Starting phenix.real_space_refine on Fri Sep 19 00:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn5_47026/09_2025/9dn5_47026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn5_47026/09_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_47026/09_2025/9dn5_47026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn5_47026/09_2025/9dn5_47026.map" model { file = "/net/cci-nas-00/data/ceres_data/9dn5_47026/09_2025/9dn5_47026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn5_47026/09_2025/9dn5_47026.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 38, 'GLN:plan1': 7, 'ASN:plan1': 11, 'TRP:plan': 1, 'PHE:plan': 8, 'TYR:plan': 3, 'ASP:plan': 22, '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: {'GLU:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 2, 'TRP:plan': 1, '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: 4.37, per 1000 atoms: 0.21 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: 1.74 Conformation dependent library (CDL) restraints added in 907.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.10 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: 5.89 Time building geometry restraints manager: 2.32 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.170 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (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 ARG 0.007 0.000 ARG A4028 TYR 0.036 0.001 TYR A2571 PHE 0.031 0.002 PHE A1734 TRP 0.034 0.002 TRP A3924 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00307 (21439) covalent geometry : angle 0.62332 (29093) hydrogen bonds : bond 0.14032 ( 1182) hydrogen bonds : angle 5.85564 ( 3486) *********************** 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 : 0.862 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: 0.1484 time to fit residues: 62.6797 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 : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1629 GLN A1665 GLN A1757 GLN A1821 ASN A1840 GLN A1899 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.125347 restraints weight = 35157.942| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.59 r_work: 0.3620 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21439 Z= 0.163 Angle : 0.548 6.530 29093 Z= 0.283 Chirality : 0.043 0.210 3352 Planarity : 0.004 0.044 3654 Dihedral : 6.255 156.327 2916 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.68 % Allowed : 7.11 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2643 helix: 1.57 (0.14), residues: 1390 sheet: -0.33 (0.29), residues: 317 loop : -0.94 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2507 TYR 0.020 0.001 TYR A2571 PHE 0.025 0.002 PHE A1734 TRP 0.019 0.001 TRP A2084 HIS 0.004 0.001 HIS A3936 Details of bonding type rmsd covalent geometry : bond 0.00377 (21439) covalent geometry : angle 0.54787 (29093) hydrogen bonds : bond 0.04077 ( 1182) hydrogen bonds : angle 4.42592 ( 3486) *********************** 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 270 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2279 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7894 (mtm110) REVERT: A 3414 MET cc_start: 0.7013 (mmt) cc_final: 0.6420 (mmt) REVERT: A 3654 LYS cc_start: 0.7451 (mttt) cc_final: 0.7025 (mtpt) REVERT: A 3885 PRO cc_start: 0.7282 (Cg_exo) cc_final: 0.7049 (Cg_endo) REVERT: A 4042 ARG cc_start: 0.5425 (tpp-160) cc_final: 0.4759 (ttt90) REVERT: A 4080 GLU cc_start: 0.5872 (tm-30) cc_final: 0.5399 (mt-10) REVERT: C 298 GLN cc_start: 0.7653 (mt0) cc_final: 0.6844 (tp40) REVERT: C 304 ASP cc_start: 0.5770 (t0) cc_final: 0.4765 (t70) REVERT: C 406 ASN cc_start: 0.7485 (m-40) cc_final: 0.5986 (p0) outliers start: 15 outliers final: 10 residues processed: 264 average time/residue: 0.1485 time to fit residues: 62.5572 Evaluate side-chains 223 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 3347 VAL Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3481 ILE Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 4029 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 249 optimal weight: 