Starting phenix.real_space_refine on Fri Apr 12 07:04:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxq_17268/04_2024/8oxq_17268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxq_17268/04_2024/8oxq_17268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxq_17268/04_2024/8oxq_17268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxq_17268/04_2024/8oxq_17268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxq_17268/04_2024/8oxq_17268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxq_17268/04_2024/8oxq_17268_updated.pdb" } resolution = 2.5 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= 0.001 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 174 5.16 5 C 15940 2.51 5 N 4288 2.21 5 O 4666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3002": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25078 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1550, 12506 Classifications: {'peptide': 1550} Link IDs: {'PTRANS': 46, 'TRANS': 1503} Chain breaks: 6 Chain: "B" Number of atoms: 12506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1550, 12506 Classifications: {'peptide': 1550} Link IDs: {'PTRANS': 46, 'TRANS': 1503} Chain breaks: 6 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3764 SG CYS A1899 73.433 40.750 29.954 1.00220.36 S ATOM 3770 SG CYS A1900 71.675 43.494 29.364 1.00216.15 S ATOM 16270 SG CYS B1899 90.081 126.253 29.972 1.00222.03 S ATOM 16276 SG CYS B1900 91.825 123.499 29.371 1.00219.12 S Time building chain proxies: 12.64, per 1000 atoms: 0.50 Number of scatterers: 25078 At special positions: 0 Unit cell: (164.374, 167.678, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 174 16.00 P 6 15.00 Mg 2 11.99 O 4666 8.00 N 4288 7.00 C 15940 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: 10.12 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3103 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1899 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1900 " pdb="ZN ZN A3103 " - pdb=" ND1 HIS A1876 " pdb=" ZN B3103 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1899 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1900 " pdb="ZN ZN B3103 " - pdb=" ND1 HIS B1876 " 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 4 sheets defined 66.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.43 Creating SS restraints... Processing helix chain 'A' and resid 1413 through 1428 Processing helix chain 'A' and resid 1432 through 1452 removed outlier: 3.610A pdb=" N ASP A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1477 Processing helix chain 'A' and resid 1485 through 1508 Processing helix chain 'A' and resid 1513 through 1515 No H-bonds generated for 'chain 'A' and resid 1513 through 1515' Processing helix chain 'A' and resid 1517 through 1528 Proline residue: A1526 - end of helix Processing helix chain 'A' and resid 1532 through 1545 Processing helix chain 'A' and resid 1553 through 1560 removed outlier: 4.435A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1584 Processing helix chain 'A' and resid 1590 through 1601 Processing helix chain 'A' and resid 1607 through 1623 removed outlier: 4.685A pdb=" N GLU A1612 " --> pdb=" O THR A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1634 removed outlier: 3.842A pdb=" N VAL A1629 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1658 Processing helix chain 'A' and resid 1664 through 1677 Processing helix chain 'A' and resid 1694 through 1702 Processing helix chain 'A' and resid 1706 through 1723 removed outlier: 4.398A pdb=" N VAL A1723 " --> pdb=" O ASN A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1742 Processing helix chain 'A' and resid 1744 through 1753 Processing helix chain 'A' and resid 1759 through 1763 Processing helix chain 'A' and resid 1792 through 1795 No H-bonds generated for 'chain 'A' and resid 1792 through 1795' Processing helix chain 'A' and resid 1802 through 1815 Processing helix chain 'A' and resid 1822 through 1831 removed outlier: 3.774A pdb=" N LEU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1827 " --> pdb=" O ILE A1823 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A1828 " --> pdb=" O LEU A1824 " (cutoff:3.500A) Proline residue: A1829 - end of helix No H-bonds generated for 'chain 'A' and resid 1822 through 1831' Processing helix chain 'A' and resid 1835 through 1851 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1857 through 1874 Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.721A pdb=" N ARG A1907 " --> pdb=" O LYS A1903 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1932 removed outlier: 3.954A pdb=" N PHE A1932 " --> pdb=" O PHE A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1947 Processing helix chain 'A' and resid 1951 through 1973 Processing helix chain 'A' and resid 1986 through 1996 Processing helix chain 'A' and resid 2001 through 2012 Processing helix chain 'A' and resid 2016 through 2019 Processing helix chain 'A' and resid 2029 through 2038 Processing helix chain 'A' and resid 2042 through 2051 Processing helix chain 'A' and resid 2057 through 2070 Processing helix chain 'A' and resid 2074 through 2087 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2124 through 2136 Processing helix chain 'A' and resid 2140 through 2159 Processing helix chain 'A' and resid 2166 through 2190 removed outlier: 3.547A pdb=" N TYR A2170 " --> pdb=" O TYR A2167 " (cutoff:3.500A) Proline residue: A2171 - end of helix removed outlier: 3.613A pdb=" N GLU A2187 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2212 Processing helix chain 'A' and resid 2217 through 2236 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2245 through 2264 Processing helix chain 'A' and resid 2269 through 2281 removed outlier: 3.576A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2290 through 2301 Processing helix chain 'A' and resid 2305 through 2322 Processing helix chain 'A' and resid 2328 through 2348 removed outlier: 4.120A pdb=" N LEU A2332 " --> pdb=" O PRO A2328 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2361 through 2370 Processing helix chain 'A' and resid 2377 through 2406 Processing helix chain 'A' and resid 2408 through 2421 Processing helix chain 'A' and resid 2437 through 2475 removed outlier: 3.959A pdb=" N GLU A2449 " --> pdb=" O LEU A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2493 removed outlier: 3.524A pdb=" N LEU A2492 " --> pdb=" O SER A2489 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2510 removed outlier: 4.463A pdb=" N MET A2509 " --> pdb=" O LYS A2505 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS A2510 " --> pdb=" O ARG A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2513 through 2516 Processing helix chain 'A' and resid 2520 through 2526 removed outlier: 3.571A pdb=" N ARG A2526 " --> pdb=" O GLN A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2551 Processing helix chain 'A' and resid 2553 through 2564 removed outlier: 5.676A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2572 Processing helix chain 'A' and