619 removed outlier: 5.111A pdb=" N ALA B1614 " --> pdb=" O ILE B1610 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL B1615 " --> pdb=" O LYS B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1627 through 1644 Processing helix chain 'B' and resid 1649 through 1651 No H-bonds generated for 'chain 'B' and resid 1649 through 1651' Processing helix chain 'B' and resid 1657 through 1663 Processing helix chain 'B' and resid 1670 through 1681 removed outlier: 3.753A pdb=" N LEU B1681 " --> pdb=" O LEU B1677 " (cutoff:3.500A) Processing helix chain 'B' and resid 1687 through 1706 Processing helix chain 'B' and resid 1710 through 1719 removed outlier: 3.595A pdb=" N GLU B1718 " --> pdb=" O SER B1714 " (cutoff:3.500A) Processing helix chain 'B' and resid 1722 through 1726 Processing helix chain 'B' and resid 1756 through 1758 No H-bonds generated for 'chain 'B' and resid 1756 through 1758' Processing helix chain 'B' and resid 1762 through 1773 removed outlier: 3.803A pdb=" N SER B1773 " --> pdb=" O ARG B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1778 through 1781 No H-bonds generated for 'chain 'B' and resid 1778 through 1781' Processing helix chain 'B' and resid 1783 through 1789 Processing helix chain 'B' and resid 1793 through 1810 Proline residue: B1799 - end of helix removed outlier: 3.651A pdb=" N LEU B1810 " --> pdb=" O LEU B1806 " (cutoff:3.500A) Processing helix chain 'B' and resid 1815 through 1827 removed outlier: 4.041A pdb=" N GLN B1825 " --> pdb=" O SER B1821 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1836 through 1851 removed outlier: 3.774A pdb=" N LEU B1841 " --> pdb=" O GLU B1837 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B1851 " --> pdb=" O LEU B1847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1860 through 1865 removed outlier: 3.992A pdb=" N ALA B1864 " --> pdb=" O ALA B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1871 through 1880 Processing helix chain 'B' and resid 1884 through 1898 Processing helix chain 'B' and resid 1916 through 1923 removed outlier: 3.727A pdb=" N ASN B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1932 Processing helix chain 'B' and resid 1939 through 1948 Processing helix chain 'B' and resid 1953 through 1968 removed outlier: 3.805A pdb=" N PHE B1958 " --> pdb=" O LYS B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1972 through 1988 removed outlier: 3.792A pdb=" N ARG B1975 " --> pdb=" O LEU B1972 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B1988 " --> pdb=" O LEU B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1991 through 1999 Processing helix chain 'B' and resid 2011 through 2021 Processing helix chain 'B' and resid 2035 through 2047 Processing helix chain 'B' and resid 2052 through 2072 Processing helix chain 'B' and resid 2077 through 2098 Processing helix chain 'B' and resid 2102 through 2121 removed outlier: 4.935A pdb=" N SER B2121 " --> pdb=" O LYS B2117 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2143 Processing helix chain 'B' and resid 2154 through 2174 Processing helix chain 'B' and resid 2178 through 2191 removed outlier: 3.734A pdb=" N LEU B2191 " --> pdb=" O ALA B2187 " (cutoff:3.500A) Processing helix chain 'B' and resid 2193 through 2196 No H-bonds generated for 'chain 'B' and resid 2193 through 2196' Processing helix chain 'B' and resid 2203 through 2217 Processing helix chain 'B' and resid 2220 through 2232 Processing helix chain 'B' and resid 2245 through 2258 Processing helix chain 'B' and resid 2264 through 2270 removed outlier: 3.829A pdb=" N GLN B2268 " --> pdb=" O PRO B2264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B2269 " --> pdb=" O ASP B2265 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2279 Processing helix chain 'B' and resid 2286 through 2303 Processing helix chain 'B' and resid 2306 through 2328 Processing helix chain 'B' and resid 2348 through 2385 Processing helix chain 'B' and