0.4980 chunk 123 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1665 GLN ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.158302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127606 restraints weight = 35104.647| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.60 r_work: 0.3653 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21439 Z= 0.105 Angle : 0.487 6.677 29093 Z= 0.251 Chirality : 0.041 0.168 3352 Planarity : 0.003 0.042 3654 Dihedral : 6.057 152.352 2916 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.86 % Allowed : 9.68 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.16), residues: 2643 helix: 1.92 (0.14), residues: 1391 sheet: -0.41 (0.28), residues: 322 loop : -0.77 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2911 TYR 0.020 0.001 TYR A2571 PHE 0.021 0.001 PHE A1734 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS A3624 Details of bonding type rmsd covalent geometry : bond 0.00229 (21439) covalent geometry : angle 0.48655 (29093) hydrogen bonds : bond 0.03429 ( 1182) hydrogen bonds : angle 4.13453 ( 3486) *********************** 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 265 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2343 ASN cc_start: 0.5703 (m-40) cc_final: 0.5419 (m-40) REVERT: A 3469 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 3523 GLU cc_start: 0.7407 (tp30) cc_final: 0.6994 (tp30) REVERT: A 3617 GLU cc_start: 0.6203 (tt0) cc_final: 0.5836 (tt0) REVERT: A 3654 LYS cc_start: 0.7454 (mttt) cc_final: 0.7044 (mtpt) REVERT: A 3835 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: A 3885 PRO cc_start: 0.7271 (Cg_exo) cc_final: 0.7049 (Cg_endo) REVERT: A 3924 TRP cc_start: 0.6382 (m100) cc_final: 0.5916 (t-100) REVERT: A 4042 ARG cc_start: 0.5389 (tpp-160) cc_final: 0.4736 (ttt90) REVERT: A 4080 GLU cc_start: 0.5695 (tm-30) cc_final: 0.5320 (mt-10) REVERT: C 298 GLN cc_start: 0.7562 (mt0) cc_final: 0.6781 (tp40) REVERT: C 304 ASP cc_start: 0.5211 (t0) cc_final: 0.4226 (t0) REVERT: C 406 ASN cc_start: 0.7440 (m-40) cc_final: 0.6036 (p0) REVERT: C 429 TYR cc_start: 0.6660 (m-80) cc_final: 0.6114 (m-80) outliers start: 19 outliers final: 13 residues processed: 258 average time/residue: 0.1481 time to fit residues: 61.8518 Evaluate side-chains 232 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 2003 LEU Chi-restraints excluded: chain A residue 2301 TRP Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2828 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3835 GLU Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 262 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3393 ASN A3821 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 = 0.4166 r_free = 0.4166 target = 0.159187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128619 restraints weight = 35040.569| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.61 r_work: 0.3669 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21439 Z= 0.098 Angle : 0.471 6.522 29093 Z= 0.242 Chirality : 0.040 0.226 3352 Planarity : 0.003 0.042 3654 Dihedral : 5.888 149.744 2916 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.86 % Allowed : 11.57 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.16), residues: 2643 helix: 2.14 (0.14), residues: 1385 sheet: -0.44 (0.28), residues: 337 loop : -0.65 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2911 TYR 0.016 0.001 TYR A3715 PHE 0.021 0.001 PHE A3313 TRP 0.021 0.001 TRP A3640 HIS 0.003 0.000 HIS A3624 Details of bonding type rmsd covalent geometry : bond 0.00211 (21439) covalent geometry : angle 0.47122 (29093) hydrogen bonds : bond 0.03174 ( 1182) hydrogen bonds : angle 3.96529 ( 3486) *********************** 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 263 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1943 LYS cc_start: 0.7407 (mttp) cc_final: 0.6850 (tptp) REVERT: A 2343 ASN cc_start: 0.5807 (m-40) cc_final: 0.5518 (m-40) REVERT: A 2852 LEU cc_start: 0.7462 (tp) cc_final: 0.7114 (tp) REVERT: A 3469 