resid 2593 through 2612 removed outlier: 4.219A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2632 Processing helix chain 'A' and resid 2637 through 2640 removed outlier: 4.580A pdb=" N THR A2640 " --> pdb=" O GLN A2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2637 through 2640' Processing helix chain 'A' and resid 2723 through 2740 Processing helix chain 'A' and resid 2743 through 2748 removed outlier: 3.610A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2780 Processing helix chain 'A' and resid 2787 through 2791 Processing helix chain 'A' and resid 2798 through 2810 removed outlier: 4.826A pdb=" N LYS A2810 " --> pdb=" O MET A2806 " (cutoff:3.500A) Processing helix chain 'A' and resid 2813 through 2825 Processing helix chain 'A' and resid 2831 through 2838 removed outlier: 3.916A pdb=" N CYS A2835 " --> pdb=" O ARG A2832 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A2837 " --> pdb=" O PHE A2834 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A2838 " --> pdb=" O CYS A2835 " (cutoff:3.500A) Processing helix chain 'A' and resid 2842 through 2866 Processing helix chain 'A' and resid 2873 through 2875 No H-bonds generated for 'chain 'A' and resid 2873 through 2875' Processing helix chain 'A' and resid 2912 through 2918 removed outlier: 3.599A pdb=" N MET A2918 " --> pdb=" O ILE A2914 " (cutoff:3.500A) Processing helix chain 'A' and resid 2926 through 2940 Processing helix chain 'A' and resid 2942 through 2953 Processing helix chain 'A' and resid 2964 through 2970 Processing helix chain 'A' and resid 3002 through 3017 Processing helix chain 'A' and resid 3028 through 3040 Processing helix chain 'A' and resid 3042 through 3047 removed outlier: 3.582A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'B' and resid 1413 through 1428 Processing helix chain 'B' and resid 1432 through 1452 removed outlier: 3.604A pdb=" N ASP B1452 " --> pdb=" O LEU B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1477 Processing helix chain 'B' and resid 1485 through 1508 Processing helix chain 'B' and resid 1513 through 1515 No H-bonds generated for 'chain 'B' and resid 1513 through 1515' Processing helix chain 'B' and resid 1517 through 1528 Proline residue: B1526 - end of helix Processing helix chain 'B' and resid 1532 through 1545 Processing helix chain 'B' and resid 1553 through 1560 removed outlier: 4.427A pdb=" N ILE B1557 " --> pdb=" O GLU B1553 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B1558 " --> pdb=" O ASN B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1572 through 1584 Processing helix chain 'B' and resid 1590 through 1601 Processing helix chain 'B' and resid 1607 through 1623 removed outlier: 4.691A pdb=" N GLU B1612 " --> pdb=" O THR B1609 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1634 removed outlier: 3.841A pdb=" N VAL B1629 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1643 through 1658 Processing helix chain 'B' and resid 1664 through 1677 Processing helix chain 'B' and resid 1694 through 1702 Processing helix chain 'B' and resid 1706 through 1723 removed outlier: 4.402A pdb=" N VAL B1723 " --> pdb=" O ASN B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1742 Processing helix chain 'B' and resid 1744 through 1753 Processing helix chain 'B' and resid 1759 through 1763 Processing helix chain 'B' and resid 1792 through 1795 No H-bonds generated for 'chain 'B' and resid 1792 through 1795' Processing helix chain 'B' and resid 1802 through 1815 Processing helix chain 'B' and resid 1822 through 1831 removed outlier: 3.775A pdb=" N LEU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B1827 " --> pdb=" O ILE B1823 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS B1828 " --> pdb=" O LEU B1824 " (cutoff:3.500A) Proline residue: B1829 - end of helix No H-bonds generated for 'chain 'B' and resid 1822 through 1831' Processing helix chain 'B' and resid 1835 through 1851 Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1857 through 1874 Processing helix chain 'B' and resid 1903 through 1918 removed outlier: 3.722A pdb=" N ARG B1907 " --> pdb=" O LYS B1903 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1927 through 1932 removed outlier: 3.956A pdb=" N PHE B1932 " --> pdb=" O PHE B1928 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1947 Processing helix chain 'B' and resid 1951 through 1973 Processing helix chain 'B' and resid 1986 through 1997 Processing helix chain 'B' and resid 2001 through 2012 Processing helix chain 'B' and resid 2016 through 2019 Processing helix chain 'B' and resid 2029 through 2038 Processing helix chain 'B' and resid 2042 through 2051 Processing helix chain 'B' and resid 2057 through 2070 Processing helix chain 'B' and resid 2074 through 2087 Processing helix chain 'B' and resid 2093 through 2105 Processing helix chain 'B' and resid 2124 through 2136 Processing helix chain 'B' and resid 2140 through 2159 Processing helix chain 'B' and resid 2166 through 2190 removed outlier: 3.568A pdb=" N TYR B2170 " --> pdb=" O TYR B2167 " (cutoff:3.500A) Proline residue: B2171 - end of helix removed outlier: 3.610A pdb=" N GLU B2187 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2212 Processing helix chain 'B' and resid 2217 through 2236 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2245 through 2264 Processing helix chain 'B' and resid 2269 through 2281 removed outlier: 3.564A pdb=" N TYR B2281 " --> pdb=" O GLN B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2290 through 2301 Processing helix chain 'B' and resid 2305 through 2322 Processing helix chain 'B' and resid 2328 through 2348 removed outlier: 4.125A pdb=" N LEU B2332 " --> pdb=" O PRO B2328 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B2333 " --> pdb=" O SER B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2359 Processing helix chain 'B' and resid 2361 through 2370 Processing helix chain 'B' and resid 2377 through 2406 Processing helix chain 'B' and resid 2408 through 2421 Processing helix chain 'B' and resid 2437 through 2475 removed outlier: 3.945A pdb=" N GLU B2449 " --> pdb=" O LEU B2445 " (cutoff:3.500A) Processing helix chain 'B' and resid 2481 through 2493 removed outlier: 3.526A pdb=" N LEU B2492 " --> pdb=" O SER B2489 " (cutoff:3.500A) Processing helix chain 'B' and resid 2498 through 2510 removed outlier: 4.468A pdb=" N MET B2509 " --> pdb=" O LYS B2505 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LYS B2510 " --> pdb=" O ARG B2506 " (cutoff:3.500A) Processing helix chain 'B' and resid 2513 through 2516 Processing helix chain 'B' and resid 2520 through 2526 removed outlier: 3.562A pdb=" N ARG B2526 " --> pdb=" O GLN B2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 2537 through 2551 Processing helix chain 'B' and resid 2553 through 2564 removed outlier: 5.668A pdb=" N PHE B2558 " --> pdb=" O HIS B2554 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE B2559 " --> pdb=" O HIS B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2568 through 2572 Processing helix