Starting phenix.real_space_refine on Wed Jun 18 17:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn5_47026/06_2025/9dn5_47026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn5_47026/06_2025/9dn5_47026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dn5_47026/06_2025/9dn5_47026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn5_47026/06_2025/9dn5_47026.map" model { file = "/net/cci-nas-00/data/ceres_data/9dn5_47026/06_2025/9dn5_47026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn5_47026/06_2025/9dn5_47026.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 94 5.16 5 C 13452 2.51 5 N 3550 2.21 5 O 3894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21000 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2333, 18190 Classifications: {'peptide': 2333} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 64, 'TRANS': 2268} Chain breaks: 13 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 551 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 8, 'GLU:plan': 38, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 392 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2697 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 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: 12.80, per 1000 atoms: 0.61 Number of scatterers: 21000 At special positions: 0 Unit cell: (100.457, 142.24, 169.799, 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 94 16.00 P 9 15.00 Mg 1 11.99 O 3894 8.00 N 3550 7.00 C 13452 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: 5.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 23 sheets defined 55.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 1433 through 1461 Processing helix chain 'A' and resid 1471 through 1494 Processing helix chain 'A' and resid 1511 through 1520 Processing helix chain 'A' and resid 1522 through 1534 removed outlier: 4.422A pdb=" N PHE A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1540 removed outlier: 3.501A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1550 Processing helix chain 'A' and resid 1558 through 1560 No H-bonds generated for 'chain 'A' and resid 1558 through 1560' Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 4.187A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.895A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1666 removed outlier: 3.712A pdb=" N THR A1666 " --> pdb=" O LYS A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 4.258A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1730 Processing helix chain 'A' and resid 1772 through 1787 Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'A' and resid 1861 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.557A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.857A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.561A 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 2046 removed outlier: 3.560A pdb=" N VAL A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2210 removed outlier: 3.833A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A2210 " --> pdb=" O THR A2206 " (cutoff:3.500A) 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: 3.845A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A2270 " --> pdb=" O PHE A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2299 Processing helix chain 'A' and resid 2300 through 2302 No H-bonds generated for 'chain 'A' and resid 2300 through 2302' Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2345 Processing helix chain 'A' and resid 2372 through 2375 removed outlier: 3.938A pdb=" N ILE A2375 " --> pdb=" O CYS A2372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2372 through 2375' Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.554A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2381 through 2385' Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.669A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.735A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A2458 " --> pdb=" O ILE A2454 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2581 through 2587 removed outlier: 6.339A pdb=" N GLU A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A2586 " --> pdb=" O PRO A2583 " (cutoff:3.500A) removed outlier: 5.327A 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: 3.781A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2656 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 removed outlier: 3.802A pdb=" N LEU A2712 " --> pdb=" O ASN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.786A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2778 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.808A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.776A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2864 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 2960 through 2980 removed outlier: 