Starting phenix.real_space_refine on Sun Jun 15 23:52:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dke_46954/06_2025/9dke_46954.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dke_46954/06_2025/9dke_46954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dke_46954/06_2025/9dke_46954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dke_46954/06_2025/9dke_46954.map" model { file = "/net/cci-nas-00/data/ceres_data/9dke_46954/06_2025/9dke_46954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dke_46954/06_2025/9dke_46954.cif" } resolution = 3.6 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 11182 2.51 5 N 2908 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17457 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2291, 17344 Classifications: {'peptide': 2291} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 63, 'TRANS': 2227} Unresolved chain links: 1 Chain breaks: 29 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1252 Unresolved non-hydrogen angles: 1546 Unresolved non-hydrogen dihedrals: 1028 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 23, 'TRP:plan': 2, 'ASP:plan': 32, 'PHE:plan': 13, 'GLU:plan': 50, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 680 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 10.36, per 1000 atoms: 0.59 Number of scatterers: 17457 At special positions: 0 Unit cell: (97.79, 163.576, 150.241, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 9 15.00 Mg 1 11.99 O 3288 8.00 N 2908 7.00 C 11182 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 2.1 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4382 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 19 sheets defined 64.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 1444 through 1461 Processing helix chain 'A' and resid 1471 through 1489 Processing helix chain 'A' and resid 1506 through 1529 removed outlier: 4.045A pdb=" N GLU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A1529 " --> pdb=" O THR A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1540 Processing helix chain 'A' and resid 1541 through 1550 Processing helix chain 'A' and resid 1561 through 1566 removed outlier: 3.600A pdb=" N MET A1565 " --> pdb=" O PHE A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.687A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 4.512A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 4.130A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1742 through 1746 removed outlier: 3.746A pdb=" N ASN A1745 " --> pdb=" O ASP A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.217A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 removed outlier: 3.728A pdb=" N LEU A1813 " --> pdb=" O PHE A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.693A pdb=" N LEU A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1853 Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 Processing helix chain 'A' and resid 1941 through 1960 removed outlier: 3.645A pdb=" N LEU A1945 " --> pdb=" O ASP A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1988 removed outlier: 3.749A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.878A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2007 through 2022 Processing helix chain 'A' and resid 2032 through 2046 Processing helix chain 'A' and resid 2051 through 2067 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2143 through 2146 removed outlier: 3.839A pdb=" N LYS A2146 " --> pdb=" O GLY A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2143 through 2146' Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2210 Processing helix chain 'A' and resid 2221 through 2236 removed outlier: 3.534A pdb=" N ILE A2226 " --> pdb=" O ILE A2222 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A2227 " --> pdb=" O SER A2223 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A2228 " --> pdb=" O SER A2224 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A2229 " --> pdb=" O LYS A2225 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A2230 " --> pdb=" O ILE A2226 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2257 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 3.631A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A2270 " --> pdb=" O PHE A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 removed outlier: 3.585A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2345 Processing helix chain 'A' and resid 2372 through 2375 Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.693A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2409 Processing helix chain 'A' and resid 2423 through 2434 Processing helix chain 'A' and resid 2454 through 2459 Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.565A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2581 through 2587 removed outlier: 6.493A pdb=" N GLU A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.538A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2619 through 2635 removed outlier: 3.505A pdb=" N THR A2623 " --> pdb=" O PRO A2619 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2658 through 2660 No H-bonds generated for 'chain 'A' and resid 2658 through 2660' Processing helix chain 'A' and resid 2665 through 2681 Processing helix chain 'A' and resid 2708 through 2727 removed outlier: 3.578A pdb=" N LEU A2712 " --> pdb=" O ASN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2778 