resid 2394 through 2404 Processing helix chain 'B' and resid 2409 through 2421 removed outlier: 5.250A pdb=" N ASN B2420 " --> pdb=" O LYS B2416 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS B2421 " --> pdb=" O LYS B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2424 through 2426 No H-bonds generated for 'chain 'B' and resid 2424 through 2426' Processing helix chain 'B' and resid 2431 through 2434 No H-bonds generated for 'chain 'B' and resid 2431 through 2434' Processing helix chain 'B' and resid 2444 through 2459 removed outlier: 3.620A pdb=" N ASP B2451 " --> pdb=" O LYS B2447 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2472 removed outlier: 5.859A pdb=" N TYR B2466 " --> pdb=" O TYR B2462 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2483 through 2499 removed outlier: 3.935A pdb=" N LYS B2499 " --> pdb=" O LYS B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2507 through 2522 Processing helix chain 'B' and resid 2541 through 2552 Processing helix chain 'B' and resid 2616 through 2635 removed outlier: 3.868A pdb=" N LYS B2634 " --> pdb=" O SER B2630 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B2635 " --> pdb=" O GLU B2631 " (cutoff:3.500A) Processing helix chain 'B' and resid 2637 through 2641 Processing helix chain 'B' and resid 2670 through 2681 Proline residue: B2676 - end of helix removed outlier: 3.897A pdb=" N GLU B2679 " --> pdb=" O MET B2675 " (cutoff:3.500A) Processing helix chain 'B' and resid 2688 through 2699 removed outlier: 3.740A pdb=" N ALA B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN B2699 " --> pdb=" O ILE B2695 " (cutoff:3.500A) Processing helix chain 'B' and resid 2703 through 2716 removed outlier: 3.876A pdb=" N ARG B2716 " --> pdb=" O ARG B2712 " (cutoff:3.500A) Processing helix chain 'B' and resid 2721 through 2728 removed outlier: 3.804A pdb=" N PHE B2725 " --> pdb=" O ARG B2722 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B2727 " --> pdb=" O PHE B2724 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B2728 " --> pdb=" O PHE B2725 " (cutoff:3.500A) Processing helix chain 'B' and resid 2732 through 2755 Processing helix chain 'B' and resid 2786 through 2789 removed outlier: 3.678A pdb=" N VAL B2789 " --> pdb=" O MET B2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2786 through 2789' Processing helix chain 'B' and resid 2802 through 2808 removed outlier: 3.501A pdb=" N GLY B2807 " --> pdb=" O ASP B2803 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET B2808 " --> pdb=" O ILE B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2816 through 2829 Processing helix chain 'B' and resid 2832 through 2843 Processing helix chain 'B' and resid 2854 through 2860 Processing helix chain 'B' and resid 2898 through 2909 Processing helix chain 'B' and resid 2916 through 2927 Processing helix chain 'B' and resid 2930 through 2933 No H-bonds generated for 'chain 'B' and resid 2930 through 2933' Processing sheet with id= A, first strand: chain 'A' and resid 2534 through 2536 Processing sheet with id= B, first strand: chain 'A' and resid 2651 through 2655 removed outlier: 6.641A pdb=" N SER A2658 " --> pdb=" O LEU A2654 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2667 through 2669 Processing sheet with id= D, first strand: chain 'B' and resid 2534 through 2536 Processing sheet with id= E, first strand: chain 'B' and resid 2651 through 2655 removed outlier: 6.641A pdb=" N SER B2658 " --> pdb=" O LEU B2654 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B2593 " --> pdb=" O VAL B2609 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 2667 through 2669 1222 hydrogen bonds defined for protein. 3564 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: 8.10 Time building geometry restraints manager: 8.