chain 'B' and resid 2593 through 2612 removed outlier: 4.196A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2614 through 2632 Processing helix chain 'B' and resid 2637 through 2640 removed outlier: 4.579A pdb=" N THR B2640 " --> pdb=" O GLN B2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2637 through 2640' Processing helix chain 'B' and resid 2723 through 2740 Processing helix chain 'B' and resid 2743 through 2748 removed outlier: 3.605A pdb=" N ARG B2748 " --> pdb=" O GLU B2744 " (cutoff:3.500A) Processing helix chain 'B' and resid 2776 through 2780 Processing helix chain 'B' and resid 2787 through 2791 Processing helix chain 'B' and resid 2798 through 2810 removed outlier: 4.825A pdb=" N LYS B2810 " --> pdb=" O MET B2806 " (cutoff:3.500A) Processing helix chain 'B' and resid 2813 through 2825 Processing helix chain 'B' and resid 2831 through 2838 removed outlier: 3.906A pdb=" N CYS B2835 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B2837 " --> pdb=" O PHE B2834 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B2838 " --> pdb=" O CYS B2835 " (cutoff:3.500A) Processing helix chain 'B' and resid 2842 through 2866 Processing helix chain 'B' and resid 2873 through 2875 No H-bonds generated for 'chain 'B' and resid 2873 through 2875' Processing helix chain 'B' and resid 2912 through 2918 removed outlier: 3.603A pdb=" N MET B2918 " --> pdb=" O ILE B2914 " (cutoff:3.500A) Processing helix chain 'B' and resid 2926 through 2940 Processing helix chain 'B' and resid 2942 through 2953 Processing helix chain 'B' and resid 2964 through 2970 Processing helix chain 'B' and resid 3002 through 3017 Processing helix chain 'B' and resid 3028 through 3040 Processing helix chain 'B' and resid 3042 through 3046 Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing sheet with id= A, first strand: chain 'A' and resid 2757 through 2759 Processing sheet with id= B, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id= C, first strand: chain 'B' and resid 2757 through 2759 Processing sheet with id= D, first strand: chain 'B' and resid 2773 through 2775 1391 hydrogen bonds defined for protein. 3903 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: 9.76 Time building geometry restraints manager: 10.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8186 1.34 - 1.46: 5057 1.46 - 1.58: 12023 1.58 - 1.69: 10 1.69 - 1.81: 264 Bond restraints: 25540 Sorted by residual: bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O5' ANP A3101 " pdb=" PA ANP A3101 " ideal model delta sigma weight residual 1.655 1.595 0.060 2.00e-02 2.50e+03 9.06e+00 ... (remaining 25535 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.12: 593 107.12 - 113.90: 14648 113.90 - 120.68: 11411 120.68 - 127.47: 7593 127.47 - 134.25: 251 Bond angle restraints: 34496 Sorted by residual: angle pdb=" O1B ANP B3101 " pdb=" PB ANP B3101 " pdb=" O3A ANP B3101 " ideal model delta sigma weight residual 103.40 114.56 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1B ANP A3101 " pdb=" PB ANP A3101 " pdb=" O3A ANP A3101 " ideal model delta sigma weight residual 103.40 114.54 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C ARG B1875 " pdb=" N HIS B1876 " pdb=" CA HIS B1876 " ideal model delta sigma weight residual 121.70 127.72 -6.02 1.80e+00 3.09e-01 1.12e+01 angle pdb=" C ARG A1875 " pdb=" N HIS A1876 " pdb=" CA HIS A1876 " ideal model delta sigma weight residual 121.70 127.67 -5.97 1.80e+00 3.09e-01 1.10e+01 angle pdb=" PA ANP A3101 " pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 125.41 134.25 -8.84 3.00e+00 1.11e-01 8.68e+00 ... (remaining 34491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14119 17.89 - 35.79: 1252 35.79 - 53.68: 163 53.68 - 71.58: 55 71.58 - 89.47: 33 Dihedral angle restraints: 15622 sinusoidal: 6504 harmonic: 9118 Sorted by residual: dihedral pdb=" CA ASP B2841 " pdb=" CB ASP B2841 " pdb=" CG ASP B2841 " pdb=" OD1 ASP B2841 " ideal model delta sinusoidal sigma weight residual -30.00 -87.18 57.18 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP A2841 " pdb=" CB ASP A2841 " pdb=" CG ASP A2841 " pdb=" OD1 ASP A2841 " ideal model delta sinusoidal sigma weight residual -30.00 -87.14 57.14 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG A2263 " pdb=" CD ARG A2263 " pdb=" NE ARG A2263 " pdb=" CZ ARG A2263 " ideal model delta sinusoidal sigma weight residual -180.00 -136.54 -43.46 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 15619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3429 0.055 - 0.110: 455 0.110 - 0.166: 18 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 3904 Sorted by residual: chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE B2055 " pdb=" N ILE B2055 " pdb=" C ILE B2055 " pdb=" CB ILE B2055 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 3901 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A2058 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C SER A2058 " -0.038 2.00e-02 2.50e+03 pdb=" O SER A2058 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A2059 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B2058 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C SER B2058 " 0.037 2.00e-02 2.50e+03 pdb=" O SER B2058 " -0.014 2.00e-02 2.50e+03 pdb=" N THR B2059 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B2504 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C MET B2504 " 0.037 2.00e-02 2.50e+03 pdb=" O MET B2504 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS B2505 " -0.012 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 208 2.66 - 3.22: 23545 3.22 - 3.78: 40176 3.78 - 4.34: 53281 4.34 - 4.90: 87710 Nonbonded interactions: 204920 Sorted by model distance: nonbonded pdb=" O ARG A1875 " pdb=" ND1 HIS A1876 " model vdw 2.094 2.520 nonbonded pdb=" O ARG B1875 " pdb=" ND1 HIS B1876 " model vdw 2.095 2.520 nonbonded pdb=" OD1 ASN A2875 " pdb="MG MG A3102 " model vdw 2.189 2.170 nonbonded pdb=" OD1 ASN B2875 " pdb="MG MG B3102 " model vdw 2.208 2.170 nonbonded pdb=" OH TYR B2969 " pdb=" O2G ANP B3101 " model vdw 2.212 2.440 ... (remaining 204915 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: 4.650 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: 14.730 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 71.940 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.150 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 25540 Z= 0.166 Angle : 0.439 11.158 34496 Z= 0.217 Chirality : 0.035 0.276 3904 Planarity : 0.003 0.045 4362 Dihedral : 13.914 89.471 9698 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.91 (0.15), residues: 3072 helix: 2.59 (0.11), residues: 2176 sheet: 1.45 (0.64), residues: 66 loop : 0.17 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2104 HIS 0.003 0.000 HIS A1951 PHE 0.014 0.001 PHE A2834 TYR 0.013 0.001 TYR B2129 ARG 0.007 0.000 ARG B1875 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1437 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8677 (tpt170) REVERT: A 1444 LEU cc_start: 0.9781 (tt) cc_final: 0.9507 (tm) REVERT: A 1489 ARG cc_start: 0.8895 (mtp180) cc_final: 0.8337 (mtp-110) REVERT: A 1518 HIS cc_start: 0.7455 (m-70) cc_final: 0.7182 (m90) REVERT: A 1559 ILE cc_start: 0.9386 (mt) cc_final: 0.9178 (mp) REVERT: A 1693 ASP cc_start: 0.8866 (m-30) cc_final: 0.8599 (t70) REVERT: A 2028 GLN cc_start: 0.9160 (mm110) cc_final: 0.8551 (mp10) REVERT: A 2030 ILE cc_start: 0.8486 (mp) cc_final: 0.8156 (mm) REVERT: A 2039 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 2139 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 2476 SER cc_start: 0.8200 (m) cc_final: 0.7997 (t) REVERT: A 2668 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8531 (pp20) REVERT: A 2744 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8717 (mm-30) REVERT: A 2900 LEU cc_start: 0.8954 (mt) cc_final: 0.8635 (mt) REVERT: A 2905 THR cc_start: 0.8906 (p) cc_final: 0.8547 (p) REVERT: A 2954 TYR cc_start: 0.8901 (m-80) cc_final: 0.8585 (m-10) REVERT: A 3004 LYS cc_start: 0.9292 (mtpp) cc_final: 0.9014 (pttp) REVERT: A 3008 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8483 (tpt170) REVERT: A 3043 LYS cc_start: 0.8579 (tptt) cc_final: 0.8324 (tptt) REVERT: A 3047 ARG cc_start: 0.8879 (mtt-85) cc_final: 0.8673 (mpp80) REVERT: B 1424 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8975 (mm-30) REVERT: B 1437 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8577 (tpt170) REVERT: B 1444 LEU cc_start: 0.9786 (tt) cc_final: 0.9479 (tm) REVERT: B 1527 LEU cc_start: 0.9455 (mt) cc_final: 0.9183 (mm) REVERT: B 1544 TYR cc_start: 0.9045 (t80) cc_final: 0.8620 (t80) REVERT: B 1581 ILE cc_start: 0.9770 (mt) cc_final: 0.9556 (tp) REVERT: B 1604 ASP cc_start: 0.7771 (t0) cc_final: 0.7530 (t0) REVERT: B 1693 ASP cc_start: 0.8942 (m-30) cc_final: 0.8690 (t70) REVERT: B 2028 GLN cc_start: 0.9134 (mm110) cc_final: 0.8433 (mp10) REVERT: B 2030 ILE cc_start: 0.8518 (mp) cc_final: 0.8209 (mm) REVERT: B 2039 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 2110 ASP cc_start: 0.8965 (m-30) cc_final: 0.8683 (p0) REVERT: B 2139 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 2476 SER cc_start: 0.8410 (m) cc_final: 0.8091 (t) REVERT: B 2744 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 2900 LEU cc_start: 0.8829 (mt) cc_final: 0.8471 (mt) REVERT: B 2954 TYR cc_start: 0.8885 (m-80) cc_final: 0.8572 (m-10) REVERT: B 3004 LYS cc_start: 0.9374 (mtpp) cc_final: 0.8844 (pttp) REVERT: B 3043 LYS cc_start: 0.8450 (tptt) cc_final: 0.8188 (tptt) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 1.6539 time to fit residues: 1053.3901 Evaluate side-chains 299 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1516 HIS A1867 GLN A2106 ASN A2197 GLN A2412 ASN A3014 GLN ** B1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1443 HIS B1516 HIS B1867 GLN B2197 GLN B2210 GLN B3014 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25540 Z= 0.230 Angle : 0.537 10.647 34496 Z= 0.267 Chirality : 0.039 0.320 3904 Planarity : 0.004 0.046 4362 Dihedral : 4.615 87.966 3424 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.33 % Allowed : 10.42 % Favored : 87.25 % 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: 2.96 (0.15), residues: 3072 helix: 2.66 (0.11), residues: 2172 sheet: 0.90 (0.65), residues: 62 loop : 0.17 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1461 HIS 0.005 0.001 HIS A2538 PHE 0.019 0.001 PHE A2571 TYR 0.020 0.001 TYR B1556 ARG 0.012 0.001 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.8731 (tp30) REVERT: A 1434 LYS cc_start: 0.9484 (tppt) cc_final: 0.9195 (tppt) REVERT: A 1437 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8721 (tpt170) REVERT: A 1489 ARG cc_start: 0.8945 (mtp180) cc_final: 0.8498 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9244 (m110) cc_final: 0.8902 (m110) REVERT: A 1693 ASP cc_start: 0.8887 (m-30) cc_final: 0.8648 (t70) REVERT: A 1822 GLU cc_start: 0.9061 (pt0) cc_final: 0.8822 (pm20) REVERT: A 1852 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8348 (pp30) REVERT: A 1967 MET cc_start: 0.8519 (mmm) cc_final: 0.8098 (mmp) REVERT: A 2025 LYS cc_start: 0.8703 (mmpt) cc_final: 0.8438 (mmpt) REVERT: A 2028 GLN cc_start: 0.9170 (mm110) cc_final: 0.8571 (mp10) REVERT: A 2066 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8943 (tm-30) REVERT: A 2139 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8110 (mm-30) REVERT: A 2744 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8833 (mm-30) REVERT: A 2881 GLN cc_start: 0.9053 (mp10) cc_final: 0.8468 (mp10) REVERT: A 2904 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: A 2962 MET cc_start: 0.9053 (tpp) cc_final: 0.8744 (tpp) REVERT: A 3004 LYS cc_start: 0.9356 (mtpp) cc_final: 0.9071 (pttp) REVERT: B 1424 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8906 (pt0) REVERT: B 1437 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8738 (tpt170) REVERT: B 1604 ASP cc_start: 0.7919 (t0) cc_final: 0.7713 (t0) REVERT: B 1636 GLN cc_start: 0.8223 (pp30) cc_final: 0.7972 (pp30) REVERT: B 1693 ASP cc_start: 0.8971 (m-30) cc_final: 0.8768 (t70) REVERT: B 1852 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8249 (pp30) REVERT: B 1988 SER cc_start: 0.9406 (t) cc_final: 0.9193 (p) REVERT: B 2025 LYS cc_start: 0.8736 (mmpt) cc_final: 0.8489 (mmpt) REVERT: B 2026 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: B 2028 GLN cc_start: 0.9160 (mm110) cc_final: 0.8502 (mp10) REVERT: B 2110 ASP cc_start: 0.8943 (m-30) cc_final: 0.8693 (p0) REVERT: B 2139 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8074 (mm-30) REVERT: B 2668 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8500 (pp20) REVERT: B 2744 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8776 (mm-30) REVERT: B 2900 LEU cc_start: 0.8958 (mt) cc_final: 0.8575 (mt) REVERT: B 2904 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8416 (mt-10) outliers start: 65 outliers final: 19 residues processed: 349 average time/residue: 1.5134 time to fit residues: 609.7143 Evaluate side-chains 285 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 261 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1573 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1810 THR Chi-restraints excluded: chain A residue 2066 GLN Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2904 GLU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain B residue 1573 ASP Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1810 THR Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2711 GLU Chi-restraints excluded: chain B residue 2904 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2069 GLN A2241 ASN ** B1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1431 ASN B2241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25540 Z= 0.279 Angle : 0.525 9.589 34496 Z= 0.264 Chirality : 0.040 0.260 3904 Planarity : 0.004 0.048 4362 Dihedral : 4.692 88.710 3424 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.65 % Allowed : 11.28 % Favored : 86.07 % 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: 2.82 (0.15), residues: 