Starting phenix.real_space_refine on Fri Sep 19 04:55:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dle_46975/09_2025/9dle_46975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dle_46975/09_2025/9dle_46975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dle_46975/09_2025/9dle_46975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dle_46975/09_2025/9dle_46975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dle_46975/09_2025/9dle_46975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dle_46975/09_2025/9dle_46975.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.024 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 101 5.16 5 C 14679 2.51 5 N 3883 2.21 5 O 4219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22892 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2300, 17945 Classifications: {'peptide': 2300} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 65, 'TRANS': 2234} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 804 Unresolved non-hydrogen dihedrals: 530 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TRP:plan': 2, 'GLU:plan': 41, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 20, 'ASN:plan1': 13, 'TYR:plan': 1, 'ARG:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 391 Chain: "C" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2777 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2057 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 11, 'TRANS': 321} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 689 Unresolved non-hydrogen angles: 886 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'TRP:plan': 6, 'ARG:plan': 13, 'ASN:plan1': 11, 'GLU:plan': 7, 'ASP:plan': 18, 'HIS:plan': 9, 'GLN:plan1': 6, 'PHE:plan': 7, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 373 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: 4.83, per 1000 atoms: 0.21 Number of scatterers: 22892 At special positions: 0 Unit cell: (111.125, 143.129, 188.468, 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 101 16.00 P 9 15.00 Mg 1 11.99 O 4219 8.00 N 3883 7.00 C 14679 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=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 980.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5682 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 31 sheets defined 49.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 1447 through 1461 Processing helix chain 'A' and resid 1471 through 1485 Processing helix chain 'A' and resid 1513 through 1523 Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 3.629A pdb=" N PHE A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1540 removed outlier: 4.050A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A1540 " --> pdb=" O PHE A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1562 through 1567 removed outlier: 3.704A pdb=" N PHE A1566 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1633 removed outlier: 3.865A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.869A 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 Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 4.383A 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 1772 through 1788 removed outlier: 4.205A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1829 through 1842 Processing helix chain 'A' and resid 1854 through 1874 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1937 Processing helix chain 'A' and resid 1942 through 1960 Processing helix chain 'A' and resid 1969 through 1988 removed outlier: 3.551A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 4.650A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.886A 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 2008 through 2022 Processing helix chain 'A' and resid 2031 through 2045 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 4.152A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 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: 3.545A 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 removed outlier: 3.562A pdb=" N ASP A2171 " --> pdb=" O ASN A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2210 Processing helix chain 'A' and resid 2221 through 2236 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 3.800A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 removed outlier: 3.828A pdb=" N HIS A2293 " --> pdb=" O GLN A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2302 Processing helix chain 'A' and resid 2306 through 2326 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2394 through 2409 Processing helix chain 'A' and resid 2423 through 2434 Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 4.009A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 removed outlier: 3.591A pdb=" N LEU A2504 " --> pdb=" O GLN A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.297A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.930A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A2635 " --> pdb=" O THR A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2766 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.562A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.775A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2844 removed outlier: 3.831A pdb=" N LEU A2843 " --> pdb=" O ILE A2840 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 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 2911 Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2949 through 2953 removed outlier: 3.518A pdb=" N LEU A2952 " --> pdb=" O ASN A2949 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A2953 " --> pdb=" O LYS A2950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2949 through 2953' Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.723A 