Processing helix chain 'A' and resid 2793 through 2809 removed outlier: 3.551A pdb=" N LYS A2809 " --> pdb=" O ASP A2805 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.644A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN A2837 " --> pdb=" O THR A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2848 through 2863 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2912 removed outlier: 3.623A pdb=" N ASN A2910 " --> pdb=" O PRO A2906 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG A2911 " --> pdb=" O ALA A2907 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS A2912 " --> pdb=" O LEU A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2949 through 2953 removed outlier: 3.666A pdb=" N VAL A2953 " --> pdb=" O LYS A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.829A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 Processing helix chain 'A' and resid 3290 through 3334 removed outlier: 4.466A pdb=" N ILE A3321 " --> pdb=" O SER A3317 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY A3322 " --> pdb=" O GLN A3318 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A3334 " --> pdb=" O TYR A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3399 removed outlier: 3.694A pdb=" N LEU A3391 " --> pdb=" O ASN A3387 " (cutoff:3.500A) Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 4.273A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.820A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3508 through 3512 Processing helix chain 'A' and resid 3521 through 3538 removed outlier: 3.589A pdb=" N ASN A3538 " --> pdb=" O LEU A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3571 removed outlier: 3.839A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3639 Proline residue: A3609 - end of helix removed outlier: 4.683A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 4.264A pdb=" N GLY A3643 " --> pdb=" O TRP A3640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3646 through 3659 removed outlier: 4.062A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A3659 " --> pdb=" O ARG A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3687 removed outlier: 3.705A pdb=" N GLU A3673 " --> pdb=" O THR A3669 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 3.856A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.630A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3743 through 3753 Processing helix chain 'A' and resid 3755 through 3767 Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3835 Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3853 Processing helix chain 'A' and resid 3853 through 3860 Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3902 through 3913 removed outlier: 3.525A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3943 removed outlier: 3.518A pdb=" N ARG A3942 " --> pdb=" O LEU A3938 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A3943 " --> pdb=" O ILE A3939 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.543A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 removed outlier: 3.533A pdb=" N VAL A3985 " --> pdb=" O PRO A3981 " (cutoff:3.500A) Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4090 Processing sheet with id=AA1, first strand: chain 'A' and resid 1386 through 1387 removed outlier: 4.092A pdb=" N GLU A1386 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A1398 " --> pdb=" O GLU A1386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1569 through 1574 Processing sheet with id=AA3, first strand: chain 'A' and resid 1733 through 1734 Processing sheet with id=AA4, first strand: chain 'A' and resid 1895 through 1897 Processing sheet with id=AA5, first strand: chain 'A' and resid 1820 through 1821 removed outlier: 6.572A pdb=" N PHE A1820 " --> pdb=" O ASP A1848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA7, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 3.703A pdb=" N ARG A2149 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A2100 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A2152 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2118 through 2119 removed outlier: 3.616A pdb=" N LEU A2119 " --> pdb=" O GLU A2124 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A2124 " --> pdb=" O LEU A2119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 2175 through 2177 removed outlier: 3.612A pdb=" N LEU A2184 " --> pdb=" O LEU A2176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2357 through 2360 removed outlier: 3.551A pdb=" N THR A2358 " --> pdb=" O SER A2369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A2369 " --> pdb=" O THR A2358 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A2360 " --> pdb=" O SER A2367 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER A2367 " --> pdb=" O VAL A2360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 2438 through 2440 removed outlier: 3.864A pdb=" N VAL A2483 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A2534 " --> pdb=" O CYS A2486 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2462 through 2463 Processing sheet with id=AB4, first strand: chain 'A' and resid 2514 through 2517 removed outlier: 3.663A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.540A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.161A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N CYS A2892 " --> pdb=" O ILE A2817 