3.802A 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 3299 Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.377A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.596A pdb=" N PHE A3356 " --> pdb=" O LEU A3352 " (cutoff:3.500A) Processing helix chain 'A' and resid 3365 through 3370 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3422 Processing helix chain 'A' and resid 3423 through 3426 removed outlier: 3.776A pdb=" N THR A3426 " --> pdb=" O GLY A3423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3423 through 3426' Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.675A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3467 Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.647A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 4.087A pdb=" N GLY A3643 " --> pdb=" O TRP A3640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.715A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3688 removed outlier: 4.448A pdb=" N THR A3688 " --> pdb=" O CYS A3684 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3728 removed outlier: 3.543A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.281A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.592A 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 3835 Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 3.686A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A3861 " --> pdb=" O LYS A3857 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3890 Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3923 through 3943 Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.643A 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 4066 through 4090 removed outlier: 4.024A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.941A pdb=" N GLY C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.527A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1734 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 5.835A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1795 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1880 Processing sheet with id=AA5, first strand: chain 'A' and resid 2099 through 2104 removed outlier: 6.099A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2118 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2360 removed outlier: 3.730A pdb=" N SER A2367 " --> pdb=" O VAL A2360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2440 through 2444 removed outlier: 6.411A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 removed outlier: 3.531A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 5.807A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.395A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 3.958A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3813 through 3815 Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4021 Processing sheet with id=AB8, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.060A pdb=" N CYS C 150 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 481 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 465 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.564A pdb=" N LYS C 162 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.818A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 256 through 264 removed outlier: 3.720A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS C 273 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP C 262 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS C 269 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 279 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR C 292 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 281 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.542A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 319 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 332 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN C 328 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 340 through 346 removed outlier: 6.954A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 422 through 426 removed outlier: 3.984A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS C 433 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 432 " --> pdb=" O ARG C 440 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3486 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: 13.57 Time building geometry restraints manager: 6.32 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: 6730 1.34 - 1.46: 4610 1.46 - 1.58: 9941 1.58 - 1.70: 12 1.70 - 1.82: 146 Bond restraints: 21439 Sorted by residual: bond pdb=" CB GLN A2289 " pdb=" CG GLN A2289 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" N GLN C 277 " pdb=" CA GLN C 277 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CA GLN A3845 " pdb=" C GLN A3845 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.80e-02 