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7968 1.36 - 1.51: 7774 1.51 - 1.66: 6866 1.66 - 1.80: 142 1.80 - 1.95: 8 Bond restraints: 22758 Sorted by residual: bond pdb=" C ASN B2539 " pdb=" N SER B2540 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.21e+00 bond pdb=" C ASN A2539 " pdb=" N SER A2540 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.21e+00 bond pdb=" C GLN A2304 " pdb=" N ASN A2305 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.61e-02 3.86e+03 4.68e+00 bond pdb=" C GLN B2304 " pdb=" N ASN B2305 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.61e-02 3.86e+03 4.68e+00 bond pdb=" CB GLU A2774 " pdb=" CG GLU A2774 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.16e+00 ... (remaining 22753 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.49: 384 105.49 - 112.68: 12350 112.68 - 119.88: 7924 119.88 - 127.07: 9872 127.07 - 134.26: 274 Bond angle restraints: 30804 Sorted by residual: angle pdb=" CA TRP A2118 " pdb=" CB TRP A2118 " pdb=" CG TRP A2118 " ideal model delta sigma weight residual 113.60 119.56 -5.96 1.90e+00 2.77e-01 9.83e+00 angle pdb=" CA TRP B2118 " pdb=" CB TRP B2118 " pdb=" CG TRP B2118 " ideal model delta sigma weight residual 113.60 119.56 -5.96 1.90e+00 2.77e-01 9.83e+00 angle pdb=" CA TRP B2940 " pdb=" CB TRP B2940 " pdb=" CG TRP B2940 " ideal model delta sigma weight residual 113.60 118.75 -5.15 1.90e+00 2.77e-01 7.33e+00 angle pdb=" CA TRP A2940 " pdb=" CB TRP A2940 " pdb=" CG TRP A2940 " ideal model delta sigma weight residual 113.60 118.75 -5.15 1.90e+00 2.77e-01 7.33e+00 angle pdb=" C LEU A2674 " pdb=" N MET A2675 " pdb=" CA MET A2675 " ideal model delta sigma weight residual 121.80 115.33 6.47 2.44e+00 1.68e-01 7.03e+00 ... (remaining 30799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.92: 12772 18.92 - 37.84: 916 37.84 - 56.76: 192 56.76 - 75.68: 28 75.68 - 94.60: 8 Dihedral angle restraints: 13916 sinusoidal: 5638 harmonic: 8278 Sorted by residual: dihedral pdb=" CA VAL B2664 " pdb=" C VAL B2664 " pdb=" N SER B2665 " pdb=" CA SER B2665 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA VAL A2664 " pdb=" C VAL A2664 " pdb=" N SER A2665 " pdb=" CA SER A2665 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA THR A2811 " pdb=" C THR A2811 " pdb=" N LYS A2812 " pdb=" CA LYS A2812 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 13913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1764 0.033 - 0.067: 1266 0.067 - 0.100: 328 0.100 - 0.134: 114 0.134 - 0.167: 18 Chirality restraints: 3490 Sorted by residual: chirality pdb=" CB ILE B2852 " pdb=" CA ILE B2852 " pdb=" CG1 ILE B2852 " pdb=" CG2 ILE B2852 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB ILE A2852 " pdb=" CA ILE A2852 " pdb=" CG1 ILE A2852 " pdb=" CG2 ILE A2852 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA PHE A2015 " pdb=" N PHE A2015 " pdb=" C PHE A2015 " pdb=" CB PHE A2015 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 3487 not shown) Planarity restraints: 3958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B2675 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B2676 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B2676 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B2676 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A2675 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO A2676 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A2676 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2676 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2731 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A2732 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2732 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2732 " 0.027 5.00e-02 4.00e+02 ... (remaining 3955 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 256 2.64 - 3.21: 20250 3.21 - 3.77: 33355 3.77 - 4.34: 48531 4.34 - 4.90: 80281 Nonbonded interactions: 182673 Sorted by model distance: nonbonded pdb=" OD1 ASP A2012 " pdb=" OG SER A2034 " model vdw 2.077 2.440 nonbonded pdb=" OD1 ASP B2012 " pdb=" OG SER B2034 " model vdw 2.077 2.440 nonbonded