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A2760 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.371A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3479 through 3481 removed outlier: 3.873A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3813 through 3815 removed outlier: 3.765A pdb=" N GLN A3842 " --> pdb=" O ILE A3814 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4020 through 4024 removed outlier: 3.906A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A4027 " --> pdb=" O ILE A4023 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3195 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: 9.01 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4366 1.33 - 1.45: 3353 1.45 - 1.57: 9945 1.57 - 1.69: 14 1.69 - 1.81: 107 Bond restraints: 17785 Sorted by residual: bond pdb=" C VAL A3946 " pdb=" N PRO A3947 " ideal model delta sigma weight residual 1.336 1.355 -0.019 9.80e-03 1.04e+04 3.64e+00 bond pdb=" C PHE A1534 " pdb=" N PRO A1535 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.80e+00 bond pdb=" CG LYS A2721 " pdb=" CD LYS A2721 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C GLY A1791 " pdb=" N GLY A1792 " ideal model delta sigma weight residual 1.331 1.322 0.009 6.60e-03 2.30e+04 1.72e+00 bond pdb=" C VAL A4024 " pdb=" N PRO A4025 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.08e-02 8.57e+03 1.50e+00 ... (remaining 17780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 23588 1.93 - 3.85: 463 3.85 - 5.78: 81 5.78 - 7.71: 29 7.71 - 9.64: 9 Bond angle restraints: 24170 Sorted by residual: angle pdb=" C LEU A3945 " pdb=" N VAL A3946 " pdb=" CA VAL A3946 " ideal model delta sigma weight residual 120.33 123.83 -3.50 8.00e-01 1.56e+00 1.91e+01 angle pdb=" N GLN A2927 " pdb=" CA GLN A2927 " pdb=" CB GLN A2927 " ideal model delta sigma weight residual 110.28 116.77 -6.49 1.55e+00 4.16e-01 1.75e+01 angle pdb=" CA ARG A3670 " pdb=" CB ARG A3670 " pdb=" CG ARG A3670 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" C LEU A2237 " pdb=" N ASP A2238 " pdb=" CA ASP A2238 " ideal model delta sigma weight residual 121.70 127.99 -6.29 1.80e+00 3.09e-01 1.22e+01 angle pdb=" CA GLN A2513 " pdb=" CB GLN A2513 " pdb=" CG GLN A2513 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 ... (remaining 24165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 10053 25.17 - 50.34: 456 50.34 - 75.51: 52 75.51 - 100.67: 6 100.67 - 125.84: 1 Dihedral angle restraints: 10568 sinusoidal: 3858 harmonic: 6710 Sorted by residual: dihedral pdb=" O1B ADP A4102 " pdb=" O3A ADP A4102 " pdb=" PB ADP A4102 " pdb=" PA ADP A4102 " ideal model delta sinusoidal sigma weight residual -60.00 65.84 -125.84 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" C2' ADP A4104 " pdb=" C1' ADP A4104 " pdb=" N9 ADP A4104 " pdb=" C4 ADP A4104 " ideal model delta sinusoidal sigma weight residual 91.55 -171.54 -96.91 1 2.00e+01 2.50e-03 2.69e+01 dihedral pdb=" CA HIS A2755 " pdb=" C HIS A2755 " pdb=" N MET A2756 " pdb=" CA MET A2756 " ideal model delta harmonic sigma weight residual 180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 10565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2210 0.049 - 0.097: 501 0.097 - 0.146: 130 0.146 - 0.195: 4 0.195 - 0.244: 1 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB ILE A3814 " pdb=" CA ILE A3814 " pdb=" CG1 ILE A3814 " pdb=" CG2 ILE A3814 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ASN A3978 " pdb=" N ASN A3978 " pdb=" C ASN A3978 " pdb=" CB ASN A3978 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CB ILE A2913 " pdb=" CA ILE A2913 " pdb=" CG1 ILE A2913 " pdb=" CG2 ILE A2913 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 2843 not shown) Planarity restraints: 3036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2988 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A2989 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A2989 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A2989 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A3508 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C PHE A3508 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A3508 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A3509 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A2619 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " -0.031 5.00e-02 4.00e+02 ... (remaining 3033 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 403 2.70 - 3.25: 17401 3.25 - 3.80: 28792 3.80 - 4.35: 34180 4.35 - 4.90: 57453 Nonbonded interactions: 138229 Sorted by model distance: nonbonded pdb=" O2B ADP A4103 " pdb="MG MG A4105 " model vdw 2.155 2.170 nonbonded pdb=" OD2 ASP A2973 " pdb=" OH TYR A3333 " model vdw 2.237 3.040 nonbonded pdb=" O PHE A1478 " pdb=" OG1 THR A1482 " model vdw 2.258 3.040 nonbonded pdb=" ND1 HIS A2274 " pdb=" OD1 ASP A2329 " model vdw 2.259 3.120 nonbonded pdb=" O SER A3755 " pdb=" OG SER A3758 " model vdw 2.263 3.040 ... (remaining 138224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.100 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 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 0.040 17786 Z= 0.153 Angle : 0.715 9.637 24170 Z= 0.383 Chirality : 0.044 0.244 2846 Planarity : 0.005 0.075 3036 Dihedral : 14.217 125.843 6186 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2228 helix: 1.01 (0.14), residues: 1345 sheet: 