3.09e+03 1.48e+00 bond pdb=" CG LYS A2402 " pdb=" CD LYS A2402 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" N PRO C 168 " pdb=" CA PRO C 168 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.18e+00 ... (remaining 21434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 28481 1.81 - 3.63: 501 3.63 - 5.44: 77 5.44 - 7.25: 28 7.25 - 9.06: 6 Bond angle restraints: 29093 Sorted by residual: angle pdb=" N VAL A2984 " pdb=" CA VAL A2984 " pdb=" C VAL A2984 " ideal model delta sigma weight residual 112.29 109.28 3.01 9.40e-01 1.13e+00 1.02e+01 angle pdb=" CA GLN C 277 " pdb=" CB GLN C 277 " pdb=" CG GLN C 277 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.81e+00 angle pdb=" CA ARG A4067 " pdb=" CB ARG A4067 " pdb=" CG ARG A4067 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.38e+00 angle pdb=" CB LYS A2402 " pdb=" CG LYS A2402 " pdb=" CD LYS A2402 " ideal model delta sigma weight residual 111.30 118.34 -7.04 2.30e+00 1.89e-01 9.37e+00 angle pdb=" CB MET A2049 " pdb=" CG MET A2049 " pdb=" SD MET A2049 " ideal model delta sigma weight residual 112.70 121.76 -9.06 3.00e+00 1.11e-01 9.13e+00 ... (remaining 29088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 12414 31.47 - 62.94: 342 62.94 - 94.40: 29 94.40 - 125.87: 0 125.87 - 157.34: 1 Dihedral angle restraints: 12786 sinusoidal: 4940 harmonic: 7846 Sorted by residual: dihedral pdb=" C2' ADP A4104 " pdb=" C1' ADP A4104 " pdb=" N9 ADP A4104 " pdb=" C4 ADP A4104 " ideal model delta sinusoidal sigma weight residual 91.55 -111.11 -157.34 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 172.16 -80.62 1 2.00e+01 2.50e-03 2.01e+01 dihedral pdb=" CA GLN A1603 " pdb=" C GLN A1603 " pdb=" N ALA A1604 " pdb=" CA ALA A1604 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 12783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2615 0.051 - 0.102: 609 0.102 - 0.152: 122 0.152 - 0.203: 3 0.203 - 0.254: 3 Chirality restraints: 3352 Sorted by residual: chirality pdb=" CB THR A1880 " pdb=" CA THR A1880 " pdb=" OG1 THR A1880 " pdb=" CG2 THR A1880 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL A2933 " pdb=" CA VAL A2933 " pdb=" CG1 VAL A2933 " pdb=" CG2 VAL A2933 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE A2768 " pdb=" CA ILE A2768 " pdb=" CG1 ILE A2768 " pdb=" CG2 ILE A2768 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3349 not shown) Planarity restraints: 3654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A2571 " -0.018 2.00e-02 2.50e+03 1.51e-02 4.58e+00 pdb=" CG TYR A2571 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A2571 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A2571 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A2571 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A2571 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A2571 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A2571 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A2619 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A3924 " 0.012 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" CG TRP A3924 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A3924 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A3924 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A3924 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A3924 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A3924 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3924 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3924 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A3924 " 0.004 2.00e-02 2.50e+03 ... (remaining 3651 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 456 2.70 - 3.25: 20199 3.25 - 3.80: 34196 3.80 - 4.35: 43335 4.35 - 4.90: 73098 Nonbonded interactions: 171284 Sorted by model distance: nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.148 2.170 nonbonded pdb=" OD1 ASP A1848 " pdb="MG MG A4105 " model vdw 2.163 2.170 nonbonded pdb=" OH TYR C 365 " pdb=" O ILE C 387 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A1832 " pdb=" OD1 ASN A1864 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A2115 " pdb=" O TYR A2162 " model vdw 2.256 3.040 ... (remaining 171279 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.450 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: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.060 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 0.038 21439 Z= 0.141 Angle : 0.623 9.063 29093 Z= 0.325 Chirality : 0.044 0.254 3352 Planarity : 0.004 0.051 3654 Dihedral : 14.320 157.338 7682 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2643 helix: 1.08 (0.14), residues: 1372 sheet: 0.15 (0.31), residues: 295 loop : -1.02 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A3924 HIS 0.005 0.001 HIS C 254 PHE 0.031 0.002 PHE A1734 TYR 0.036 0.001 TYR