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 3523 GLU cc_start: 0.7424 (tp30) cc_final: 0.7043 (tp30) REVERT: A 3617 GLU cc_start: 0.6160 (tt0) cc_final: 0.5879 (tt0) REVERT: A 3654 LYS cc_start: 0.7513 (mttt) cc_final: 0.7107 (mtpt) REVERT: A 3695 LYS cc_start: 0.6971 (mttt) cc_final: 0.6765 (mttm) REVERT: A 3835 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: A 3885 PRO cc_start: 0.7207 (Cg_exo) cc_final: 0.6991 (Cg_endo) REVERT: A 3893 ASP cc_start: 0.7520 (m-30) cc_final: 0.6864 (t0) REVERT: A 3924 TRP cc_start: 0.6559 (m100) cc_final: 0.6277 (t-100) REVERT: A 4042 ARG cc_start: 0.5335 (tpp-160) cc_final: 0.4742 (ttt90) REVERT: A 4080 GLU cc_start: 0.5603 (tm-30) cc_final: 0.5283 (mt-10) REVERT: C 298 GLN cc_start: 0.7557 (mt0) cc_final: 0.6825 (tp40) REVERT: C 304 ASP cc_start: 0.5204 (t0) cc_final: 0.4294 (t70) REVERT: C 406 ASN cc_start: 0.7443 (m-40) cc_final: 0.5948 (p0) REVERT: C 429 TYR cc_start: 0.6524 (m-80) cc_final: 0.5952 (m-80) outliers start: 19 outliers final: 16 residues processed: 256 average time/residue: 0.1531 time to fit residues: 62.8610 Evaluate side-chains 234 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 2003 LEU Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2828 LEU Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3488 VAL Chi-restraints excluded: chain A residue 3765 ASN 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 256 VAL 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 193 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 243 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 237 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 GLN A1665 GLN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.155280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.124652 restraints weight = 35123.525| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.59 r_work: 0.3612 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1632 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= 0.148 Angle : 0.529 8.281 29093 Z= 0.270 Chirality : 0.042 0.177 3352 Planarity : 0.003 0.038 3654 Dihedral : 6.027 150.262 2916 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.40 % Allowed : 12.33 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.16), residues: 2643 helix: 2.05 (0.14), residues: 1394 sheet: -0.60 (0.28), residues: 327 loop : -0.69 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4067 TYR 0.016 0.001 TYR A1643 PHE 0.023 0.002 PHE A3313 TRP 0.023 0.001 TRP A3640 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00348 (21439) covalent geometry : angle 0.52950 (29093) hydrogen bonds : bond 0.03459 ( 1182) hydrogen bonds : angle 3.98395 ( 3486) *********************** 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 261 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 1943 LYS cc_start: 0.7608 (mttp) cc_final: 0.6977 (mtpp) REVERT: A 2257 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.4463 (t80) REVERT: A 2852 LEU cc_start: 0.7431 (tp) cc_final: 0.7215 (tp) REVERT: A 3523 GLU cc_start: 0.7520 (tp30) cc_final: 0.7149 (tp30) REVERT: A 3617 GLU cc_start: 0.6245 (tt0) cc_final: 0.6036 (tt0) REVERT: A 3654 LYS cc_start: 0.7463 (mttt) cc_final: 0.7052 (mtpt) REVERT: A 3695 LYS cc_start: 0.6957 (mttt) cc_final: 0.6751 (mttm) REVERT: A 3835 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: A 4042 ARG cc_start: 0.5432 (tpp-160) cc_final: 0.4752 (ttt90) REVERT: A 4080 GLU cc_start: 0.5792 (tm-30) cc_final: 0.5378 (mt-10) REVERT: C 298 GLN cc_start: 0.7588 (mt0) cc_final: 0.6829 (tp40) REVERT: C 304 ASP cc_start: 0.5649 (t0) cc_final: 0.4620 (t0) REVERT: C 406 ASN cc_start: 0.7527 (m-40) cc_final: 0.5979 (p0) REVERT: C 429 TYR cc_start: 0.6621 (m-80) cc_final: 0.6030 (m-80) REVERT: C 479 MET cc_start: 0.6510 (mmp) cc_final: 0.6109 (mmm) outliers start: 31 outliers final: 17 residues processed: 251 average time/residue: 0.1514 time to fit residues: 60.8918 Evaluate side-chains 234 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 2003 LEU Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2257 