0.21 (0.39), residues: 169 loop : -0.98 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.009 0.001 HIS A2735 PHE 0.037 0.002 PHE A2972 TYR 0.035 0.002 TYR A2234 ARG 0.010 0.001 ARG A3944 Details of bonding type rmsd hydrogen bonds : bond 0.14204 ( 1085) hydrogen bonds : angle 5.52765 ( 3195) covalent geometry : bond 0.00305 (17785) covalent geometry : angle 0.71497 (24170) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1396 LEU cc_start: 0.6672 (pp) cc_final: 0.6050 (mp) REVERT: A 1400 TRP cc_start: 0.3060 (p-90) cc_final: 0.1996 (t60) REVERT: A 1828 TYR cc_start: 0.6827 (t80) cc_final: 0.6393 (t80) REVERT: A 1913 LYS cc_start: 0.6437 (ttpp) cc_final: 0.6150 (tptp) REVERT: A 1918 GLU cc_start: 0.7488 (mp0) cc_final: 0.7108 (mm-30) REVERT: A 2107 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8170 (mmmm) REVERT: A 2546 MET cc_start: 0.5969 (mtt) cc_final: 0.5715 (mtt) REVERT: A 2746 ASP cc_start: 0.8053 (t0) cc_final: 0.7499 (t0) REVERT: A 2756 MET cc_start: 0.6795 (ttp) cc_final: 0.6329 (ptp) REVERT: A 2762 SER cc_start: 0.8683 (t) cc_final: 0.8453 (m) REVERT: A 3487 ASP cc_start: 0.5004 (t0) cc_final: 0.4396 (t0) REVERT: A 3767 PHE cc_start: 0.5592 (t80) cc_final: 0.5230 (t80) REVERT: A 3888 LEU cc_start: 0.7006 (mp) cc_final: 0.6286 (pp) REVERT: A 4009 LYS cc_start: 0.7685 (tttt) cc_final: 0.6834 (ttmm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2641 time to fit residues: 90.6995 Evaluate side-chains 158 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 179 optimal weight: 40.0000 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1629 GLN A2975 ASN A3517 HIS A3685 GLN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3843 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3890 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.133783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.109500 restraints weight = 52306.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111993 restraints weight = 30783.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.113645 restraints weight = 21955.239| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 17786 Z= 0.340 Angle : 0.820 10.000 24170 Z= 0.428 Chirality : 0.049 0.214 2846 Planarity : 0.006 0.088 3036 Dihedral : 8.119 124.924 2466 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.59 % Allowed : 10.58 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2228 helix: 0.88 (0.14), residues: 1339 sheet: 0.02 (0.39), residues: 173 loop : -1.18 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A3850 HIS 0.007 0.002 HIS A3517 PHE 0.028 0.003 PHE A1916 TYR 0.032 0.003 TYR A1790 ARG 0.008 0.001 ARG A3942 Details of bonding type rmsd hydrogen bonds : bond 0.05320 ( 1085) hydrogen bonds : angle 5.04048 ( 3195) covalent geometry : bond 0.00774 (17785) covalent geometry : angle 0.81988 (24170) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1396 LEU cc_start: 0.6890 (pp) cc_final: 0.5999 (mp) REVERT: A 1453 TYR cc_start: 0.6271 (m-10) cc_final: 0.5924 (m-80) REVERT: A 1562 MET cc_start: 0.6540 (pmm) cc_final: 0.6174 (ptp) REVERT: A 1828 TYR cc_start: 0.7307 (t80) cc_final: 0.6758 (t80) REVERT: A 1918 GLU cc_start: 0.7511 (mp0) cc_final: 0.7107 (mm-30) REVERT: A 2072 LEU cc_start: 0.7562 (mt) cc_final: 0.7189 (mp) REVERT: A 2762 SER cc_start: 0.8853 (t) cc_final: 0.8541 (m) REVERT: A 3487 ASP cc_start: 0.5985 (t0) cc_final: 0.5648 (t0) REVERT: A 3639 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7442 (t-90) REVERT: A 3987 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7133 (t0) REVERT: A 4009 LYS cc_start: 0.7760 (tttt) cc_final: 0.6942 (ttmm) outliers start: 28 outliers final: 13 residues processed: 190 average time/residue: 0.2432 time to fit residues: 76.9456 Evaluate side-chains 159 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2641 LEU Chi-restraints excluded: chain A residue 2767 THR Chi-restraints excluded: chain A residue 2970 ILE Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3639 HIS Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3987 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 16 optimal weight: 0.8980 chunk 217 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2959 GLN A2975 ASN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3975 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.139518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.115627 restraints weight = 51386.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.118472 restraints weight = 28445.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.120378 restraints weight = 19434.393| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17786 Z= 0.113 Angle : 0.568 9.329 24170 Z= 0.285 Chirality : 0.040 0.200 2846 Planarity : 0.004 0.062 3036 Dihedral : 7.585 126.496 2466 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.48 % Allowed : 12.23 % Favored : 86.29 % 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: 1.01 (0.18), residues: 2228 helix: 1.59 (0.14), residues: 1350 sheet: 0.15 (0.39), residues: 165 loop : -0.98 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2084 HIS 0.004 0.001 HIS A1965 PHE 0.024 0.001 PHE A2972 TYR 0.022 0.002 TYR A2558 ARG 0.006 0.000 ARG A2507 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1085) hydrogen bonds : angle 4.41631 ( 3195) covalent geometry : bond 0.00237 (17785) covalent geometry : angle 0.56818 (24170) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1396 LEU cc_start: 0.6678 (pp) cc_final: 0.5762 (mp) REVERT: A 1453 TYR cc_start: 0.6107 (m-10) cc_final: 0.5757 (m-80) REVERT: A 1562 MET cc_start: 0.6361 (pmm) cc_final: 0.5832 (ptp) REVERT: A 1828 TYR cc_start: 0.7039 (t80) cc_final: 0.6552 (t80) REVERT: A 1918 GLU cc_start: 0.7401 (mp0) cc_final: 0.7014 (mm-30) REVERT: A 2072 LEU cc_start: 0.7335 (mt) cc_final: 0.7101 (mp) REVERT: A 2746 ASP cc_start: 0.7995 (t0) cc_final: 0.7680 (t0) REVERT: A 2762 SER cc_start: 0.8840 (t) cc_final: 0.8559 (m) REVERT: A 2927 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 3639 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7395 (t-90) REVERT: A 3686 PHE cc_start: 0.7654 (m-80) cc_final: 0.7274 (m-10) REVERT: A 4009 LYS cc_start: 0.7729 (tttt) cc_final: 0.6926 (ttmm) outliers start: 26 outliers final: 9 residues processed: 195 average time/residue: 0.2407 time to fit residues: 78.4283 Evaluate side-chains 165 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3639 HIS Chi-restraints excluded: chain A residue 3776 ASP Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 134 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 152 optimal weight: 8.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2959 GLN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.138614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.114807 restraints weight = 51413.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.117520 restraints weight = 29513.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.119329 restraints weight = 20590.936| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17786 Z= 0.126 Angle : 0.563 9.251 24170 Z= 0.282 Chirality : 0.040 0.201 2846 Planarity : 0.004 0.060 3036 Dihedral : 7.374 125.619 2466 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 14.05 % Favored : 84.24 % 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: 1.19 (0.18), residues: 2228 helix: 1.74 (0.14), residues: 1353 sheet: 0.13 (0.39), residues: 170 loop : -0.92 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.005 0.001 HIS A2553 PHE 0.018 0.001 PHE A2972 TYR 0.027 0.001 TYR A2234 ARG 0.005 0.000 ARG A2552 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1085) hydrogen bonds : angle 4.28453 ( 3195) covalent geometry : bond 0.00279 (17785) covalent geometry : angle 0.56328 (24170) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6192 (m-10) cc_final: 0.5839 (m-80) REVERT: A 1562 MET cc_start: 0.6323 (pmm) cc_final: 0.5957 (ptp) REVERT: A 1828 TYR cc_start: 0.7057 (t80) cc_final: 0.6549 (t80) REVERT: A 1918 GLU cc_start: 0.7484 (mp0) cc_final: 0.6762 (mm-30) REVERT: A 2072 LEU cc_start: 0.7419 (mt) cc_final: 0.7132 (mp) REVERT: A 2107 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8189 (mmmm) REVERT: A 2513 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8149 (tp-100) REVERT: A 2746 ASP cc_start: 0.8134 (t0) cc_final: 0.7556 (t0) REVERT: A 2762 SER cc_start: 0.8840 (t) cc_final: 0.8558 (m) REVERT: A 2914 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5970 (mt) REVERT: A 3686 PHE cc_start: 0.7697 (m-80) cc_final: 0.7331 (m-10) REVERT: A 3968 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 4009 LYS cc_start: 0.7768 (tttt) cc_final: 0.6929 (ttmm) outliers start: 30 outliers final: 21 residues processed: 194 average time/residue: 0.2362 time to fit residues: 76.6748 Evaluate side-chains 180 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1811 GLN Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2163 VAL Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3776 ASP Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 67 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2975 ASN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3975 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.132278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.108022 restraints weight = 53045.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110493 restraints weight = 31177.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.112047 restraints weight = 22218.071| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 17786 Z= 0.302 Angle : 0.778 12.393 24170 Z= 0.403 Chirality : 0.047 0.228 2846 Planarity : 0.005 0.069 3036 Dihedral : 8.115 105.520 2466 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.30 % Allowed : 15.13 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2228 helix: 0.94 (0.14), residues: 1354 sheet: -0.42 (0.38), residues: 175 loop : -1.35 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A3850 HIS 0.006 0.002 HIS A3413 PHE 0.038 0.003 PHE A3767 TYR 0.027 0.003 TYR A2234 ARG 0.007 0.001 ARG A3942 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 1085) hydrogen bonds : angle 4.93820 ( 3195) covalent geometry : bond 0.00695 (17785) covalent geometry : angle 0.77781 (24170) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6397 (m-10) cc_final: 0.6042 (m-80) REVERT: A 1828 TYR cc_start: 0.7307 (t80) cc_final: 0.6917 (t80) REVERT: A 1918 GLU cc_start: 0.7516 (mp0) cc_final: 0.7146 (mm-30) REVERT: A 2546 MET cc_start: 0.6619 (mtt) cc_final: 0.6176 (mtt) REVERT: A 2762 SER cc_start: 0.8803 (t) cc_final: 0.8495 (m) REVERT: A 2971 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7376 (m-70) REVERT: A 3384 LEU cc_start: 0.7915 (mm) cc_final: 0.7657 (mm) REVERT: A 3968 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7795 (mm) REVERT: A 4009 LYS cc_start: 0.7754 (tttt) cc_final: 0.6941 (ttmm) outliers start: 58 outliers final: 38 residues processed: 205 average time/residue: 0.2331 time to fit residues: 80.5277 Evaluate side-chains 187 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1811 GLN Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2084 TRP Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2163 VAL Chi-restraints excluded: chain A residue 2219 VAL Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2767 THR Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3397 VAL Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3508 PHE Chi-restraints excluded: chain A residue 3635 PHE Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3698 MET Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3710 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 100 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 98 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2959 GLN A2975 ASN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3975 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.137206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.113374 restraints weight = 51775.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.116039 restraints weight = 29727.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.117870 restraints weight = 20764.660| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17786 Z= 0.125 Angle : 0.588 9.355 24170 Z= 0.295 Chirality : 0.041 0.231 2846 Planarity : 0.004 0.062 3036 Dihedral : 7.561 108.292 2466 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.28 % Allowed : 16.95 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2228 helix: 1.53 (0.14), residues: 1362 sheet: -0.22 (0.39), residues: 170 loop : -1.05 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A3911 HIS 0.004 0.001 HIS A1965 PHE 0.023 0.001 PHE A2877 TYR 0.024 0.002 TYR A2234 ARG 0.003 0.000 ARG A2507 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1085) hydrogen bonds : angle 4.41604 ( 3195) covalent geometry : bond 0.00275 (17785) covalent geometry : angle 0.58770 (24170) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6250 (m-10) cc_final: 0.5959 (m-80) REVERT: A 1828 TYR cc_start: 0.7099 (t80) cc_final: 0.6749 (t80) REVERT: A 1918 GLU cc_start: 0.7414 (mp0) cc_final: 0.7166 (mp0) REVERT: A 2072 LEU cc_start: 0.7501 (mt) cc_final: 0.7118 (mp) REVERT: A 2107 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8315 (mmmm) REVERT: A 2762 SER cc_start: 0.8856 (t) cc_final: 0.8564 (m) REVERT: A 3888 LEU cc_start: 0.7402 (mt) cc_final: 0.6620 (pp) REVERT: A 3968 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7410 (mm) REVERT: A 4009 LYS cc_start: 0.7758 (tttt) cc_final: 0.6941 (ttmm) outliers start: 40 outliers final: 27 residues processed: 199 average time/residue: 0.2338 time to fit residues: 77.8669 Evaluate side-chains 186 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain A residue 1838 ILE Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2318 ILE Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3508 PHE Chi-restraints excluded: chain A residue 3635 PHE Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3682 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 101 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1811 GLN A2959 GLN A2975 ASN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.135161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.111146 restraints weight = 51956.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113715 restraints weight = 30253.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.115478 restraints weight = 21367.591| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17786 Z= 0.180 Angle : 0.633 11.146 24170 Z= 0.321 Chirality : 0.043 0.218 2846 Planarity : 0.004 0.063 3036 Dihedral : 7.512 103.888 2466 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.96 % Allowed : 16.78 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2228 helix: 1.49 (0.14), residues: 1364 sheet: -0.29 (0.39), residues: 170 loop : -1.11 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A3911 HIS 0.004 0.001 HIS A1965 PHE 0.015 0.002 PHE A2972 TYR 0.022 0.002 TYR A2234 ARG 0.003 0.000 ARG A3942 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 1085) hydrogen bonds : angle 4.49902 ( 3195) covalent geometry : bond 0.00413 (17785) covalent geometry : angle 0.63348 (24170) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6257 (m-10) cc_final: 0.5941 (m-80) REVERT: A 1828 TYR cc_start: 0.7265 (t80) cc_final: 0.6889 (t80) REVERT: A 1918 GLU cc_start: 0.7467 (mp0) cc_final: 0.6570 (mm-30) REVERT: A 2008 ASP cc_start: 0.7522 (m-30) cc_final: 0.7081 (m-30) REVERT: A 2107 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8366 (mmmm) REVERT: A 2482 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7476 (tt) REVERT: A 2762 SER cc_start: 0.8849 (t) cc_final: 0.8545 (m) REVERT: A 2914 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.6068 (mt) REVERT: A 2971 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7477 (m-70) REVERT: A 3686 PHE cc_start: 0.7677 (m-80) cc_final: 0.7164 (m-80) REVERT: A 3968 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7541 (mm) REVERT: A 4009 LYS