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 3319 removed outlier: 3.627A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A3319 " --> pdb=" O LYS A3315 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 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 3381 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 3.827A pdb=" N VAL A3417 " --> pdb=" O HIS A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3424 through 3426 No H-bonds generated for 'chain 'A' and resid 3424 through 3426' Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 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 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 removed outlier: 3.745A pdb=" N ASN A3538 " --> pdb=" O LEU A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 4.166A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3618 Processing helix chain 'A' and resid 3619 through 3639 Processing helix chain 'A' and resid 3646 through 3659 removed outlier: 3.610A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3671 through 3687 Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.383A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) 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 3836 removed outlier: 4.215A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3847 through 3859 removed outlier: 4.925A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.573A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3903 through 3912 Processing helix chain 'A' and resid 3922 through 3944 removed outlier: 3.986A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 4.398A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 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 4091 removed outlier: 3.730A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'B' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1571 through 1573 Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.114A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A1847 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A1792 " --> pdb=" O VAL A1894 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A1896 " --> pdb=" O GLY A1792 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.519A pdb=" N THR A1886 " --> pdb=" O ILE A1879 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 3.530A pdb=" N VAL A2153 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 removed outlier: 3.775A pdb=" N ARG A2126 " --> pdb=" O SER A2117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2176 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.072A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2464 removed outlier: 4.187A pdb=" N LEU A2474 " --> pdb=" O ASN A2463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2514 through 2516 Processing sheet with id=AB3, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.544A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.183A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.380A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER A3498 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A3407 " --> pdb=" O SER A3498 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3471 through 3472 removed outlier: 3.631A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3811 through 3814 removed outlier: 5.879A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.956A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.447A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 481 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU C 464 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY C 483 " --> pdb=" O ASN C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.595A pdb=" N PHE C 171 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 172 " --> pdb=" O TYR C 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 201 through 205 removed outlier: 5.896A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.512A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 270 " --> pdb=" O TRP C 282 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.775A pdb=" N SER C 302 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 340 through 346 removed outlier: 6.782A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 411 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 420 through 426 Processing sheet with id=AC7, first strand: chain 'B' and resid 150 through 153 removed outlier: 3.543A pdb=" N ASN B 490 " --> pdb=" O THR B 482 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.995A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 201 through 208 removed outlier: 3.592A pdb=" N SER B 203 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 247 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.887A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 279 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 292 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 281 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.547A pdb=" N SER B 302 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 340 through 346 removed outlier: 4.743A pdb=" N TYR B 372 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B 373 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE B 382 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR B 412 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 384 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 420 through 426 removed outlier: 3.730A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 452 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS B 441 " --> pdb=" O LEU B 450 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3570 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: 5.65 