A2571 ARG 0.007 0.000 ARG A4028 Details of bonding type rmsd hydrogen bonds : bond 0.14032 ( 1182) hydrogen bonds : angle 5.85564 ( 3486) covalent geometry : bond 0.00307 (21439) covalent geometry : angle 0.62332 (29093) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7331 (mttp) cc_final: 0.6825 (tptp) REVERT: A 2032 LYS cc_start: 0.7391 (mmtt) cc_final: 0.6897 (mmtt) REVERT: A 2932 MET cc_start: 0.8019 (mtp) cc_final: 0.7698 (mtp) REVERT: A 3414 MET cc_start: 0.6871 (mmt) cc_final: 0.6480 (mmt) REVERT: A 3469 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6722 (tm-30) REVERT: A 3617 GLU cc_start: 0.6092 (tt0) cc_final: 0.5757 (tt0) REVERT: A 3654 LYS cc_start: 0.7391 (mttt) cc_final: 0.6959 (mtpt) REVERT: A 3700 MET cc_start: 0.7148 (ttp) cc_final: 0.6738 (ttp) REVERT: A 4042 ARG cc_start: 0.5293 (tpp-160) cc_final: 0.4672 (ttt90) REVERT: A 4080 GLU cc_start: 0.5599 (tm-30) cc_final: 0.5333 (mt-10) REVERT: C 406 ASN cc_start: 0.7442 (m-40) cc_final: 0.5999 (p0) REVERT: C 429 TYR cc_start: 0.6554 (m-80) cc_final: 0.6031 (m-80) REVERT: C 488 LYS cc_start: 0.7673 (mptt) cc_final: 0.6975 (pttt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3377 time to fit residues: 143.9826 Evaluate side-chains 221 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1665 GLN A1757 GLN A1821 ASN A1840 GLN A1899 ASN A2536 ASN A3988 HIS ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.152701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121820 restraints weight = 35476.326| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.60 r_work: 0.3568 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21439 Z= 0.229 Angle : 0.623 7.605 29093 Z= 0.323 Chirality : 0.045 0.228 3352 Planarity : 0.004 0.043 3654 Dihedral : 6.452 155.955 2916 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.90 % Allowed : 8.01 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2643 helix: 1.39 (0.14), residues: 1391 sheet: -0.41 (0.29), residues: 313 loop : -1.04 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2084 HIS 0.007 0.001 HIS A3936 PHE 0.032 0.002 PHE A1734 TYR 0.023 0.002 TYR A2571 ARG 0.004 0.001 ARG A2507 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 1182) hydrogen bonds : angle 4.47474 ( 3486) covalent geometry : bond 0.00541 (21439) covalent geometry : angle 0.62306 (29093) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2058 MET cc_start: 0.7264 (mmp) cc_final: 0.6926 (mmp) REVERT: A 2279 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7970 (mtm110) REVERT: A 3414 MET cc_start: 0.7104 (mmt) cc_final: 0.6484 (mmt) REVERT: A 3617 GLU cc_start: 0.6289 (tt0) cc_final: 0.5915 (tt0) REVERT: A 3654 LYS cc_start: 0.7459 (mttt) cc_final: 0.7038 (mtpt) REVERT: A 3702 MET cc_start: 0.6513 (mtp) cc_final: 0.5998 (mtp) REVERT: A 3885 PRO cc_start: 0.7415 (Cg_exo) cc_final: 0.7206 (Cg_endo) REVERT: A 4042 ARG cc_start: 0.5521 (tpp-160) cc_final: 0.4886 (ttt90) REVERT: C 298 GLN cc_start: 0.7823 (mt0) cc_final: 0.6942 (tp40) REVERT: C 304 ASP cc_start: 0.5823 (t0) cc_final: 0.5545 (t0) REVERT: C 406 ASN cc_start: 0.7573 (m-40) cc_final: 0.5978 (p0) outliers start: 20 outliers final: 12 residues processed: 265 average time/residue: 0.3280 time to fit residues: 138.1858 Evaluate side-chains 221 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 12 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1629 GLN A1665 GLN A1899 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.155009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124384 restraints weight = 34943.938| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.59 r_work: 0.3607 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21439 Z= 0.130 Angle : 0.515 6.874 29093 Z= 0.266 Chirality : 0.041 0.177 3352 Planarity : 0.003 0.041 3654 Dihedral : 6.225 152.071 2916 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.13 % Allowed : 10.31 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2643 helix: 1.74 (0.14), residues: 1393 sheet: -0.53 (0.28), residues: 321 loop : -0.88 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2084 HIS 0.004 0.001 HIS C 347 PHE 0.026 0.001 PHE A3763 TYR 0.024 0.001 TYR A2571 ARG 0.003 0.000 ARG A2183 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1182) hydrogen bonds : angle 4.21033 ( 3486) covalent geometry : bond 0.00297 (21439) covalent geometry : angle 0.51457 (29093) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7633 (mttp) cc_final: 0.7023 (mtpp) REVERT: A 2343 ASN cc_start: 0.5760 (m-40) cc_final: 0.5469 (m-40) REVERT: A 3414 MET cc_start: 0.7128 (mmt) cc_final: 0.6368 (mmt) REVERT: A 3654 LYS cc_start: 0.7478 (mttt) cc_final: 0.7064 (mtpt) REVERT: A 3835 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: A 3885 PRO cc_start: 0.7433 (Cg_exo) cc_final: 0.7223 (Cg_endo) REVERT: A 3924 TRP cc_start: 