3072 helix: 2.54 (0.11), residues: 2164 sheet: 0.85 (0.64), residues: 62 loop : 0.17 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1461 HIS 0.003 0.001 HIS B2111 PHE 0.021 0.001 PHE B1491 TYR 0.023 0.001 TYR A1508 ARG 0.018 0.001 ARG A2642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 282 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8724 (tp30) REVERT: A 1434 LYS cc_start: 0.9521 (tppt) cc_final: 0.9235 (tppt) REVERT: A 1437 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8765 (tpt170) REVERT: A 1449 LEU cc_start: 0.9300 (mp) cc_final: 0.9073 (mp) REVERT: A 1489 ARG cc_start: 0.8958 (mtp-110) cc_final: 0.8483 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9247 (m110) cc_final: 0.8897 (m110) REVERT: A 1655 SER cc_start: 0.9401 (m) cc_final: 0.9048 (p) REVERT: A 1693 ASP cc_start: 0.8920 (m-30) cc_final: 0.8676 (t70) REVERT: A 1822 GLU cc_start: 0.9122 (pt0) cc_final: 0.8893 (pm20) REVERT: A 1991 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8469 (pp20) REVERT: A 2028 GLN cc_start: 0.9139 (mm110) cc_final: 0.8511 (mp10) REVERT: A 2139 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 2157 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 2443 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.7951 (ptm160) REVERT: A 2744 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8895 (mm-30) REVERT: A 2962 MET cc_start: 0.9072 (tpp) cc_final: 0.8818 (tpp) REVERT: A 3004 LYS cc_start: 0.9412 (mtpp) cc_final: 0.9140 (pttp) REVERT: B 1424 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9012 (mm-30) REVERT: B 1434 LYS cc_start: 0.9514 (tppt) cc_final: 0.9268 (tppt) REVERT: B 1437 ARG cc_start: 0.9239 (ttp80) cc_final: 0.8817 (tpt170) REVERT: B 1554 ASN cc_start: 0.9069 (m110) cc_final: 0.8666 (m110) REVERT: B 1636 GLN cc_start: 0.8293 (pp30) cc_final: 0.8053 (pp30) REVERT: B 1693 ASP cc_start: 0.8960 (m-30) cc_final: 0.8754 (t70) REVERT: B 1701 LYS cc_start: 0.9061 (pttp) cc_final: 0.8805 (pptt) REVERT: B 1720 ASN cc_start: 0.9122 (m-40) cc_final: 0.8881 (m-40) REVERT: B 2025 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8380 (mmpt) REVERT: B 2028 GLN cc_start: 0.9144 (mm110) cc_final: 0.8412 (mp10) REVERT: B 2139 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8107 (mm-30) REVERT: B 2157 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: B 2550 MET cc_start: 0.9135 (mmp) cc_final: 0.8913 (mmp) REVERT: B 2668 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8655 (pp20) REVERT: B 2744 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8896 (mm-30) REVERT: B 2904 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8524 (mt-10) outliers start: 74 outliers final: 26 residues processed: 324 average time/residue: 1.5218 time to fit residues: 566.2589 Evaluate side-chains 283 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 252 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1573 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1810 THR Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1991 GLU Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1556 TYR Chi-restraints excluded: chain B residue 1573 ASP Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1810 THR Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2667 MET Chi-restraints excluded: chain B residue 2711 GLU Chi-restraints excluded: chain B residue 2904 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 189 optimal weight: 0.3980 chunk 283 optimal weight: 0.7980 chunk 299 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 268 optimal weight: 0.0020 chunk 80 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B1416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25540 Z= 0.142 Angle : 0.482 11.162 34496 Z= 0.239 Chirality : 0.038 0.358 3904 Planarity : 0.003 0.049 4362 Dihedral : 4.587 85.598 3424 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 12.43 % Favored : 85.53 % 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: 2.80 (0.16), residues: 3072 helix: 2.54 (0.11), residues: 2166 sheet: 0.95 (0.64), residues: 62 loop : 0.10 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1461 HIS 0.004 0.001 HIS B1443 PHE 0.011 0.001 PHE A2571 TYR 0.016 0.001 TYR A1556 ARG 0.009 0.000 ARG B1585 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 279 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8701 (tp30) REVERT: A 1434 LYS cc_start: 0.9516 (tppt) cc_final: 0.9285 (tppt) REVERT: A 1436 HIS cc_start: 0.9391 (t70) cc_final: 0.9033 (t-90) REVERT: A 1437 ARG cc_start: 0.9150 (ttp80) cc_final: 0.8765 (tpt170) REVERT: A 1449 LEU cc_start: 0.9312 (mt) cc_final: 0.9037 (mp) REVERT: A 1489 ARG cc_start: 0.8968 (mtp-110) cc_final: 0.8291 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9286 (m110) cc_final: 0.8949 (m110) REVERT: A 1655 SER cc_start: 0.9406 (m) cc_final: 0.9078 (p) REVERT: A 1693 ASP cc_start: 0.8932 (m-30) cc_final: 0.8713 (t70) REVERT: A 1701 LYS cc_start: 0.8991 (pttp) cc_final: 0.8705 (pptt) REVERT: A 2025 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8316 (mmpt) REVERT: A 2028 GLN cc_start: 0.9135 (mm110) cc_final: 0.8478 (mp10) REVERT: A 2139 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 2157 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: A 2443 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8078 (ptm160) REVERT: A 2744 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8876 (mm-30) REVERT: A 2962 MET cc_start: 0.9081 (tpp) cc_final: 0.8851 (tpp) REVERT: A 3004 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9126 (pttp) REVERT: B 1424 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8966 (mm-30) REVERT: B 1434 LYS cc_start: 0.9529 (tppt) cc_final: 0.9104 (tppp) REVERT: B 1437 ARG cc_start: 0.9209 (ttp80) cc_final: 0.8747 (tpt170) REVERT: B 1554 ASN cc_start: 0.9070 (m110) cc_final: 0.8658 (m110) REVERT: B 1636 GLN cc_start: 0.8355 (pp30) cc_final: 0.8106 (pp30) REVERT: B 1655 SER cc_start: 0.9431 (m) cc_final: 0.9078 (p) REVERT: B 1701 LYS cc_start: 0.9022 (pttp) cc_final: 0.8778 (pptt) REVERT: B 1720 ASN cc_start: 0.9117 (m-40) cc_final: 0.8887 (m-40) REVERT: B 2028 GLN cc_start: 0.9157 (mm110) cc_final: 0.8498 (mp10) REVERT: B 2139 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8098 (mm-30) REVERT: B 2157 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: B 2561 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9314 (mm) REVERT: B 2744 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8848 (mm-30) REVERT: B 2904 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8495 (mt-10) outliers start: 57 outliers final: 20 residues processed: 314 average time/residue: 1.4554 time to fit residues: 527.2844 Evaluate side-chains 279 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 254 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2904 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 123 optimal weight: 0.0060 chunk 255 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN ** B1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25540 Z= 