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7378 1.34 - 1.46: 5411 1.46 - 1.58: 10419 1.58 - 1.70: 11 1.70 - 1.82: 154 Bond restraints: 23373 Sorted by residual: bond pdb=" C VAL A3946 " pdb=" N PRO A3947 " ideal model delta sigma weight residual 1.334 1.368 -0.035 2.34e-02 1.83e+03 2.18e+00 bond pdb=" CA THR A2518 " pdb=" C THR A2518 " ideal model delta sigma weight residual 1.520 1.535 -0.015 1.23e-02 6.61e+03 1.46e+00 bond pdb=" C2' ADP A4103 " pdb=" C3' ADP A4103 " ideal model delta sigma weight residual 1.524 1.500 0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" CB PHE A2404 " pdb=" CG PHE A2404 " ideal model delta sigma weight residual 1.502 1.475 0.027 2.30e-02 1.89e+03 1.43e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.22e+00 ... (remaining 23368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 31288 2.01 - 4.02: 385 4.02 - 6.03: 73 6.03 - 8.03: 18 8.03 - 10.04: 7 Bond angle restraints: 31771 Sorted by residual: angle pdb=" N ILE A1467 " pdb=" CA ILE A1467 " pdb=" C ILE A1467 " ideal model delta sigma weight residual 113.20 108.99 4.21 9.60e-01 1.09e+00 1.92e+01 angle pdb=" C ASP C 228 " pdb=" N LEU C 229 " pdb=" CA LEU C 229 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 angle pdb=" N LEU A2491 " pdb=" CA LEU A2491 " pdb=" C LEU A2491 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 angle pdb=" C ASP C 316 " pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 122.08 127.77 -5.69 1.47e+00 4.63e-01 1.50e+01 angle pdb=" C1' ADP A4103 " pdb=" C2' ADP A4103 " pdb=" C3' ADP A4103 " ideal model delta sigma weight residual 111.00 100.96 10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 31766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 12902 22.36 - 44.71: 878 44.71 - 67.06: 63 67.06 - 89.42: 19 89.42 - 111.77: 3 Dihedral angle restraints: 13865 sinusoidal: 5132 harmonic: 8733 Sorted by residual: dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 -156.68 -111.77 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" O2A ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PA ADP A4104 " pdb=" PB ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 43.35 -103.34 1 2.00e+01 2.50e-03 2.95e+01 dihedral pdb=" C5' ADP A4103 " pdb=" O5' ADP A4103 " pdb=" PA ADP A4103 " pdb=" O2A ADP A4103 " ideal model delta sinusoidal sigma weight residual -60.00 -152.99 92.99 1 2.00e+01 2.50e-03 2.53e+01 ... (remaining 13862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2941 0.053 - 0.107: 631 0.107 - 0.160: 112 0.160 - 0.213: 4 0.213 - 0.267: 1 Chirality restraints: 3689 Sorted by residual: chirality pdb=" C3' ADP A4103 " pdb=" C2' ADP A4103 " pdb=" C4' ADP A4103 " pdb=" O3' ADP A4103 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C2' ADP A4103 " pdb=" C1' ADP A4103 " pdb=" C3' ADP A4103 " pdb=" O2' ADP A4103 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA LEU A2491 " pdb=" N LEU A2491 " pdb=" C LEU A2491 " pdb=" CB LEU A2491 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 3686 not shown) Planarity restraints: 4002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2485 " 0.020 2.00e-02 2.50e+03 2.05e-02 7.32e+00 pdb=" CG PHE A2485 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A2485 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A2485 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A2485 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A2485 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A2485 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A2619 " -0.096 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 delta sigma weight rms_deltas residual plane pdb=" C LEU A2491 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A2492 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A2492 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2492 " -0.031 5.00e-02 4.00e+02 ... (remaining 3999 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 191 2.60 - 3.17: 18263 3.17 - 3.75: 36301 3.75 - 4.32: 47184 4.32 - 4.90: 80439 Nonbonded interactions: 182378 Sorted by model distance: nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 2.019 2.170 nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.048 2.170 nonbonded pdb=" O ILE A3903 " pdb=" OG1 THR A3906 " model vdw 2.213 3.040 nonbonded pdb=" O GLY A1988 " pdb=" OG1 THR A1993 " model vdw 2.221 3.040 nonbonded pdb=" OG SER C 377 " pdb=" OD1 ASP C 379 " model vdw 2.221 3.040 ... (remaining 182373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 139 through 211 or (resid 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 238 or (resid 239 through 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 3 or (resid 244 and (name N or name CA or name C or name O or name CB )) or resi \ d 245 through 494)) selection = (chain 'C' and ((resid 139 through 143 and (name N or name CA or name C or name \ O or name CB )) or resid 144 or (resid 145 through 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 or (resid 159 through 160 and (name \ N or name CA or name C or name O or name CB )) or resid 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 173 or \ (resid 174 through 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 through 177 or (resid 178 and (name N or name CA or name C or name \ O or name CB )) or resid 179 through 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 188 or (resid 189 and (name \ N or name CA or name C or name O or name CB )) or resid 190 through 198 or (res \ id 199 through 200 and (name N or name CA or name C or name O or name CB )) or r \ esid 201 through 202 or (resid 203 and (name N or name CA or name C or name O or \ name CB )) or resid 204 through 211 or resid 217 through 228 or (resid 229 and \ (name