0.6533 (m100) cc_final: 0.6123 (t-100) REVERT: A 4042 ARG cc_start: 0.5471 (tpp-160) cc_final: 0.4870 (ttt90) REVERT: C 298 GLN cc_start: 0.7708 (mt0) cc_final: 0.6826 (tp40) REVERT: C 304 ASP cc_start: 0.5540 (t0) cc_final: 0.5269 (t0) REVERT: C 406 ASN cc_start: 0.7512 (m-40) cc_final: 0.5993 (p0) outliers start: 25 outliers final: 14 residues processed: 253 average time/residue: 0.3188 time to fit residues: 130.8689 Evaluate side-chains 225 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 119 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 chunk 251 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 GLN A1899 ASN A2536 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.156916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126467 restraints weight = 35106.783| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.58 r_work: 0.3636 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21439 Z= 0.104 Angle : 0.483 6.742 29093 Z= 0.248 Chirality : 0.041 0.157 3352 Planarity : 0.003 0.041 3654 Dihedral : 6.034 149.125 2916 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.08 % Allowed : 12.29 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2643 helix: 2.03 (0.14), residues: 1386 sheet: -0.48 (0.28), residues: 336 loop : -0.74 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.004 0.001 HIS A3624 PHE 0.022 0.001 PHE A3313 TYR 0.028 0.001 TYR A2571 ARG 0.003 0.000 ARG A2911 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 1182) hydrogen bonds : angle 4.01839 ( 3486) covalent geometry : bond 0.00227 (21439) covalent geometry : angle 0.48291 (29093) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7669 (mttp) cc_final: 0.7071 (mtpp) REVERT: A 2343 ASN cc_start: 0.5762 (m-40) cc_final: 0.5449 (m-40) REVERT: A 3414 MET cc_start: 0.6917 (mmt) cc_final: 0.6163 (mmt) REVERT: A 3469 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6665 (tm-30) REVERT: A 3523 GLU cc_start: 0.7459 (tp30) cc_final: 0.7073 (tp30) REVERT: A 3617 GLU cc_start: 0.6204 (tt0) cc_final: 0.5885 (tt0) REVERT: A 3638 PHE cc_start: 0.7436 (m-80) cc_final: 0.6976 (m-10) REVERT: A 3654 LYS cc_start: 0.7476 (mttt) cc_final: 0.7059 (mtpt) REVERT: A 3835 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: A 3893 ASP cc_start: 0.7498 (m-30) cc_final: 0.6818 (t0) REVERT: A 3924 TRP cc_start: 0.6582 (m100) cc_final: 0.6353 (t-100) REVERT: A 4042 ARG cc_start: 0.5499 (tpp-160) cc_final: 0.4925 (ttt90) REVERT: C 298 GLN cc_start: 0.7621 (mt0) cc_final: 0.6821 (tp40) REVERT: C 304 ASP cc_start: 0.5333 (t0) cc_final: 0.4368 (t0) REVERT: C 406 ASN cc_start: 0.7489 (m-40) cc_final: 0.5904 (p0) REVERT: C 429 TYR cc_start: 0.6625 (m-80) cc_final: 0.6070 (m-80) outliers start: 24 outliers final: 15 residues processed: 258 average time/residue: 0.3169 time to fit residues: 132.8238 Evaluate side-chains 227 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 15 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 265 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1665 GLN A1899 ASN ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2536 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.149902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119004 restraints weight = 35782.563| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.63 r_work: 0.3534 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 21439 Z= 0.264 Angle : 0.645 10.265 29093 Z= 0.330 Chirality : 0.046 0.290 3352 Planarity : 0.004 0.041 3654 Dihedral : 6.438 151.682 2916 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.03 % Allowed : 13.10 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2643 helix: 1.64 (0.14), residues: 1389 sheet: -0.83 (0.28), residues: 324 loop : -0.94 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1607 HIS 0.006 0.001 HIS A3936 PHE 0.031 0.002 PHE A1734 TYR 0.026 0.002 TYR A2571 ARG 0.006 0.001 ARG A2183 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 1182) hydrogen bonds : angle 4.29211 ( 3486) covalent geometry : bond 0.00631 (21439) covalent geometry : angle 0.64466 (29093) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 1943 LYS cc_start: 0.7810 (mttp) cc_final: 0.7373 (mtpp) REVERT: A 2343 ASN cc_start: 0.5917 (m-40) cc_final: 0.5573 (m-40) REVERT: A 2817 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8612 (mm) REVERT: A 3414 MET cc_start: 0.7143 (mmt) cc_final: 0.6289 (mmt) REVERT: A 3617 GLU cc_start: 0.6425 (tt0) cc_final: 0.6067 (tt0) REVERT: A 3654 LYS cc_start: 0.7459 (mttt) cc_final: 0.7044 (mtpt) REVERT: A 3835 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: A 3924 TRP cc_start: 0.6863 (m100) cc_final: 0.6583 (t-100) REVERT: A 4042 ARG cc_start: 0.5661 (tpp-160) cc_final: 0.5024 (ttt90) REVERT: C 277 GLN cc_start: 0.6797 (pm20) cc_final: 0.6532 (pm20) REVERT: C 298 GLN