0.206 Angle : 0.506 10.710 34496 Z= 0.249 Chirality : 0.039 0.318 3904 Planarity : 0.003 0.049 4362 Dihedral : 4.568 82.589 3424 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.11 % Allowed : 13.22 % Favored : 84.67 % 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: 2.83 (0.16), residues: 3072 helix: 2.56 (0.11), residues: 2164 sheet: 1.02 (0.65), residues: 62 loop : 0.14 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1461 HIS 0.003 0.001 HIS B2538 PHE 0.015 0.001 PHE A2143 TYR 0.011 0.001 TYR B1696 ARG 0.010 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 267 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8711 (tp30) REVERT: A 1434 LYS cc_start: 0.9562 (tppt) cc_final: 0.9171 (tppp) REVERT: A 1436 HIS cc_start: 0.9409 (t70) cc_final: 0.9048 (t-90) REVERT: A 1437 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8723 (tpt170) REVERT: A 1449 LEU cc_start: 0.9355 (mt) cc_final: 0.9057 (mp) REVERT: A 1489 ARG cc_start: 0.8971 (mtp-110) cc_final: 0.8280 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9295 (m110) cc_final: 0.8949 (m110) REVERT: A 1655 SER cc_start: 0.9416 (m) cc_final: 0.9080 (p) REVERT: A 1693 ASP cc_start: 0.8932 (m-30) cc_final: 0.8731 (t70) REVERT: A 1967 MET cc_start: 0.8477 (mmm) cc_final: 0.8083 (mmp) REVERT: A 2025 LYS cc_start: 0.8730 (mmpt) cc_final: 0.8524 (mmpt) REVERT: A 2028 GLN cc_start: 0.9148 (mm110) cc_final: 0.8522 (mp10) REVERT: A 2107 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8621 (mtm) REVERT: A 2139 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 2157 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: A 2193 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8932 (p) REVERT: A 2200 GLU cc_start: 0.9013 (pt0) cc_final: 0.8717 (pp20) REVERT: A 2443 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8102 (ptm160) REVERT: A 3004 LYS cc_start: 0.9432 (mtpp) cc_final: 0.9134 (pttp) REVERT: B 1424 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8879 (pt0) REVERT: B 1434 LYS cc_start: 0.9577 (tppt) cc_final: 0.9159 (tppp) REVERT: B 1437 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8801 (tpt170) REVERT: B 1527 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9058 (mm) REVERT: B 1530 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 1554 ASN cc_start: 0.9156 (m110) cc_final: 0.8754 (m110) REVERT: B 1636 GLN cc_start: 0.8386 (pp30) cc_final: 0.8177 (pp30) REVERT: B 1655 SER cc_start: 0.9441 (m) cc_final: 0.9093 (p) REVERT: B 1701 LYS cc_start: 0.9062 (pttp) cc_final: 0.8809 (pptt) REVERT: B 1720 ASN cc_start: 0.9117 (m-40) cc_final: 0.8867 (m-40) REVERT: B 2007 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 2025 LYS cc_start: 0.8830 (mmpt) cc_final: 0.8551 (mmpt) REVERT: B 2028 GLN cc_start: 0.9150 (mm110) cc_final: 0.8504 (mp10) REVERT: B 2139 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8146 (mm-30) REVERT: B 2157 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 2443 ARG cc_start: 0.8528 (ptm160) cc_final: 0.8082 (ppp80) REVERT: B 2504 MET cc_start: 0.9145 (tpt) cc_final: 0.8839 (tpt) REVERT: B 2561 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9253 (mm) outliers start: 59 outliers final: 23 residues processed: 302 average time/residue: 1.4839 time to fit residues: 517.9222 Evaluate side-chains 280 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 249 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1527 LEU Chi-restraints excluded: chain B residue 1530 GLU Chi-restraints excluded: chain B residue 1573 ASP Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1810 THR Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2806 MET Chi-restraints excluded: chain B residue 2965 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 299 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 138 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B1416 GLN ** B1852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25540 Z= 0.151 Angle : 0.504 12.257 34496 Z= 0.245 Chirality : 0.038 0.321 3904 Planarity : 0.003 0.052 4362 Dihedral : 4.528 83.367 3424 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 14.26 % Favored : 83.95 % 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: 2.83 (0.16), residues: 3072 helix: 2.57 (0.11), residues: 2160 sheet: 1.05 (0.65), residues: 62 loop : 0.10 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1461 HIS 0.004 0.001 HIS B1443 PHE 0.011 0.001 PHE A2143 TYR 0.028 0.001 TYR B1696 ARG 0.011 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.9073 (pt0) REVERT: A 1434 LYS cc_start: 0.9563 (tppt) cc_final: 0.9162 (tppp) REVERT: A 1436 HIS cc_start: 0.9406 (t70) cc_final: 0.9073 (t-90) REVERT: A 1437 ARG cc_start: 0.9188 (ttp80) cc_final: 0.8712 (tpt170) REVERT: A 1449 LEU cc_start: 0.9389 (mt) cc_final: 0.9069 (mp) REVERT: A 1489 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8285 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9323 (m110) cc_final: 0.8992 (m110) REVERT: A 1655 SER cc_start: 0.9422 (m) cc_final: 0.9114 (p) REVERT: A 2028 GLN cc_start: 0.9150 (mm110) cc_final: 0.8532 (mp10) REVERT: A 2139 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 2157 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: A 2443 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.8149 (ptm160) REVERT: A 3004 LYS cc_start: 0.9430 (mtpp) cc_final: 0.9131 (pttp) REVERT: B 1424 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8884 (pt0) REVERT: B 1434 LYS cc_start: 0.9585 (tppt) cc_final: 0.9161 (tppp) REVERT: B 1437 ARG cc_start: 0.9254 (ttp80) cc_final: 0.8813 (tpt170) REVERT: B 1554 ASN cc_start: 0.9161 (m110) cc_final: 0.8761 (m110) REVERT: B 1636 GLN cc_start: 0.8363 (pp30) cc_final: 0.8144 (pp30) REVERT: B 1655 SER cc_start: 0.9441 (m) cc_final: 0.9112 (p) REVERT: B 1701 LYS cc_start: 0.9089 (pttp) cc_final: 0.8838 (pptt) REVERT: B 1720 ASN cc_start: 0.9111 (m-40) cc_final: 0.8886 (m-40) REVERT: B 2025 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8573 (mmpt) REVERT: B 2028 GLN cc_start: 0.9151 (mm110) cc_final: 0.8499 (mp10) REVERT: B 2139 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 2157 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 2443 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8106 (ppp80) REVERT: B 2504 MET cc_start: 0.9148 (tpt) cc_final: 0.8846 (tpt) REVERT: B 2561 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9206 (mm) outliers start: 50 outliers final: 19 residues processed: 293 average time/residue: 1.4796 time to fit residues: 499.8528 Evaluate side-chains 273 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 250 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2482 MET Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1556 TYR Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2806 MET Chi-restraints excluded: chain B residue 2965 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 219 optimal weight: 0.1980 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN ** B1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25540 