N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB )) or resid 232 through 25 \ 2 or (resid 253 through 254 and (name N or name CA or name C or name O or name C \ B )) or resid 255 or (resid 256 through 258 and (name N or name CA or name C or \ name O or name CB )) or resid 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 265 or (resid 266 through 267 and \ (name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 through 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 through 273 or (resid 274 through 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 or (resid 283 and (name N or name CA o \ r name C or name O or name CB )) or resid 284 through 288 or (resid 289 through \ 294 and (name N or name CA or name C or name O or name CB )) or resid 295 or (re \ sid 296 through 299 and (name N or name CA or name C or name O or name CB )) or \ resid 300 or (resid 301 through 302 and (name N or name CA or name C or name O o \ r name CB )) or resid 303 through 304 or (resid 305 through 306 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 307 through 311 and (name N o \ r name CA or name C or name O or name CB )) or resid 312 through 313 or (resid 3 \ 14 through 326 and (name N or name CA or name C or name O or name CB )) or (resi \ d 327 through 332 and (name N or name CA or name C or name O or name CB )) or re \ sid 333 or (resid 334 and (name N or name CA or name C or name O or name CB )) o \ r resid 335 or (resid 336 through 343 and (name N or name CA or name C or name O \ or name CB )) or resid 344 through 345 or (resid 346 through 350 and (name N or \ name CA or name C or name O or name CB )) or (resid 355 through 367 and (name N \ or name CA or name C or name O or name CB )) or resid 368 through 369 or (resid \ 370 through 372 and (name N or name CA or name C or name O or name CB )) or res \ id 373 or (resid 374 through 382 and (name N or name CA or name C or name O or n \ ame CB )) or resid 383 or (resid 384 and (name N or name CA or name C or name O \ or name CB )) or resid 385 or (resid 386 through 387 and (name N or name CA or n \ ame C or name O or name CB )) or resid 388 or (resid 389 and (name N or name CA \ or name C or name O or name CB )) or (resid 405 through 414 and (name N or name \ CA or name C or name O or name CB )) or resid 415 or (resid 416 through 420 and \ (name N or name CA or name C or name O or name CB )) or resid 421 or (resid 422 \ and (name N or name CA or name C or name O or name CB )) or resid 423 through 42 \ 4 or (resid 425 through 426 and (name N or name CA or name C or name O or name C \ B )) or resid 427 or (resid 428 through 429 and (name N or name CA or name C or \ name O or name CB )) or resid 430 or (resid 431 and (name N or name CA or name C \ or name O or name CB )) or resid 432 through 434 or (resid 435 through 443 and \ (name N or name CA or name C or name O or name CB )) or resid 444 or (resid 445 \ through 446 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 7 or (resid 448 through 458 and (name N or name CA or name C or name O or name C \ B )) or resid 459 or (resid 460 through 467 and (name N or name CA or name C or \ name O or name CB )) or resid 468 or (resid 469 and (name N or name CA or name C \ or name O or name CB )) or resid 470 or (resid 471 through 476 and (name N or n \ ame CA or name C or name O or name CB )) or resid 477 through 479 or (resid 480 \ and (name N or name CA or name C or name O or name CB )) or resid 481 through 48 \ 4 or (resid 485 through 490 and (name N or name CA or name C or name O or name C \ B )) or resid 491 through 492 or (resid 493 through 494 and (name N or name CA o \ r name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.410 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 0.037 23373 Z= 0.147 Angle : 0.601 10.044 31771 Z= 0.301 Chirality : 0.044 0.267 3689 Planarity : 0.004 0.056 4002 Dihedral : 14.332 111.774 8183 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 2945 helix: 0.98 (0.13), residues: 1380 sheet: 0.08 (0.26), residues: 462 loop : -1.04 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3543 TYR 0.018 0.001 TYR A2571 PHE 0.045 0.002 PHE A2485 TRP 0.028 0.001 TRP C 299 HIS 0.005 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00333 (23373) covalent geometry : angle 0.60074 (31771) hydrogen bonds : bond 0.15323 ( 1226) hydrogen bonds : angle 6.36223 ( 3570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1963 MET cc_start: 0.7994 (mtp) cc_final: 0.7631 (mtt) REVERT: A 2166 MET cc_start: 0.7801 (ppp) cc_final: 0.7597 (ppp) REVERT: A 2403 ILE cc_start: 0.8669 (tp) cc_final: 0.8429 (tp) REVERT: A 2658 ASP cc_start: 0.8680 (m-30) cc_final: 0.8415 (m-30) REVERT: A 2805 ASP cc_start: 0.8063 (t0) cc_final: 0.7542 (t0) REVERT: A 2880 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 372 TYR cc_start: 0.8552 (m-80) cc_final: 0.8342 (m-10) REVERT: B 217 LYS cc_start: 0.7309 (tptp) cc_final: 0.6846 (mttt) REVERT: B 242 LYS cc_start: 0.9096 (ptmt) cc_final: 0.8383 (pttm) REVERT: B 261 ILE cc_start: 0.8259 (mm) cc_final: 0.8019 (tt) REVERT: B 478 GLN cc_start: 0.8706 (pt0) cc_final: 0.7287 (tp40) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1298 time to fit residues: 56.0499 Evaluate side-chains 190 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1629 GLN A1788 GLN A2777 ASN A3613 ASN A3826 GLN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS B 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106414 restraints weight = 43215.372| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.91 r_work: 0.3416 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23373 Z= 0.195 Angle : 0.581 8.908 31771 Z= 0.298 Chirality : 0.044 0.256 3689 Planarity : 