PHE 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 3481 ILE 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 256 VAL Chi-restraints excluded: chain C residue 279 VAL 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 96 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 219 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.158071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128499 restraints weight = 35075.984| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.67 r_work: 0.3650 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21439 Z= 0.099 Angle : 0.486 11.124 29093 Z= 0.246 Chirality : 0.040 0.154 3352 Planarity : 0.003 0.038 3654 Dihedral : 5.857 146.565 2916 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.26 % Allowed : 12.65 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.17), residues: 2643 helix: 2.24 (0.14), residues: 1385 sheet: -0.54 (0.27), residues: 334 loop : -0.58 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4028 TYR 0.018 0.001 TYR A1643 PHE 0.023 0.001 PHE A3313 TRP 0.025 0.001 TRP A3640 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00215 (21439) covalent geometry : angle 0.48599 (29093) hydrogen bonds : bond 0.03120 ( 1182) hydrogen bonds : angle 3.86258 ( 3486) *********************** 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 264 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 1943 LYS cc_start: 0.7654 (mttp) cc_final: 0.7046 (mtpp) REVERT: A 2257 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.4484 (t80) REVERT: A 2343 ASN cc_start: 0.5752 (m-40) cc_final: 0.5510 (m-40) REVERT: A 3523 GLU cc_start: 0.7480 (tp30) cc_final: 0.7154 (tp30) REVERT: A 3654 LYS cc_start: 0.7528 (mttt) cc_final: 0.7124 (mtpt) REVERT: A 3695 LYS cc_start: 0.6929 (mttt) cc_final: 0.6727 (mttm) REVERT: A 3702 MET cc_start: 0.6438 (mtp) cc_final: 0.5939 (mtp) REVERT: A 3835 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: A 3893 ASP cc_start: 0.7492 (m-30) cc_final: 0.6811 (t0) REVERT: A 4042 ARG cc_start: 0.5352 (tpp-160) cc_final: 0.4814 (ttt90) REVERT: C 298 GLN cc_start: 0.7495 (mt0) cc_final: 0.6817 (tp40) REVERT: C 304 ASP cc_start: 0.5352 (t0) cc_final: 0.4406 (t0) REVERT: C 406 ASN cc_start: 0.7501 (m-40) cc_final: 0.5960 (p0) REVERT: C 429 TYR cc_start: 0.6496 (m-80) cc_final: 0.5931 (m-80) REVERT: C 453 TRP cc_start: 0.7930 (m-90) cc_final: 0.7609 (m-90) REVERT: C 479 MET cc_start: 0.6608 (mmp) cc_final: 0.6200 (mmm) outliers start: 28 outliers final: 21 residues processed: 251 average time/residue: 0.1461 time to fit residues: 59.2322 Evaluate side-chains 238 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1572 ILE 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 2103 VAL Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2301 TRP Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3788 MET 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 185 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE 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 103 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 248 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2282 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.158245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.128825 restraints weight = 34926.387| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.67 r_work: 0.3658 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21439 Z= 0.101 Angle : 0.486 9.598 29093 Z= 0.247 Chirality : 0.041 0.201 3352 Planarity : 0.003 0.039 3654 Dihedral : 5.801 145.398 2916 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.44 % Allowed : 13.32 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.17), residues: 2643 helix: 2.28 (0.14), residues: 1386 sheet: -0.53 (0.27), residues: 336 loop : -0.54 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2299 TYR 0.019 0.001 TYR A1643 PHE 0.027 0.001 PHE A3313 TRP 0.025 0.001 TRP A3640 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00223 (21439) covalent geometry : angle 0.48594 (29093) hydrogen bonds : bond 0.03067 ( 1182) hydrogen bonds : angle 3.82532 ( 3486) *********************** 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 262 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7544 (mm) REVERT: A 1943 LYS cc_start: 0.7709 (mttp) cc_final: 0.7316 (mtpp) REVERT: A 2257 PHE cc_start: 0.5926 (OUTLIER) cc_final: 0.4440 (t80) REVERT: A 2343 ASN cc_start: 0.5833 (m-40) cc_final: 0.5586 (m-40) REVERT: A 2932 MET cc_start: 0.8187 (mtp) cc_final: 0.7823 (mtp) REVERT: A 3414 MET cc_start: 0.7114 (mmt) cc_final: 0.6624 (mmt) REVERT: A 3523 GLU cc_start: 0.7475 (tp30) cc_final: 0.7157 (tp30) REVERT: A 3654 LYS cc_start: 0.7547 (mttt) cc_final: 0.7142 (mtpt) REVERT: A 3702 MET cc_start: 0.6507 (mtp) cc_final: 0.6032 (mtp) REVERT: A 3835 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: A 3893 ASP cc_start: 0.7523 (m-30) cc_final: 0.6928 (t0) REVERT: A 4042 ARG cc_start: 0.5405 (tpp-160) cc_final: 0.4898 (ttt90) REVERT: A 4080 GLU cc_start: 0.5239 (tm-30) cc_final: 0.4988 (mt-10) REVERT: C 298 GLN cc_start: 0.7444 (mt0) cc_final: 0.6794 (tp40) REVERT: C 304 ASP cc_start: 0.5355 (t0) cc_final: 0.4420 (t0) REVERT: C 406 ASN cc_start: 0.7480 (m-40) cc_final: 0.5940 (p0) REVERT: C 429 TYR cc_start: 0.6521 (m-80) cc_final: 0.5952 (m-80) REVERT: C 453 TRP cc_start: 0.7921 (m-90) cc_final: 0.7693 (m-90) outliers start: 32 outliers final: 23 residues processed: 246 average time/residue: 0.1458 time to fit residues: 57.3048 Evaluate side-chains 238 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1572 ILE 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 2003 LEU Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2301 TRP Chi-restraints excluded: chain A residue 2428 MET Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2828 LEU Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 3788 MET 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 185 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE 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 174 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 175 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.157844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127317 restraints weight = 34839.135| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.59 r_work: 0.3649 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21439 Z= 0.110 Angle : 0.502 9.430 29093 Z= 0.253 Chirality : 0.041 0.431 3352 Planarity : 0.003 0.038 3654 Dihedral : 5.793 144.766 2916 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.76 % Allowed : 13.10 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.17), residues: 2643 helix: 2.27 (0.14), residues: 1389 sheet: -0.51 (0.27), residues: 337 loop : -0.53 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4067 TYR 0.021 0.001 TYR A3715 PHE 0.036 0.001 PHE A2550 TRP 0.028 0.001 TRP A3640 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00251 (21439) covalent geometry : angle 0.50174 (29093) hydrogen bonds : bond 0.03104 ( 1182) hydrogen bonds : angle 3.82301 ( 3486) *********************** 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 258 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 1943 LYS cc_start: 0.7712 (mttp) cc_final: 0.7272 (mtpp) REVERT: A 2257 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.4432 (t80) REVERT: A 2343 ASN cc_start: 0.5894 (m-40) cc_final: 0.5627 (m-40) REVERT: A 2738 MET cc_start: 0.7796 (ttt) cc_final: 0.7560 (ttt) REVERT: A 2932 MET cc_start: 0.8218 (mtp) cc_final: 0.7806 (mtp) REVERT: A 3523 GLU cc_start: 0.7530 (tp30) cc_final: 0.7214 (tp30) REVERT: A 3654 LYS cc_start: 0.7557 (mttt) cc_final: 0.7157 (mtpt) REVERT: A 3835 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: A 3893 ASP cc_start: 0.7476 (m-30) cc_final: 0.6829 (t0) REVERT: A 4042 ARG cc_start: 0.5376 (tpp-160) cc_final: 0.4848 (ttt90) REVERT: C 298 GLN cc_start: 0.7489 (mt0) cc_final: 0.6839 (tp40) REVERT: C 304 ASP cc_start: 0.5513 (t0) cc_final: 0.5304 (t0) REVERT: C 406 ASN cc_start: 0.7481 (m-40) cc_final: 