cc_start: 0.7741 (mt0) cc_final: 0.6812 (tp40) REVERT: C 406 ASN cc_start: 0.7519 (m-40) cc_final: 0.5895 (p0) outliers start: 45 outliers final: 29 residues processed: 255 average time/residue: 0.3133 time to fit residues: 130.7898 Evaluate side-chains 232 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1619 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2817 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3788 MET Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 242 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 0.0870 chunk 232 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 259 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1899 ASN A2536 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS C 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.154985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124611 restraints weight = 34910.895| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.57 r_work: 0.3616 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21439 Z= 0.110 Angle : 0.507 8.462 29093 Z= 0.259 Chirality : 0.041 0.157 3352 Planarity : 0.003 0.041 3654 Dihedral : 6.115 145.885 2916 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.53 % Allowed : 14.18 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2643 helix: 2.03 (0.14), residues: 1379 sheet: -0.77 (0.27), residues: 341 loop : -0.70 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A2084 HIS 0.004 0.001 HIS A3624 PHE 0.024 0.001 PHE A3313 TYR 0.026 0.001 TYR A2571 ARG 0.003 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1182) hydrogen bonds : angle 4.01694 ( 3486) covalent geometry : bond 0.00242 (21439) covalent geometry : angle 0.50679 (29093) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7685 (mttp) cc_final: 0.7252 (mtpp) REVERT: A 2126 ARG cc_start: 0.6545 (ttp-170) cc_final: 0.6316 (ttp80) REVERT: A 2257 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.4716 (t80) REVERT: A 2343 ASN cc_start: 0.5990 (m-40) cc_final: 0.5681 (m-40) REVERT: A 3414 MET cc_start: 0.7101 (mmt) cc_final: 0.6550 (mmt) REVERT: A 3469 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6786 (tm-30) REVERT: A 3523 GLU cc_start: 0.7454 (tp30) cc_final: 0.7117 (tp30) REVERT: A 3617 GLU cc_start: 0.6305 (tt0) cc_final: 0.5949 (tt0) REVERT: A 3654 LYS cc_start: 0.7483 (mttt) cc_final: 0.7078 (mtpt) REVERT: A 3700 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5771 (ttm) REVERT: A 3835 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: A 4042 ARG cc_start: 0.5528 (tpp-160) cc_final: 0.4930 (ttt90) REVERT: C 298 GLN cc_start: 0.7591 (mt0) cc_final: 0.6839 (tp40) REVERT: C 406 ASN cc_start: 0.7535 (m-40) cc_final: 0.5900 (p0) REVERT: C 429 TYR cc_start: 0.6707 (m-80) cc_final: 0.6151 (m-80) outliers start: 34 outliers final: 22 residues processed: 247 average time/residue: 0.3175 time to fit residues: 128.9324 Evaluate side-chains 234 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2257 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 3347 VAL Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3788 MET Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 148 optimal weight: 0.0040 chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124233 restraints weight = 35092.653| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.58 r_work: 0.3606 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21439 Z= 0.121 Angle : 0.514 8.056 29093 Z= 0.262 Chirality : 0.041 0.312 3352 Planarity : 0.003 0.040 3654 Dihedral : 6.065 146.051 2916 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.62 % Allowed : 14.76 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2643 helix: 2.11 (0.14), residues: 1379 sheet: -0.82 (0.27), residues: 337 loop : -0.67 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.007 0.001 HIS C 254 PHE 0.027 0.001 PHE A3313 TYR 0.022 0.001 TYR A2571 ARG 0.004 0.000 ARG A4067 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 1182) hydrogen bonds : angle 3.96237 ( 3486) covalent geometry : bond 0.00278 (21439) covalent geometry : angle 0.51445 (29093) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7702 (mttp) cc_final: 0.7271 (mtpp) REVERT: A 2032 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7279 (mmmt) REVERT: A 2126 ARG cc_start: 0.6555 (ttp-170) cc_final: 0.6325 (ttp80) REVERT: A 2257 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.4770 (t80) REVERT: A 2343 ASN cc_start: 0.6017 (m-40) cc_final: 0.5699 (m-40) REVERT: A 3414 MET cc_start: 0.6984 (mmt) cc_final: 0.6439 (mmt) REVERT: A 3523 GLU cc_start: 0.7468 (tp30) cc_final: 0.7135 (tp30) REVERT: A 3617 GLU cc_start: 0.6246 (tt0) cc_final: 0.5924 (tt0) REVERT: A 3654 LYS cc_start: 0.7479 (mttt) cc_final: 0.7078 (mtpt) REVERT: A 3835 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: A 4042 ARG cc_start: 