0.004 0.049 4002 Dihedral : 6.468 117.261 3223 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.81 % Allowed : 8.96 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2945 helix: 1.54 (0.14), residues: 1395 sheet: -0.26 (0.25), residues: 478 loop : -0.93 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3543 TYR 0.021 0.001 TYR A2571 PHE 0.019 0.002 PHE A2485 TRP 0.031 0.002 TRP A1607 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00453 (23373) covalent geometry : angle 0.58144 (31771) hydrogen bonds : bond 0.03994 ( 1226) hydrogen bonds : angle 4.84829 ( 3570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 2151 TRP cc_start: 0.7470 (m-10) cc_final: 0.7094 (m100) REVERT: A 2166 MET cc_start: 0.7623 (ppp) cc_final: 0.7393 (ppp) REVERT: A 2658 ASP cc_start: 0.8838 (m-30) cc_final: 0.8609 (m-30) REVERT: A 2797 MET cc_start: 0.8393 (ptp) cc_final: 0.8146 (ptm) REVERT: A 2805 ASP cc_start: 0.8166 (t0) cc_final: 0.7649 (t0) REVERT: A 3873 MET cc_start: 0.6460 (ttm) cc_final: 0.6199 (ttt) REVERT: C 228 ASP cc_start: 0.7590 (t0) cc_final: 0.7169 (t0) REVERT: C 372 TYR cc_start: 0.8610 (m-80) cc_final: 0.8215 (m-10) REVERT: B 217 LYS cc_start: 0.7329 (tptp) cc_final: 0.6817 (mttt) REVERT: B 242 LYS cc_start: 0.9099 (ptmt) cc_final: 0.8367 (pttm) REVERT: B 261 ILE cc_start: 0.8313 (mm) cc_final: 0.8053 (tt) REVERT: B 478 GLN cc_start: 0.8869 (pt0) cc_final: 0.7404 (tp40) outliers start: 19 outliers final: 15 residues processed: 235 average time/residue: 0.1310 time to fit residues: 51.3558 Evaluate side-chains 205 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 237 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 HIS ** 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 = 0.4024 r_free = 0.4024 target = 0.141779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106377 restraints weight = 43063.947| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.92 r_work: 0.3412 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23373 Z= 0.159 Angle : 0.545 8.225 31771 Z= 0.276 Chirality : 0.043 0.219 3689 Planarity : 0.004 0.046 4002 Dihedral : 6.396 117.205 3223 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.24 % Allowed : 12.44 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2945 helix: 1.78 (0.14), residues: 1392 sheet: -0.27 (0.25), residues: 468 loop : -0.94 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3543 TYR 0.020 0.001 TYR A2571 PHE 0.023 0.001 PHE A2485 TRP 0.025 0.001 TRP A1607 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00371 (23373) covalent geometry : angle 0.54458 (31771) hydrogen bonds : bond 0.03600 ( 1226) hydrogen bonds : angle 4.60725 ( 3570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 2151 TRP cc_start: 0.7342 (m-10) cc_final: 0.7050 (m100) REVERT: A 2166 MET cc_start: 0.7586 (ppp) cc_final: 0.7355 (ppp) REVERT: A 2797 MET cc_start: 0.8409 (ptp) cc_final: 0.8167 (ptm) REVERT: A 2805 ASP cc_start: 0.8159 (t0) cc_final: 0.7691 (t0) REVERT: A 3656 VAL cc_start: 0.7592 (t) cc_final: 0.7242 (t) REVERT: C 228 ASP cc_start: 0.7699 (t0) cc_final: 0.7219 (t0) REVERT: C 372 TYR cc_start: 0.8595 (m-80) cc_final: 0.8235 (m-10) REVERT: B 217 LYS cc_start: 0.7355 (tptp) cc_final: 0.6802 (mttt) REVERT: B 261 ILE cc_start: 0.8331 (mm) cc_final: 0.8070 (tt) REVERT: B 373 CYS cc_start: 0.7650 (p) cc_final: 0.7096 (t) REVERT: B 478 GLN cc_start: 0.8802 (pt0) cc_final: 0.7361 (tp40) outliers start: 29 outliers final: 24 residues processed: 227 average time/residue: 0.1319 time to fit residues: 49.8283 Evaluate side-chains 217 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain B residue 163 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 42 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 HIS ** 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 = 0.4043 r_free = 0.4043 target = 0.143357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.108217 restraints weight = 42869.074| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.91 r_work: 0.3441 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23373 Z= 0.111 Angle : 0.508 10.215 31771 Z= 0.255 Chirality : 0.042 0.164 3689 Planarity : 0.003 0.042 4002 Dihedral : 6.192 116.921 3223 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.07 % Allowed : 14.02 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.16), residues: 2945 helix: 1.95 (0.14), residues: 1397 sheet: -0.24 (0.25), residues: 471 loop : -0.89 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3543 TYR 0.018 0.001 TYR A2571 PHE 0.018 0.001 PHE A2972 TRP 0.024 0.001 TRP A1607 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00251 (23373) covalent geometry : angle 0.50799 (31771) hydrogen bonds : bond 0.03234 ( 1226) hydrogen bonds : angle 4.38654 ( 3570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1739 ASP cc_start: 0.7589 (p0) cc_final: 0.7090 (t0) REVERT: A 1945 LEU cc_start: 0.7763 (tp) cc_final: 0.7330 (tp) REVERT: A 2151 TRP cc_start: 0.7261 (m-10) cc_final: 0.6960 (m100) REVERT: A 2166 MET cc_start: 0.7532 (ppp) cc_final: 0.7320 (ppp) REVERT: A 2216 SER cc_start: 0.8710 (p) cc_final: 0.8389 (p) REVERT: A 2797 MET cc_start: 0.8399 (ptp) cc_final: 0.8190 (ptm) REVERT: A 2805 ASP cc_start: 0.8126 (t0) cc_final: 0.7618 (t0) REVERT: A 3656 VAL cc_start: 0.7442 (t) cc_final: 0.7112 (t) REVERT: C 228 ASP cc_start: 0.7675 (t0) cc_final: 0.7168 (t0) REVERT: C 372 TYR cc_start: 0.8556 (m-80) cc_final: 0.8218 (m-10) REVERT: B 217 LYS cc_start: 0.7344 (tptp) cc_final: 0.6807 (mttt) REVERT: B 261 ILE cc_start: 0.8274 (mm) cc_final: 0.8021 (tt) REVERT: B 373 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6863 (t) REVERT: B 478 GLN cc_start: 0.8769 (pt0) cc_final: 0.7271 (tp40) outliers start: 