0.5937 (p0) REVERT: C 429 TYR cc_start: 0.6531 (m-80) cc_final: 0.5949 (m-80) REVERT: C 453 TRP cc_start: 0.7879 (m-90) cc_final: 0.7675 (m-90) outliers start: 39 outliers final: 28 residues processed: 241 average time/residue: 0.1460 time to fit residues: 56.9081 Evaluate side-chains 243 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1572 ILE 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 2003 LEU Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2301 TRP Chi-restraints excluded: chain A residue 2428 MET 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 2828 LEU Chi-restraints excluded: chain A residue 2939 GLU Chi-restraints excluded: chain A residue 2980 MET 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 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 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE 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 20 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2282 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.157293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126733 restraints weight = 34793.967| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.58 r_work: 0.3642 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21439 Z= 0.117 Angle : 0.511 9.280 29093 Z= 0.258 Chirality : 0.041 0.270 3352 Planarity : 0.003 0.037 3654 Dihedral : 5.823 144.415 2916 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.49 % Allowed : 13.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.17), residues: 2643 helix: 2.28 (0.14), residues: 1386 sheet: -0.49 (0.27), residues: 350 loop : -0.51 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4067 TYR 0.019 0.001 TYR A1643 PHE 0.035 0.001 PHE A2550 TRP 0.028 0.001 TRP A3640 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00272 (21439) covalent geometry : angle 0.51135 (29093) hydrogen bonds : bond 0.03139 ( 1182) hydrogen bonds : angle 3.83539 ( 3486) *********************** 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 259 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7516 (mm) REVERT: A 1943 LYS cc_start: 0.7682 (mttp) cc_final: 0.7249 (mtpp) REVERT: A 2343 ASN cc_start: 0.5866 (m-40) cc_final: 0.5592 (m-40) REVERT: A 2738 MET cc_start: 0.7833 (ttt) cc_final: 0.7412 (ttm) REVERT: A 2932 MET cc_start: 0.8265 (mtp) cc_final: 0.7838 (mtp) REVERT: A 3523 GLU cc_start: 0.7557 (tp30) cc_final: 0.7226 (tp30) REVERT: A 3654 LYS cc_start: 0.7491 (mttt) cc_final: 0.7091 (mtpt) REVERT: A 3700 MET cc_start: 0.6875 (tpp) cc_final: 0.6558 (mmm) REVERT: A 3701 THR cc_start: 0.8531 (t) cc_final: 0.7924 (p) REVERT: A 3835 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: A 3893 ASP cc_start: 0.7477 (m-30) cc_final: 0.6821 (t0) REVERT: A 4042 ARG cc_start: 0.5334 (tpp-160) cc_final: 0.4808 (ttt90) REVERT: A 4080 GLU cc_start: 0.5360 (tm-30) cc_final: 0.5127 (mt-10) REVERT: C 298 GLN cc_start: 0.7491 (mt0) cc_final: 0.6840 (tp40) REVERT: C 304 ASP cc_start: 0.5579 (t0) cc_final: 0.5369 (t0) REVERT: C 406 ASN cc_start: 0.7499 (m-40) cc_final: 0.5945 (p0) REVERT: C 429 TYR cc_start: 0.6589 (m-80) cc_final: 0.5989 (m-80) REVERT: C 479 MET cc_start: 0.6393 (mmp) cc_final: 0.5939 (mmm) outliers start: 33 outliers final: 27 residues processed: 244 average time/residue: 0.1517 time to fit residues: 59.1100 Evaluate side-chains 245 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 2003 LEU Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2428 MET 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 2828 LEU Chi-restraints excluded: chain A residue 2939 GLU Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3347 VAL Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3788 MET 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 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE 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 226 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 248 optimal weight: 0.0060 chunk 134 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.157958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127480 