0.5522 (tpp-160) cc_final: 0.4939 (ttt90) REVERT: C 298 GLN cc_start: 0.7588 (mt0) cc_final: 0.6832 (tp40) REVERT: C 406 ASN cc_start: 0.7518 (m-40) cc_final: 0.5882 (p0) REVERT: C 429 TYR cc_start: 0.6633 (m-80) cc_final: 0.6082 (m-80) outliers start: 36 outliers final: 31 residues processed: 245 average time/residue: 0.3210 time to fit residues: 130.4511 Evaluate side-chains 239 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2257 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 2733 VAL Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3788 MET Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2634 ASN C 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.155929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125461 restraints weight = 35160.068| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.59 r_work: 0.3630 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21439 Z= 0.106 Angle : 0.499 7.667 29093 Z= 0.254 Chirality : 0.041 0.211 3352 Planarity : 0.003 0.040 3654 Dihedral : 5.963 144.316 2916 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.71 % Allowed : 14.94 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2643 helix: 2.20 (0.14), residues: 1384 sheet: -0.76 (0.27), residues: 336 loop : -0.62 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2084 HIS 0.007 0.001 HIS C 254 PHE 0.030 0.001 PHE A3313 TYR 0.020 0.001 TYR A2571 ARG 0.007 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 1182) hydrogen bonds : angle 3.89462 ( 3486) covalent geometry : bond 0.00238 (21439) covalent geometry : angle 0.49866 (29093) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7692 (mttp) cc_final: 0.7274 (mtpp) REVERT: A 2126 ARG cc_start: 0.6570 (ttp-170) cc_final: 0.6338 (ttp80) REVERT: A 2257 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.4770 (t80) REVERT: A 2343 ASN cc_start: 0.5980 (m-40) cc_final: 0.5667 (m-40) REVERT: A 2402 LYS cc_start: 0.7059 (tppt) cc_final: 0.6751 (tppt) REVERT: A 2494 LEU cc_start: 0.8567 (mt) cc_final: 0.8351 (mp) REVERT: A 2932 MET cc_start: 0.8169 (mtp) cc_final: 0.7752 (mtp) REVERT: A 3390 PHE cc_start: 0.7903 (m-80) cc_final: 0.7585 (m-80) REVERT: A 3414 MET cc_start: 0.6911 (mmt) cc_final: 0.6358 (mmt) REVERT: A 3523 GLU cc_start: 0.7511 (tp30) cc_final: 0.7186 (tp30) REVERT: A 3617 GLU cc_start: 0.6209 (tt0) cc_final: 0.6008 (tt0) REVERT: A 3654 LYS cc_start: 0.7471 (mttt) cc_final: 0.7072 (mtpt) REVERT: A 3695 LYS cc_start: 0.7238 (mttm) cc_final: 0.6893 (mttt) REVERT: A 3835 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: A 4042 ARG cc_start: 0.5514 (tpp-160) cc_final: 0.4944 (ttt90) REVERT: C 298 GLN cc_start: 0.7585 (mt0) cc_final: 0.6836 (tp40) REVERT: C 406 ASN cc_start: 0.7514 (m-40) cc_final: 0.5889 (p0) REVERT: C 429 TYR cc_start: 0.6545 (m-80) cc_final: 0.6008 (m-80) outliers start: 38 outliers final: 29 residues processed: 255 average time/residue: 0.3147 time to fit residues: 132.3386 Evaluate side-chains 246 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2257 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 2944 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3788 MET Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 213 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 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 = 0.4122 r_free = 0.4122 target = 0.155168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124651 restraints weight = 35155.109| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.59 r_work: 0.3614 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21439 Z= 0.125 Angle : 0.521 8.010 29093 Z= 0.265 Chirality : 0.042 0.328 3352 Planarity : 0.003 0.040 3654 Dihedral : 5.984 146.050 2916 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.76 % Allowed : 14.99 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2643 helix: 2.14 (0.14), residues: 1389 sheet: -0.59 (0.28), residues: 338 loop : -0.64 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 PHE 0.039 0.001 PHE A3763 TYR 0.020 0.001 TYR A2571 ARG 0.006 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 1182) hydrogen bonds : angle 3.91180 ( 3486) covalent geometry : bond 0.00290 (21439) covalent geometry : angle 0.52148 (29093) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1804 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8289 (mm-30) REVERT: A 1943 LYS cc_start: 0.7693 (mttp) cc_final: 0.7261 (mtpp) REVERT: A 2126 ARG cc_start: 0.6528 (ttp-170) cc_final: 0.6265 (ttp80) REVERT: A 2257 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.4883 (t80) REVERT: A 2343 ASN cc_start: 0.6008 (m-40) cc_final: 0.5687 (m-40) REVERT: A 2402 LYS cc_start: 0.7108 (tppt) cc_final: 0.6794 (tppt) REVERT: A 2932 MET cc_start: 0.8175 (mtp) cc_final: 0.7744 (mtp) REVERT: A 3390 PHE cc_start: 0.7953 (m-80) cc_final: 