25 outliers final: 21 residues processed: 232 average time/residue: 0.1325 time to fit residues: 51.0314 Evaluate side-chains 218 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 227 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 85 optimal weight: 0.0370 chunk 262 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2068 GLN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105487 restraints weight = 42941.273| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.86 r_work: 0.3397 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23373 Z= 0.182 Angle : 0.556 9.267 31771 Z= 0.282 Chirality : 0.043 0.161 3689 Planarity : 0.003 0.044 4002 Dihedral : 6.389 117.663 3223 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.14 % Allowed : 15.31 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2945 helix: 1.87 (0.14), residues: 1397 sheet: -0.39 (0.25), residues: 463 loop : -0.96 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3543 TYR 0.020 0.001 TYR A2571 PHE 0.018 0.002 PHE A3530 TRP 0.025 0.001 TRP C 299 HIS 0.005 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00430 (23373) covalent geometry : angle 0.55563 (31771) hydrogen bonds : bond 0.03523 ( 1226) hydrogen bonds : angle 4.41562 ( 3570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 1739 ASP cc_start: 0.7621 (p0) cc_final: 0.7138 (t0) REVERT: A 2166 MET cc_start: 0.7632 (ppp) cc_final: 0.7346 (ppp) REVERT: A 2216 SER cc_start: 0.8698 (p) cc_final: 0.8375 (p) REVERT: A 2797 MET cc_start: 0.8397 (ptp) cc_final: 0.8011 (ptp) REVERT: A 3650 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6361 (tt) REVERT: A 3656 VAL cc_start: 0.7473 (t) cc_final: 0.7164 (t) REVERT: C 228 ASP cc_start: 0.7755 (t0) cc_final: 0.7168 (t0) REVERT: C 372 TYR cc_start: 0.8620 (m-80) cc_final: 0.8258 (m-10) REVERT: B 217 LYS cc_start: 0.7349 (tptp) cc_final: 0.6804 (mttt) REVERT: B 261 ILE cc_start: 0.8389 (mm) cc_final: 0.8109 (tt) REVERT: B 373 CYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7112 (t) REVERT: B 478 GLN cc_start: 0.8693 (pt0) cc_final: 0.7228 (tp40) outliers start: 50 outliers final: 38 residues processed: 237 average time/residue: 0.1341 time to fit residues: 53.3910 Evaluate side-chains 235 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3551 LEU Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 46 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** 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 = 0.3992 r_free = 0.3992 target = 0.139275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104059 restraints weight = 43190.936| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.85 r_work: 0.3376 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23373 Z= 0.205 Angle : 0.588 9.817 31771 Z= 0.298 Chirality : 0.044 0.171 3689 Planarity : 0.004 0.044 4002 Dihedral : 6.531 118.273 3223 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.57 % Allowed : 16.30 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2945 helix: 1.82 (0.14), residues: 1397 sheet: -0.56 (0.25), residues: 463 loop : -1.03 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2136 TYR 0.021 0.001 TYR A2571 PHE 0.021 0.002 PHE A2972 TRP 0.025 0.002 TRP C 299 HIS 0.006 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00484 (23373) covalent geometry : angle 0.58804 (31771) hydrogen bonds : bond 0.03661 ( 1226) hydrogen bonds : angle 4.47606 ( 3570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.825 Fit side-chains REVERT: A 1739 ASP cc_start: 0.7594 (p0) cc_final: 0.7143 (t0) REVERT: A 1786 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7703 (mm) REVERT: A 1945 LEU cc_start: 0.7670 (tt) cc_final: 0.6665 (tp) REVERT: A 2166 MET cc_start: 0.7635 (ppp) cc_final: 0.7315 (ppp) REVERT: A 2216 SER cc_start: 0.8678 (p) cc_final: 0.8349 (p) REVERT: A 2797 MET cc_start: 0.8429 (ptp) cc_final: 0.7993 (ptp) REVERT: A 2978 GLN cc_start: 0.8299 (tm-30) cc_final: 0.8086 (tt0) REVERT: A 3484 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6317 (p-80) REVERT: A 3648 GLN cc_start: 0.7581 (tt0) cc_final: 0.7290 (tt0) REVERT: A 3656 VAL cc_start: 0.7467 (t) cc_final: 0.7178 (t) REVERT: C 228 ASP cc_start: 0.7739 (t0) cc_final: 0.7184 (t0) REVERT: C 372 TYR cc_start: 0.8661 (m-80) cc_final: 0.8221 (m-10) REVERT: B 217 LYS cc_start: 0.7293 (tptp) cc_final: 0.6775 (mttt) REVERT: B 261 ILE cc_start: 0.8471 (mm) cc_final: 0.8169 (tt) REVERT: B 373 CYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7195 (t) REVERT: B 478 GLN cc_start: 0.8687 (pt0) cc_final: 0.7231 (tp40) outliers start: 60 outliers final: 45 residues processed: 243 average time/residue: 0.1348 time to fit residues: 55.2688 Evaluate side-chains 239 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3484 HIS Chi-restraints excluded: chain A residue 3551 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 123 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2501 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.141755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106453 restraints weight = 42978.321| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.89 r_work: 0.3414 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23373 Z= 0.119 Angle : 0.524 7.718 31771 Z= 0.264 Chirality : 0.042 0.160 3689 Planarity : 0.003 0.042 4002 Dihedral : 6.076 117.853 3223 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.97 % Allowed : 17.