restraints weight = 34970.655| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.59 r_work: 0.3652 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21439 Z= 0.107 Angle : 0.516 9.834 29093 Z= 0.259 Chirality : 0.041 0.241 3352 Planarity : 0.003 0.038 3654 Dihedral : 5.795 143.730 2916 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.40 % Allowed : 13.82 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.17), residues: 2643 helix: 2.32 (0.14), residues: 1385 sheet: -0.45 (0.27), residues: 350 loop : -0.49 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3342 TYR 0.023 0.001 TYR A1643 PHE 0.031 0.001 PHE A3313 TRP 0.031 0.001 TRP A3640 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00243 (21439) covalent geometry : angle 0.51596 (29093) hydrogen bonds : bond 0.03094 ( 1182) hydrogen bonds : angle 3.83806 ( 3486) ********************** 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: 31 poor density : 225 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7510 (mm) REVERT: A 1943 LYS cc_start: 0.7671 (mttp) cc_final: 0.7235 (mtpp) REVERT: A 2257 PHE cc_start: 0.5954 (OUTLIER) cc_final: 0.4560 (t80) REVERT: A 2343 ASN cc_start: 0.5847 (m-40) cc_final: 0.5578 (m-40) REVERT: A 2932 MET cc_start: 0.8248 (mtp) cc_final: 0.7818 (mtp) REVERT: A 3469 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6784 (tm-30) REVERT: A 3523 GLU cc_start: 0.7569 (tp30) cc_final: 0.7254 (tp30) REVERT: A 3654 LYS cc_start: 0.7477 (mttt) cc_final: 0.7083 (mtpt) REVERT: A 3701 THR cc_start: 0.8594 (t) cc_final: 0.8003 (p) REVERT: A 3835 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: A 3893 ASP cc_start: 0.7469 (m-30) cc_final: 0.6829 (t0) REVERT: A 4042 ARG cc_start: 0.5325 (tpp-160) cc_final: 0.4802 (ttt90) REVERT: C 298 GLN cc_start: 0.7469 (mt0) cc_final: 0.6843 (tp40) REVERT: C 304 ASP cc_start: 0.5466 (t0) cc_final: 0.5265 (t0) REVERT: C 406 ASN cc_start: 0.7496 (m-40) cc_final: 0.5946 (p0) REVERT: C 429 TYR cc_start: 0.6558 (m-80) cc_final: 0.5967 (m-80) REVERT: C 479 MET cc_start: 0.6440 (mmp) cc_final: 0.6005 (mmm) outliers start: 31 outliers final: 27 residues processed: 239 average time/residue: 0.1518 time to fit residues: 57.8463 Evaluate side-chains 249 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1572 ILE 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 2003 LEU Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2428 MET 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 2828 LEU Chi-restraints excluded: chain A residue 2856 LEU Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3499 CYS Chi-restraints excluded: chain A residue 3788 MET 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 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 423 ILE 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 159 optimal weight: 0.7980 chunk 46 optimal weight: 0.0000 chunk 234 optimal weight: 4.9990 chunk 81 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.159509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129174 restraints weight = 34734.004| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.57 r_work: 0.3674 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21439 Z= 0.098 Angle : 0.506 9.236 29093 Z= 0.254 Chirality : 0.041 0.216 3352 Planarity : 0.003 0.039 3654 Dihedral : 5.707 142.526 2916 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.31 % Allowed : 14.13 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.17), residues: 2643 helix: 2.37 (0.14), residues: 1389 sheet: -0.38 (0.27), residues: 350 loop : -0.48 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2830 TYR 0.020 0.001 TYR A1643 PHE 0.031 0.001 PHE A3313 TRP 0.030 0.001 TRP A3640 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00213 (21439) covalent geometry : angle 0.50571 (29093) hydrogen bonds : bond 0.02957 ( 1182) hydrogen bonds : angle 3.79613 ( 3486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.01 seconds wall clock time: 90 minutes 48.23 seconds (5448.23 seconds total)