Z= 0.156 Angle : 0.520 14.906 34496 Z= 0.251 Chirality : 0.038 0.370 3904 Planarity : 0.003 0.050 4362 Dihedral : 4.505 85.459 3424 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.76 % Allowed : 14.79 % Favored : 83.45 % 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: 2.82 (0.16), residues: 3072 helix: 2.56 (0.11), residues: 2160 sheet: 0.99 (0.65), residues: 62 loop : 0.12 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1461 HIS 0.003 0.001 HIS A1443 PHE 0.013 0.001 PHE A1491 TYR 0.024 0.001 TYR B1696 ARG 0.008 0.000 ARG B2642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 261 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9077 (pt0) REVERT: A 1434 LYS cc_start: 0.9571 (tppt) cc_final: 0.9166 (tppp) REVERT: A 1436 HIS cc_start: 0.9380 (t70) cc_final: 0.9010 (t-90) REVERT: A 1437 ARG cc_start: 0.9215 (ttp80) cc_final: 0.8759 (tpt170) REVERT: A 1489 ARG cc_start: 0.8955 (mtp-110) cc_final: 0.8270 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9322 (m110) cc_final: 0.8988 (m110) REVERT: A 1655 SER cc_start: 0.9417 (m) cc_final: 0.9102 (p) REVERT: A 1967 MET cc_start: 0.8464 (mmm) cc_final: 0.8074 (mmp) REVERT: A 2028 GLN cc_start: 0.9135 (mm110) cc_final: 0.8475 (mp10) REVERT: A 2139 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 2157 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: A 2200 GLU cc_start: 0.8981 (pt0) cc_final: 0.8668 (pp20) REVERT: A 2443 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8171 (ptm160) REVERT: A 3004 LYS cc_start: 0.9432 (mtpp) cc_final: 0.9132 (pttp) REVERT: B 1424 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8896 (pt0) REVERT: B 1434 LYS cc_start: 0.9591 (tppt) cc_final: 0.9163 (tppp) REVERT: B 1437 ARG cc_start: 0.9280 (ttp80) cc_final: 0.8832 (tpt170) REVERT: B 1554 ASN cc_start: 0.9207 (m110) cc_final: 0.8814 (m110) REVERT: B 1636 GLN cc_start: 0.8352 (pp30) cc_final: 0.8144 (pp30) REVERT: B 1655 SER cc_start: 0.9442 (m) cc_final: 0.9118 (p) REVERT: B 1701 LYS cc_start: 0.9094 (pttp) cc_final: 0.8865 (pptt) REVERT: B 1720 ASN cc_start: 0.9116 (m-40) cc_final: 0.8896 (m-40) REVERT: B 2028 GLN cc_start: 0.9147 (mm110) cc_final: 0.8499 (mp10) REVERT: B 2139 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8089 (mm-30) REVERT: B 2157 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 2479 GLU cc_start: 0.8878 (tp30) cc_final: 0.8223 (tp30) REVERT: B 2532 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: B 2561 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9192 (mm) outliers start: 49 outliers final: 20 residues processed: 288 average time/residue: 1.4119 time to fit residues: 471.3206 Evaluate side-chains 278 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1556 TYR Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2806 MET Chi-restraints excluded: chain B residue 2965 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 178 optimal weight: 0.7980 chunk 90 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN B1416 GLN ** B1852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25540 Z= 0.191 Angle : 0.550 16.723 34496 Z= 0.263 Chirality : 0.039 0.410 3904 Planarity : 0.003 0.050 4362 Dihedral : 4.514 87.106 3424 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.58 % Allowed : 15.19 % Favored : 83.24 % 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: 2.81 (0.16), residues: 3072 helix: 2.54 (0.11), residues: 2168 sheet: 1.04 (0.65), residues: 62 loop : 0.12 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1461 HIS 0.005 0.001 HIS A1443 PHE 0.013 0.001 PHE A2143 TYR 0.022 0.001 TYR B1696 ARG 0.012 0.000 ARG B3008 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 261 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.9111 (pt0) REVERT: A 1434 LYS cc_start: 0.9577 (tppt) cc_final: 0.9170 (tppp) REVERT: A 1436 HIS cc_start: 0.9391 (t70) cc_final: 0.9037 (t-90) REVERT: A 1437 ARG cc_start: 0.9254 (ttp80) cc_final: 0.8800 (tpt170) REVERT: A 1489 ARG cc_start: 0.8965 (mtp-110) cc_final: 0.8305 (mtp-110) REVERT: A 1491 PHE cc_start: 0.9176 (t80) cc_final: 0.8900 (t80) REVERT: A 1554 ASN cc_start: 0.9331 (m110) cc_final: 0.8999 (m110) REVERT: A 1655 SER cc_start: 0.9421 (m) cc_final: 0.9100 (p) REVERT: A 1967 MET cc_start: 0.8464 (mmm) cc_final: 0.8078 (mmp) REVERT: A 2028 GLN cc_start: 0.9137 (mm110) cc_final: 0.8488 (mp10) REVERT: A 2139 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 2157 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: A 2200 GLU cc_start: 0.9003 (pt0) cc_final: 0.8673 (pp20) REVERT: A 2443 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8210 (ptm160) REVERT: A 2532 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7186 (mmm) REVERT: A 3004 LYS cc_start: 0.9440 (mtpp) cc_final: 0.9135 (pttp) REVERT: B 1424 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8931 (pt0) REVERT: B 1434 LYS cc_start: 0.9601 (tppt) cc_final: 0.9172 (tppp) REVERT: B 1437 ARG cc_start: 0.9304 (ttp80) cc_final: 0.8856 (tpt170) REVERT: B 1554 ASN cc_start: 0.9210 (m110) cc_final: 0.8817 (m110) REVERT: B 1655 SER cc_start: 0.9442 (m) cc_final: 0.9112 (p) REVERT: B 1701 LYS cc_start: 0.9091 (pttp) cc_final: 0.8860 (pptt) REVERT: B 1720 ASN cc_start: 0.9121 (m-40) cc_final: 0.8901 (m-40) REVERT: B 2028 GLN cc_start: 0.9125 (mm110) cc_final: 0.8435 (mp10) REVERT: B 2139 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 2157 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: B 2443 ARG cc_start: 0.8614 (ptm160) cc_final: 0.8189 (ppp80) REVERT: B 2479 GLU cc_start: 0.8887 (tp30) cc_final: 0.8156 (tp30) REVERT: B 2532 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7640 (mmm) REVERT: B 2561 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9193 (mm) outliers start: 44 outliers final: 20 residues processed: 286 average time/residue: 1.4464 time to fit residues: 478.5623 Evaluate side-chains 273 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2452 LEU Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2806 MET Chi-restraints excluded: chain B residue 2965 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 8.9990 chunk 286 optimal weight: 0.0980 chunk 261 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 263 optimal weight: 0.0270 chunk 277 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN ** B1852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25540 Z= 0.156 Angle : 0.547 14.619 34496 Z= 0.262 Chirality : 0.038 0.374 3904 Planarity : 0.003 0.050 4362 Dihedral : 4.513 88.718 3424 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.54 % Allowed : 15.44 % Favored : 83.02 % 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: 2.82 (0.16), residues: 3072 helix: 2.56 (0.11), residues: 2164 sheet: 1.08 (0.65), residues: 62 loop : 0.12 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1461 HIS 0.003 0.001 HIS A1443 PHE 0.013 0.001 PHE B1491 TYR 0.021 0.001 TYR B1696 ARG 0.009 0.000 ARG B1575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 259 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.9103 (pt0) REVERT: A 1434 LYS cc_start: 0.9576 (tppt) cc_final: 0.9172 (tppp) REVERT: A 1436 HIS cc_start: 0.9376 (t70) cc_final: 0.9065 (t-90) REVERT: A 1437 ARG cc_start: 0.9246 (ttp80) cc_final: 0.8789 (tpt170) REVERT: A 1489 ARG cc_start: 0.8958 (mtp-110) cc_final: 0.8322 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9329 (m110) cc_final: 0.9002 (m110) REVERT: A 1655 SER cc_start: 0.9417 (m) cc_final: 0.9105 (p) REVERT: A 2028 GLN cc_start: 0.9137 (mm110) cc_final: 0.8452 (mp10) REVERT: A 2139 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 2157 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: A 2200 GLU cc_start: 0.8996 (pt0) cc_final: 0.8668 (pp20) REVERT: A 2443 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.8233 (ptm160) REVERT: A 2532 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7233 (mmm) REVERT: A 3004 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9129 (pttp) REVERT: B 1424 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8887 (pt0) REVERT: B 1434 LYS cc_start: 0.9599 (tppt) cc_final: 0.9173 (tppp) REVERT: B 1437 ARG cc_start: 0.9314 (ttp80) cc_final: 0.8855 (tpt170) REVERT: B 1554 ASN cc_start: 0.9176 (m110) cc_final: 0.8801 (m110) REVERT: B 1655 SER cc_start: 0.9430 (m) cc_final: 0.9109 (p) REVERT: B 1701 LYS cc_start: 0.9099 (pttp) cc_final: 0.8875 (pptt) REVERT: B 1720 ASN cc_start: 0.9110 (m-40) cc_final: 0.8890 (m-40) REVERT: B 2028 GLN cc_start: 0.9129 (mm110) cc_final: 0.8424 (mp10) REVERT: B 2139 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 2157 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: B 2479 GLU cc_start: 0.8883 (tp30) cc_final: 0.8157 (tp30) REVERT: B 2532 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7670 (mmm) REVERT: B 2561 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9172 (mm) outliers start: 43 outliers final: 18 residues processed: 283 average time/residue: 1.4559 time to fit residues: 478.0317 Evaluate side-chains 275 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2163 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2962 MET Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2806 MET Chi-restraints excluded: chain B residue 2962 MET Chi-restraints excluded: chain B residue 2965 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN A2241 ASN ** B1852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25540 Z= 0.193 Angle : 0.571 17.308 34496 Z= 0.273 Chirality : 0.039 0.383 3904 Planarity : 0.003 0.050 4362 Dihedral : 4.551 89.813 3424 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.33 % Allowed : 15.87 % Favored : 82.81 % 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: 2.81 (0.16), residues: 3072 helix: 2.54 (0.11), residues: 2166 sheet: 1.06 (0.65), residues: 62 loop : 0.13 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1461 HIS 0.005 0.001 HIS A1876 PHE 0.013 0.001 PHE A2143 TYR 0.022 0.001 TYR A1556 ARG 0.013 0.000 ARG B3008 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1424 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9120 (pt0) REVERT: A 1434 LYS cc_start: 0.9577 (tppt) cc_final: 0.9168 (tppp) REVERT: A 1436 HIS cc_start: 0.9341 (t70) cc_final: 0.8976 (t-90) REVERT: A 1437 ARG cc_start: 0.9268 (ttp80) cc_final: 0.8831 (tpt170) REVERT: A 1489 ARG cc_start: 0.8945 (mtp-110) cc_final: 0.8304 (mtp-110) REVERT: A 1554 ASN cc_start: 0.9319 (m110) cc_final: 0.8994 (m110) REVERT: A 1655 SER cc_start: 0.9418 (m) cc_final: 0.9098 (p) REVERT: A 1967 MET cc_start: 0.8469 (mmm) cc_final: 0.8100 (mmp) REVERT: A 2007 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 2025 LYS cc_start: 0.8692 (mmpt) cc_final: 0.8416 (mmpt) REVERT: A 2028 GLN cc_start: 0.9130 (mm110) cc_final: 0.8471 (mp10) REVERT: A 2139 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 2157 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: A 2200 GLU cc_start: 0.8997 (pt0) cc_final: 0.8681 (pp20) REVERT: A 2443 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8265 (ptm160) REVERT: A 2532 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7691 (mmm) REVERT: A 3004 LYS cc_start: 0.9447 (mtpp) cc_final: 0.9139 (pttp) REVERT: B 1424 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8904 (pt0) REVERT: B 1434 LYS cc_start: 0.9605 (tppt) cc_final: 0.9203 (tppp) REVERT: B 1437 ARG cc_start: 0.9305 (ttp80) cc_final: 0.8838 (tpt170) REVERT: B 1554 ASN cc_start: 0.9199 (m110) cc_final: 0.8818 (m110) REVERT: B 1655 SER cc_start: 0.9432 (m) cc_final: 0.9102 (p) REVERT: B 1701 LYS cc_start: 0.9111 (pttp) cc_final: 0.8876 (pptt) REVERT: B 1720 ASN cc_start: 0.9122 (m-40) cc_final: 0.8903 (m-40) REVERT: B 2025 LYS cc_start: 0.8701 (mmpt) cc_final: 0.8459 (mmpt) REVERT: B 2028 GLN cc_start: 0.9116 (mm110) cc_final: 0.8428 (mp10) REVERT: B 2139 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 2157 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: B 2479 GLU cc_start: 0.8891 (tp30) cc_final: 0.8166 (tp30) REVERT: B 2532 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: B 2561 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9165 (mm) outliers start: 37 outliers final: 22 residues processed: 275 average time/residue: 1.4823 time to fit residues: 475.7630 Evaluate side-chains 269 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 GLU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2310 SER Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2962 MET Chi-restraints excluded: chain A residue 2965 LEU Chi-restraints excluded: chain A residue 2970 LEU Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2157 GLU Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2310 SER Chi-restraints excluded: chain B residue 2332 LEU Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2806 MET Chi-restraints excluded: chain B residue 2962 MET Chi-restraints excluded: chain B residue 2965 LEU Chi-restraints excluded: chain B residue 2970 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 4.9990 chunk 261 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2066 GLN A2241 ASN A2269 GLN A2412 ASN ** B1852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2066 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058461 restraints weight = 51958.706| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.15 r_work: 0.2660 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25540 Z= 0.290 Angle : 0.594 14.922 34496 Z= 0.285 Chirality : 0.041 0.375 3904 Planarity : 0.003 0.050 4362 Dihedral : 4.592 89.343 3424 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.43 % Allowed : 16.15 % Favored : 82.41 % 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: 2.78 (0.16), residues: 3072 helix: 2.52 (0.11), residues: 2154 sheet: 0.89 (0.61), residues: 66 loop : 0.16 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A1461 HIS 0.005 0.001 HIS A1443 PHE 0.016 0.001 PHE A2143 TYR 0.020 0.001 TYR B1696 ARG 0.009 0.000 ARG B1575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9654.04 seconds wall clock time: 174 minutes 10.81 seconds (10450.81 seconds total)