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.16), residues: 2945 helix: 2.02 (0.14), residues: 1398 sheet: -0.48 (0.25), residues: 477 loop : -0.90 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2136 TYR 0.018 0.001 TYR A2571 PHE 0.025 0.001 PHE A2972 TRP 0.031 0.001 TRP A2151 HIS 0.003 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00272 (23373) covalent geometry : angle 0.52404 (31771) hydrogen bonds : bond 0.03241 ( 1226) hydrogen bonds : angle 4.29561 ( 3570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 1655 MET cc_start: 0.7852 (ttp) cc_final: 0.7578 (tmm) REVERT: A 1739 ASP cc_start: 0.7598 (p0) cc_final: 0.7125 (t0) REVERT: A 1786 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 1945 LEU cc_start: 0.7548 (tt) cc_final: 0.6656 (tp) REVERT: A 2166 MET cc_start: 0.7592 (ppp) cc_final: 0.7280 (ppp) REVERT: A 2216 SER cc_start: 0.8710 (p) cc_final: 0.8379 (p) REVERT: A 2797 MET cc_start: 0.8418 (ptp) cc_final: 0.8087 (ptp) REVERT: A 2978 GLN cc_start: 0.8237 (tm-30) cc_final: 0.8023 (tt0) REVERT: A 3484 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6133 (p-80) REVERT: A 3650 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6347 (tt) REVERT: A 3656 VAL cc_start: 0.7282 (t) cc_final: 0.6993 (t) REVERT: C 228 ASP cc_start: 0.7683 (t0) cc_final: 0.7158 (t0) REVERT: C 372 TYR cc_start: 0.8589 (m-80) cc_final: 0.8142 (m-10) REVERT: B 217 LYS cc_start: 0.7270 (tptp) cc_final: 0.6779 (mttt) REVERT: B 261 ILE cc_start: 0.8391 (mm) cc_final: 0.8104 (tt) REVERT: B 373 CYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6975 (t) REVERT: B 478 GLN cc_start: 0.8668 (pt0) cc_final: 0.7212 (tp40) outliers start: 46 outliers final: 34 residues processed: 239 average time/residue: 0.1314 time to fit residues: 52.1112 Evaluate side-chains 233 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3484 HIS Chi-restraints excluded: chain A residue 3551 LEU Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 54 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 206 optimal weight: 9.9990 chunk 267 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2501 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104967 restraints weight = 43988.466| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.15 r_work: 0.3382 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23373 Z= 0.187 Angle : 0.575 8.738 31771 Z= 0.290 Chirality : 0.044 0.176 3689 Planarity : 0.003 0.043 4002 Dihedral : 6.152 118.283 3223 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.49 % Allowed : 16.60 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2945 helix: 1.91 (0.14), residues: 1399 sheet: -0.56 (0.25), residues: 465 loop : -0.99 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3445 TYR 0.020 0.001 TYR A2571 PHE 0.019 0.002 PHE A3530 TRP 0.034 0.002 TRP A2151 HIS 0.005 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00443 (23373) covalent geometry : angle 0.57504 (31771) hydrogen bonds : bond 0.03513 ( 1226) hydrogen bonds : angle 4.35763 ( 3570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 1655 MET cc_start: 0.7851 (ttp) cc_final: 0.7599 (tmm) REVERT: A 1739 ASP cc_start: 0.7534 (p0) cc_final: 0.7080 (t0) REVERT: A 1786 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 1945 LEU cc_start: 0.7621 (tt) cc_final: 0.6729 (tp) REVERT: A 2166 MET cc_start: 0.7695 (ppp) cc_final: 0.7364 (ppp) REVERT: A 2216 SER cc_start: 0.8636 (p) cc_final: 0.8317 (p) REVERT: A 2797 MET cc_start: 0.8425 (ptp) cc_final: 0.8017 (ptp) REVERT: A 3484 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6320 (p-80) REVERT: A 3648 GLN cc_start: 0.7625 (tt0) cc_final: 0.7325 (tt0) REVERT: A 3650 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6324 (tt) REVERT: A 3656 VAL cc_start: 0.7449 (t) cc_final: 0.7163 (t) REVERT: C 228 ASP cc_start: 0.7803 (t0) cc_final: 0.7275 (t0) REVERT: C 372 TYR cc_start: 0.8659 (m-80) cc_final: 0.8162 (m-10) REVERT: B 217 LYS cc_start: 0.7342 (tptp) cc_final: 0.6834 (mttt) REVERT: B 261 ILE cc_start: 0.8435 (mm) cc_final: 0.8108 (tt) REVERT: B 373 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7217 (t) REVERT: B 478 GLN cc_start: 0.8714 (pt0) cc_final: 0.7255 (tp40) outliers start: 58 outliers final: 44 residues processed: 244 average time/residue: 0.1360 time to fit residues: 56.3308 Evaluate side-chains 245 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2960 THR Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3484 HIS Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3551 LEU Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 173 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 290 optimal weight: 40.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 HIS ** 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 = 0.4030 r_free = 0.4030 target = 0.141031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106700 restraints weight = 44100.672| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.07 r_work: 0.3428 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23373 Z= 0.116 Angle : 0.529 8.814 31771 Z= 0.265 Chirality : 0.042 0.159 3689 Planarity : 0.003 0.043 4002 Dihedral : 5.907 117.535 3223 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.10 % Allowed : 17.32 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.16), residues: 2945 helix: 2.08 (0.14), residues: 1397 sheet: -0.49 (0.25), residues: 480 loop : -0.88 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3445 TYR 0.017 0.001 TYR A2571 PHE 0.024 0.001 PHE A2972 TRP 0.024 0.001 TRP A2084 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00265 (23373) covalent geometry : angle 0.52892 (31771) hydrogen bonds : bond 0.03149 ( 1226) hydrogen bonds : angle 4.22674 ( 3570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 1655 MET cc_start: 0.7831 (ttp) cc_final: 0.7569 (tmm) REVERT: A 1739 ASP cc_start: 0.7483 (p0) cc_final: 0.7030 (t0) REVERT: A 1786 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7707 (mm) REVERT: A 1945 LEU cc_start: 0.7493 (tt) cc_final: 