pdb=" OD2 ASP A2190 " pdb=" OG SER B1965 " model vdw 2.126 2.440 nonbonded pdb=" OG SER A1965 " pdb=" OD2 ASP B2190 " model vdw 2.126 2.440 nonbonded pdb=" OG SER A2244 " pdb=" OD2 ASP A2247 " model vdw 2.173 2.440 ... (remaining 182668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.020 Extract box with map and model: 9.790 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 58.810 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.009 0.083 22758 Z= 0.620 Angle : 0.685 14.267 30804 Z= 0.372 Chirality : 0.047 0.167 3490 Planarity : 0.004 0.056 3958 Dihedral : 13.865 94.596 8528 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.63 % Allowed : 7.18 % Favored : 89.19 % 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: -2.12 (0.14), residues: 2792 helix: -0.77 (0.10), residues: 1948 sheet: -0.85 (0.65), residues: 72 loop : -2.86 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2940 HIS 0.006 0.001 HIS B1512 PHE 0.022 0.002 PHE A2015 TYR 0.018 0.002 TYR B2673 ARG 0.005 0.001 ARG B2019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 378 time to evaluate : 2.589 Fit side-chains REVERT: A 1433 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (tmm) REVERT: A 1463 ASP cc_start: 0.7320 (m-30) cc_final: 0.7088 (m-30) REVERT: A 1507 LYS cc_start: 0.8020 (mttt) cc_final: 0.7731 (mtpt) REVERT: A 1818 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7642 (ttp80) REVERT: A 1883 MET cc_start: 0.8765 (mtp) cc_final: 0.8552 (mtm) REVERT: A 1899 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6609 (ptp-170) REVERT: A 2068 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7490 (mtm110) REVERT: A 2176 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7655 (mmp80) REVERT: A 2191 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 2247 ASP cc_start: 0.7601 (p0) cc_final: 0.7102 (p0) REVERT: A 2304 GLN cc_start: 0.7926 (pt0) cc_final: 0.7406 (mp10) REVERT: A 2317 ASN cc_start: 0.6612 (m-40) cc_final: 0.6304 (m110) REVERT: A 2365 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7298 (ttp80) REVERT: A 2368 GLN cc_start: 0.7944 (tp40) cc_final: 0.7640 (mm-40) REVERT: A 2393 ASN cc_start: 0.8286 (m-40) cc_final: 0.8051 (m110) REVERT: A 2487 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 2502 LYS cc_start: 0.8336 (mttt) cc_final: 0.7957 (tttp) REVERT: A 2522 MET cc_start: 0.8713 (mmp) cc_final: 0.8362 (mmm) REVERT: A 2561 GLN cc_start: 0.8910 (mt0) cc_final: 0.8638 (mt0) REVERT: A 2613 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6525 (p0) REVERT: A 2637 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8166 (tpt90) REVERT: A 2693 LYS cc_start: 0.8222 (tttt) cc_final: 0.7936 (ttpt) REVERT: A 2752 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 2808 MET cc_start: 0.9164 (mtt) cc_final: 0.8728 (mtt) REVERT: B 1433 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8091 (tmm) REVERT: B 1463 ASP cc_start: 0.7323 (m-30) cc_final: 0.7089 (m-30) REVERT: B 1507 LYS cc_start: 0.8021 (mttt) cc_final: 0.7730 (mtpt) REVERT: B 1818 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7639 (ttp80) REVERT: B 1883 MET cc_start: 0.8766 (mtp) cc_final: 0.8552 (mtm) REVERT: B 1899 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6601 (ptp-170) REVERT: B 2068 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7490 (mtm110) REVERT: B 2176 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7654 (mmp80) REVERT: B 2191 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 2247 ASP cc_start: 0.7599 (p0) cc_final: 0.7097 (p0) REVERT: B 2304 GLN cc_start: 0.7925 (pt0) cc_final: 0.7410 (mp10) REVERT: B 2317 ASN cc_start: 0.6618 (m-40) cc_final: 0.6307 (m110) REVERT: B 2365 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7298 (ttp80) REVERT: B 2368 GLN cc_start: 0.7943 (tp40) cc_final: 0.7639 (mm-40) REVERT: B 2393 ASN cc_start: 0.8286 (m-40) cc_final: 0.8048 (m110) REVERT: B 2487 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: B 2502 LYS cc_start: 0.8338 (mttt) cc_final: 0.7958 (tttp) REVERT: B 2522 MET cc_start: 0.8712 (mmp) cc_final: 0.8363 (mmm) REVERT: B 2561 GLN cc_start: 0.8912 (mt0) cc_final: 0.8642 (mt0) REVERT: B 2613 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6533 (p0) REVERT: B 2637 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8163 (tpt90) REVERT: B 2693 LYS cc_start: 0.8221 (tttt) cc_final: 0.7938 (ttpt) REVERT: B 2752 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8734 (tt) REVERT: B 2808 MET cc_start: 0.9181 (mtt) cc_final: 0.8750 (mtt) outliers start: 88 outliers final: 34 residues processed: 452 average time/residue: 1.6076 time to fit residues: 808.5278 Evaluate side-chains 330 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 282 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1899 ARG Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 1936 ASP Chi-restraints excluded: chain A residue 2076 ASN Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2485 SER Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1650 ASP Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1899 ARG Chi-restraints excluded: chain B residue 1935 GLN Chi-restraints excluded: chain B residue 1936 ASP Chi-restraints excluded: chain B residue 2076 ASN Chi-restraints excluded: chain B residue 2077 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2485 SER Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2600 THR Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2637 ARG Chi-restraints excluded: chain B residue 2713 VAL Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2993 > 50: distance: 105 - 111: 21.454 distance: 111 - 112: 14.495 distance: 112 - 113: 14.873 distance: 112 - 115: 27.536 distance: 113 - 114: 25.874 distance: 113 - 118: 11.060 distance: 115 - 116: 30.590 distance: 115 - 117: 18.598 distance: 118 - 119: 16.601 distance: 119 - 120: 6.415 distance: 119 - 122: 8.403 distance: 120 - 121: 27.442 distance: 120 - 130: 12.841 distance: 122 - 123: 10.550 distance: 123 - 124: 10.883 distance: 123 - 125: 11.960 distance: 124 - 126: 8.546 distance: 125 - 127: 11.288 distance: 126 - 128: 6.642 distance: 127 - 128: 19.256 distance: 128 - 129: 21.545 distance: 130 - 131: 16.575 distance: 131 - 132: 14.487 distance: 131 - 134: 17.831 distance: 132 - 133: 14.803 distance: 132 - 139: 20.528 distance: 134 - 135: 25.434 distance: 135 - 136: 9.238 distance: 136 - 137: 10.983 distance: 137 - 138: 14.929 distance: 139 - 140: 10.069 distance: 140 - 141: 18.276 distance: 140 - 143: 16.256 distance: 141 - 142: 23.960 distance: 141 - 146: 25.630 distance: 143 - 144: 16.252 distance: 143 - 145: 21.101 distance: 146 - 147: 24.141 distance: 146 - 201: 17.990 distance: 147 - 148: 15.664 distance: 147 - 150: 23.117 distance: 148 - 149: 14.885 distance: 148 - 154: 23.072 distance: 149 - 198: 22.861 distance: 150 - 151: 24.983 distance: 151 - 152: 27.525 distance: 151 - 153: 17.993 distance: 154 - 155: 16.855 distance: 154 - 160: 12.841 distance: 155 - 156: 3.043 distance: 155 - 158: 3.562 distance: 156 - 157: 16.768 distance: 156 - 161: 22.046 distance: 158 - 159: 18.704 distance: 159 - 160: 22.919 distance: 161 - 162: 16.770 distance: 161 - 191: 18.857 distance: 162 - 163: 16.773 distance: 162 - 165: 17.184 distance: 163 - 164: 19.501 distance: 163 - 169: 34.163 distance: 165 - 166: 15.102 distance: 166 - 167: 24.401 distance: 166 - 168: 24.982 distance: 169 - 170: 10.071 distance: 170 - 171: 15.227 distance: 170 - 173: 37.006 distance: 171 - 172: 49.120 distance: 171 - 176: 7.774 distance: 173 - 174: 12.550 distance: 173 - 175: 22.616 distance: 176 - 177: 6.467 distance: 177 - 178: 42.811 distance: 177 - 180: 40.370 distance: 178 - 179: 31.500 distance: 178 - 182: 20.044 distance: 180 - 181: 36.311 distance: 182 - 183: 8.391 distance: 183 - 184: 5.999 distance: 183 - 186: 24.848 distance: 184 - 185: 4.313 distance: 184 - 188: 5.177 distance: 186 - 187: 23.439