0.7639 (m-80) REVERT: A 3414 MET cc_start: 0.6917 (mmt) cc_final: 0.6372 (mmt) REVERT: A 3523 GLU cc_start: 0.7520 (tp30) cc_final: 0.7192 (tp30) REVERT: A 3638 PHE cc_start: 0.7301 (m-80) cc_final: 0.6887 (m-10) REVERT: A 3654 LYS cc_start: 0.7478 (mttt) cc_final: 0.7081 (mtpt) REVERT: A 3835 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6868 (pm20) REVERT: A 4042 ARG cc_start: 0.5543 (tpp-160) cc_final: 0.4951 (ttt90) REVERT: C 298 GLN cc_start: 0.7603 (mt0) cc_final: 0.6863 (tp40) REVERT: C 406 ASN cc_start: 0.7459 (m-40) cc_final: 0.5835 (p0) REVERT: C 429 TYR cc_start: 0.6563 (m-80) cc_final: 0.6014 (m-80) outliers start: 39 outliers final: 33 residues processed: 244 average time/residue: 0.3020 time to fit residues: 121.2336 Evaluate side-chains 244 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2257 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 2733 VAL Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3348 ILE Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3788 MET Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 199 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 252 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124259 restraints weight = 34921.952| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.56 r_work: 0.3611 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21439 Z= 0.130 Angle : 0.537 10.466 29093 Z= 0.271 Chirality : 0.042 0.325 3352 Planarity : 0.003 0.040 3654 Dihedral : 6.007 146.192 2916 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.62 % Allowed : 15.26 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2643 helix: 2.09 (0.14), residues: 1396 sheet: -0.59 (0.28), residues: 338 loop : -0.67 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 PHE 0.043 0.001 PHE A3763 TYR 0.021 0.001 TYR A2571 ARG 0.006 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 1182) hydrogen bonds : angle 3.92988 ( 3486) covalent geometry : bond 0.00303 (21439) covalent geometry : angle 0.53666 (29093) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1804 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 1943 LYS cc_start: 0.7704 (mttp) cc_final: 0.7273 (mtpp) REVERT: A 2126 ARG cc_start: 0.6519 (ttp-170) cc_final: 0.6216 (ttp80) REVERT: A 2257 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.4918 (t80) REVERT: A 2343 ASN cc_start: 0.5936 (m-40) cc_final: 0.5619 (m-40) REVERT: A 2402 LYS cc_start: 0.7122 (tppt) cc_final: 0.6811 (tppt) REVERT: A 2932 MET cc_start: 0.8200 (mtp) cc_final: 0.7765 (mtp) REVERT: A 3390 PHE cc_start: 0.8002 (m-80) cc_final: 0.7691 (m-80) REVERT: A 3414 MET cc_start: 0.6897 (mmt) cc_final: 0.6405 (mmt) REVERT: A 3523 GLU cc_start: 0.7575 (tp30) cc_final: 0.7259 (tp30) REVERT: A 3654 LYS cc_start: 0.7477 (mttt) cc_final: 0.7080 (mtpt) REVERT: A 3695 LYS cc_start: 0.7128 (mttm) cc_final: 0.6758 (mttt) REVERT: A 3835 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: A 4042 ARG cc_start: 0.5572 (tpp-160) cc_final: 0.4966 (ttt90) REVERT: C 298 GLN cc_start: 0.7647 (mt0) cc_final: 0.6876 (tp40) REVERT: C 406 ASN cc_start: 0.7479 (m-40) cc_final: 0.5854 (p0) REVERT: C 429 TYR cc_start: 0.6556 (m-80) cc_final: 0.6010 (m-80) outliers start: 36 outliers final: 34 residues processed: 245 average time/residue: 0.3320 time to fit residues: 134.5609 Evaluate side-chains 253 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2257 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 2733 VAL Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3348 ILE Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3788 MET Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 213 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 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 = 0.4101 r_free = 0.4101 target = 0.153453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122597 restraints weight = 35380.887| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.62 r_work: 0.3581 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21439 Z= 0.162 Angle : 0.563 8.856 29093 Z= 0.287 Chirality : 0.043 0.341 3352 Planarity : 0.003 0.039 3654 Dihedral : 6.104 146.974 2916 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.67 % Allowed : 15.57 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2643 helix: 2.01 (0.14), residues: 1395 sheet: -0.68 (0.27), residues: 338 loop : -0.73 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 324 HIS 0.005 0.001 HIS C 336 PHE 0.041 0.002 PHE A3763 TYR 0.022 0.001 TYR A2571 ARG 0.006 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 1182) hydrogen bonds : angle 4.00391 ( 3486) covalent geometry : bond 0.00384 (21439) covalent geometry : angle 0.56348 (29093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10313.45 seconds wall clock time: 179 minutes 37.22 seconds (10777.22 seconds total)