0.6720 (tp) REVERT: A 2216 SER cc_start: 0.8686 (p) cc_final: 0.8370 (p) REVERT: A 2797 MET cc_start: 0.8400 (ptp) cc_final: 0.8097 (ptp) REVERT: A 2805 ASP cc_start: 0.8052 (t0) cc_final: 0.7595 (t0) REVERT: A 2978 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8080 (tt0) REVERT: A 3484 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6134 (p-80) REVERT: A 3650 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6417 (tt) REVERT: A 3656 VAL cc_start: 0.7305 (t) cc_final: 0.7014 (t) REVERT: A 4005 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7478 (tm-30) REVERT: A 4090 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: C 228 ASP cc_start: 0.7674 (t0) cc_final: 0.7172 (t0) REVERT: C 372 TYR cc_start: 0.8574 (m-80) cc_final: 0.8090 (m-10) REVERT: B 217 LYS cc_start: 0.7381 (tptp) cc_final: 0.6879 (mttt) REVERT: B 261 ILE cc_start: 0.8321 (mm) cc_final: 0.8045 (tt) REVERT: B 373 CYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7131 (t) REVERT: B 478 GLN cc_start: 0.8698 (pt0) cc_final: 0.7259 (tp40) outliers start: 49 outliers final: 42 residues processed: 242 average time/residue: 0.1336 time to fit residues: 54.3094 Evaluate side-chains 248 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3484 HIS Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3551 LEU Chi-restraints excluded: chain A residue 3567 LEU Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain A residue 4090 GLN Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 12 optimal weight: 0.1980 chunk 269 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** 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 = 0.4021 r_free = 0.4021 target = 0.140283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.105937 restraints weight = 44059.926| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.05 r_work: 0.3416 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23373 Z= 0.137 Angle : 0.540 9.550 31771 Z= 0.272 Chirality : 0.042 0.159 3689 Planarity : 0.003 0.043 4002 Dihedral : 5.883 117.996 3223 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 17.50 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2945 helix: 2.05 (0.14), residues: 1398 sheet: -0.46 (0.25), residues: 474 loop : -0.90 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3445 TYR 0.020 0.001 TYR A1643 PHE 0.021 0.001 PHE A2972 TRP 0.025 0.001 TRP A2151 HIS 0.003 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00320 (23373) covalent geometry : angle 0.54010 (31771) hydrogen bonds : bond 0.03245 ( 1226) hydrogen bonds : angle 4.22546 ( 3570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5890 Ramachandran restraints generated. 2945 Oldfield, 0 Emsley, 2945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 1655 MET cc_start: 0.7829 (ttp) cc_final: 0.7556 (tmm) REVERT: A 1739 ASP cc_start: 0.7485 (p0) cc_final: 0.7039 (t0) REVERT: A 1786 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 1945 LEU cc_start: 0.7508 (tt) cc_final: 0.6735 (tp) REVERT: A 2216 SER cc_start: 0.8656 (p) cc_final: 0.8342 (p) REVERT: A 2797 MET cc_start: 0.8419 (ptp) cc_final: 0.8114 (ptp) REVERT: A 2978 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8110 (tt0) REVERT: A 3484 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6222 (p-80) REVERT: A 3650 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6360 (tt) REVERT: A 3656 VAL cc_start: 0.7356 (t) cc_final: 0.7070 (t) REVERT: A 4005 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7482 (tm-30) REVERT: A 4090 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: C 228 ASP cc_start: 0.7725 (t0) cc_final: 0.7186 (t0) REVERT: C 372 TYR cc_start: 0.8597 (m-80) cc_final: 0.8099 (m-10) REVERT: B 217 LYS cc_start: 0.7392 (tptp) cc_final: 0.6867 (mttt) REVERT: B 261 ILE cc_start: 0.8329 (mm) cc_final: 0.8055 (tt) REVERT: B 373 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7132 (t) REVERT: B 478 GLN cc_start: 0.8715 (pt0) cc_final: 0.7261 (tp40) outliers start: 49 outliers final: 39 residues processed: 234 average time/residue: 0.1283 time to fit residues: 51.2875 Evaluate side-chains 243 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1790 TYR Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2203 THR Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2654 ARG Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3484 HIS Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3551 LEU Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3906 THR Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain A residue 4090 GLN Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 257 optimal weight: 0.0060 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1851 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104058 restraints weight = 44222.611| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.09 r_work: 0.3376 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23373 Z= 0.209 Angle : 0.603 9.912 31771 Z= 0.307 Chirality : 0.044 0.170 3689 Planarity : 0.004 0.046 4002 Dihedral : 6.165 118.505 3223 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.40 % Allowed : 17.32 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2945 helix: 1.89 (0.14), residues: 1398 sheet: -0.65 (0.25), residues: 471 loop : -1.02 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2654 TYR 0.025 0.002 TYR A1643 PHE 0.021 0.002 PHE A3530 TRP 0.035 0.002 TRP A2151 HIS 0.006 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00493 (23373) covalent geometry : angle 0.60335 (31771) hydrogen bonds : bond 0.03655 ( 1226) hydrogen bonds : angle 4.38865 ( 3570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4932.64 seconds wall clock time: 85 minutes 25.70 seconds (5125.70 seconds total)