cc_start: 0.7802 (tttt) cc_final: 0.6974 (ttmm) outliers start: 52 outliers final: 37 residues processed: 213 average time/residue: 0.2317 time to fit residues: 82.8056 Evaluate side-chains 202 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1811 GLN Chi-restraints excluded: chain A residue 1838 ILE Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2318 ILE Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3508 PHE Chi-restraints excluded: chain A residue 3635 PHE Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3682 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3710 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3841 LEU Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 174 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1811 GLN A2264 ASN A2975 ASN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.136557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.112676 restraints weight = 52064.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.115254 restraints weight = 30061.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.117080 restraints weight = 21224.393| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17786 Z= 0.138 Angle : 0.605 10.398 24170 Z= 0.303 Chirality : 0.042 0.253 2846 Planarity : 0.004 0.064 3036 Dihedral : 7.347 104.110 2466 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.73 % Allowed : 17.41 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2228 helix: 1.64 (0.14), residues: 1357 sheet: -0.27 (0.39), residues: 170 loop : -1.05 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2301 HIS 0.004 0.001 HIS A1965 PHE 0.022 0.001 PHE A2877 TYR 0.021 0.002 TYR A2234 ARG 0.002 0.000 ARG A2507 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 1085) hydrogen bonds : angle 4.38689 ( 3195) covalent geometry : bond 0.00313 (17785) covalent geometry : angle 0.60453 (24170) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6259 (m-10) cc_final: 0.5933 (m-80) REVERT: A 1828 TYR cc_start: 0.7253 (t80) cc_final: 0.6905 (t80) REVERT: A 1918 GLU cc_start: 0.7430 (mp0) cc_final: 0.7156 (mp0) REVERT: A 2107 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8360 (mmmm) REVERT: A 2482 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7440 (tt) REVERT: A 2762 SER cc_start: 0.8844 (t) cc_final: 0.8557 (m) REVERT: A 2914 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6188 (mt) REVERT: A 2971 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7435 (m-70) REVERT: A 3686 PHE cc_start: 0.7664 (m-80) cc_final: 0.7124 (m-80) REVERT: A 3888 LEU cc_start: 0.7204 (mp) cc_final: 0.6366 (pp) REVERT: A 3968 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7483 (mm) REVERT: A 4009 LYS cc_start: 0.7785 (tttt) cc_final: 0.6947 (ttmm) outliers start: 48 outliers final: 37 residues processed: 208 average time/residue: 0.2416 time to fit residues: 84.5409 Evaluate side-chains 198 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1811 GLN Chi-restraints excluded: chain A residue 1838 ILE Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2318 ILE Chi-restraints excluded: chain A residue 2322 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2827 PHE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3508 PHE Chi-restraints excluded: chain A residue 3635 PHE Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3682 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3841 LEU Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 170 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 158 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1811 GLN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.137213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.113375 restraints weight = 52025.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.116040 restraints weight = 29892.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.117848 restraints weight = 20869.515| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17786 Z= 0.130 Angle : 0.605 12.598 24170 Z= 0.301 Chirality : 0.042 0.259 2846 Planarity : 0.004 0.064 3036 Dihedral : 7.146 100.645 2466 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.84 % Allowed : 17.80 % Favored : 79.35 % 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: 1.08 (0.18), residues: 2228 helix: 1.71 (0.14), residues: 1360 sheet: -0.23 (0.39), residues: 170 loop : -1.03 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A3911 HIS 0.005 0.001 HIS A1965 PHE 0.023 0.001 PHE A2877 TYR 0.020 0.001 TYR A2234 ARG 0.002 0.000 ARG A2507 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1085) hydrogen bonds : angle 4.31562 ( 3195) covalent geometry : bond 0.00294 (17785) covalent geometry : angle 0.60533 (24170) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6226 (m-10) cc_final: 0.5869 (m-80) REVERT: A 1668 GLU cc_start: 0.4359 (pm20) cc_final: 0.4144 (tp30) REVERT: A 1918 GLU cc_start: 0.7433 (mp0) cc_final: 0.6503 (mm-30) REVERT: A 2107 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8366 (mmmm) REVERT: A 2482 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7501 (tt) REVERT: A 2546 MET cc_start: 0.5903 (mtt) cc_final: 0.5556 (mtt) REVERT: A 2762 SER cc_start: 0.8851 (t) cc_final: 0.8553 (m) REVERT: A 2914 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.6065 (mt) REVERT: A 2971 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7395 (m-70) REVERT: A 3888 LEU cc_start: 0.7210 (mp) cc_final: 0.6382 (pp) REVERT: A 3968 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7559 (mm) REVERT: A 4009 LYS cc_start: 0.7788 (tttt) cc_final: 0.6944 (ttmm) outliers start: 50 outliers final: 41 residues processed: 211 average time/residue: 0.2484 time to fit residues: 88.4360 Evaluate side-chains 203 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1680 ILE Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1838 ILE Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2318 ILE Chi-restraints excluded: chain A residue 2322 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3356 PHE Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3397 VAL Chi-restraints excluded: chain A residue 3508 PHE Chi-restraints excluded: chain A residue 3635 PHE Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3682 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3710 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3841 LEU Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 195 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 189 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1811 GLN ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.138171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.114451 restraints weight = 51889.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.117108 restraints weight = 29843.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.118965 restraints weight = 20838.987| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17786 Z= 0.119 Angle : 0.591 10.296 24170 Z= 0.294 Chirality : 0.041 0.276 2846 Planarity : 0.004 0.064 3036 Dihedral : 6.874 94.950 2466 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.33 % Allowed : 18.43 % Favored : 79.24 % 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: 1.23 (0.18), residues: 2228 helix: 1.84 (0.14), residues: 1358 sheet: -0.08 (0.39), residues: 172 loop : -1.00 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A3911 HIS 0.005 0.001 HIS A1965 PHE 0.024 0.001 PHE A2877 TYR 0.031 0.001 TYR A2234 ARG 0.002 0.000 ARG A2744 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1085) hydrogen bonds : angle 4.24560 ( 3195) covalent geometry : bond 0.00265 (17785) covalent geometry : angle 0.59113 (24170) Misc. bond : bond 0.00018 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 TYR cc_start: 0.6229 (m-10) cc_final: 0.5890 (m-80) REVERT: A 1918 GLU cc_start: 0.7396 (mp0) cc_final: 0.6495 (mm-30) REVERT: A 2107 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8310 (mmmm) REVERT: A 2746 ASP cc_start: 0.7935 (t0) cc_final: 0.7405 (t0) REVERT: A 2762 SER cc_start: 0.8856 (t) cc_final: 0.8565 (m) REVERT: A 2914 ILE cc_start: 0.6347 (OUTLIER) cc_final: 0.6049 (mt) REVERT: A 2971 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7471 (m-70) REVERT: A 3888 LEU cc_start: 0.7206 (mp) cc_final: 0.6386 (pp) REVERT: A 3968 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 4009 LYS cc_start: 0.7798 (tttt) cc_final: 0.6923 (ttmm) outliers start: 41 outliers final: 35 residues processed: 202 average time/residue: 0.2462 time to fit residues: 83.2133 Evaluate side-chains 200 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1680 ILE Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1838 ILE Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2318 ILE Chi-restraints excluded: chain A residue 2322 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2927 GLN Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 2988 SER Chi-restraints excluded: chain A residue 3356 PHE Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3397 VAL Chi-restraints excluded: chain A residue 3508 PHE Chi-restraints excluded: chain A residue 3635 PHE Chi-restraints excluded: chain A residue 3645 SER Chi-restraints excluded: chain A residue 3682 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3841 LEU Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4004 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 123 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 197 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.138017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.114352 restraints weight = 51729.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116980 restraints weight = 29823.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.118780 restraints weight = 20957.360| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17786 Z= 0.124 Angle : 0.593 12.643 24170 Z= 0.294 Chirality : 0.041 0.262 2846 Planarity : 0.004 0.061 3036 Dihedral : 6.672 89.478 2466 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.56 % Allowed : 18.49 % Favored : 78.95 % 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: 1.27 (0.18), residues: 2228 helix: 1.88 (0.14), residues: 1359 sheet: -0.08 (0.39), residues: 172 loop : -1.00 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A3911 HIS 0.005 0.001 HIS A1965 PHE 0.023 0.001 PHE A2877 TYR 0.030 0.001 TYR A2234 ARG 0.002 0.000 ARG A3944 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1085) hydrogen bonds : angle 4.19979 ( 3195) covalent geometry : bond 0.00278 (17785) covalent geometry : angle 0.59343 (24170) Misc. bond : bond 0.00018 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5879.98 seconds wall clock time: 102 minutes 41.28 seconds (6161.28 seconds total)