Starting phenix.real_space_refine on Fri Sep 19 07:23:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn7_47032/09_2025/9dn7_47032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn7_47032/09_2025/9dn7_47032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dn7_47032/09_2025/9dn7_47032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn7_47032/09_2025/9dn7_47032.map" model { file = "/net/cci-nas-00/data/ceres_data/9dn7_47032/09_2025/9dn7_47032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn7_47032/09_2025/9dn7_47032.cif" } resolution = 3.25 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= 0.031 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 109 5.16 5 C 15232 2.51 5 N 4033 2.21 5 O 4388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s 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: 23772 Number of models: 1 Model: "" Number of chains: 4 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: "B" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2769 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2700 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 5, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.83, per 1000 atoms: 0.20 Number of scatterers: 23772 At special positions: 0 Unit cell: (101.346, 136.906, 189.357, 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 109 16.00 P 9 15.00 Mg 1 11.99 O 4388 8.00 N 4033 7.00 C 15232 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: 1.79 Conformation dependent library (CDL) restraints added in 920.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5756 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 31 sheets defined 50.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 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 1522 removed outlier: 3.585A pdb=" N SER A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A1522 " --> pdb=" O MET A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1534 Processing helix chain 'A' and resid 1535 through 1540 removed outlier: 3.571A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1555 through 1560 removed outlier: 4.208A pdb=" N SER A1559 " --> pdb=" O HIS A1555 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1555 through 1560' Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1633 removed outlier: 3.920A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A1633 " --> pdb=" O GLN A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.767A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1689 removed outlier: 3.930A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (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 1788 removed outlier: 4.195A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.514A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1850 through 1853' 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: 3.599A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1959 removed outlier: 3.597A pdb=" N LEU A1945 " --> pdb=" O ASP A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1981 Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2003 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 Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2079 through 2096 removed outlier: 3.508A pdb=" N THR A2083 " --> pdb=" O GLY A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2129 through 2140 removed outlier: 3.738A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) 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 2208 Processing helix chain 'A' and resid 2221 through 2237 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2258 through 2269 removed outlier: 3.920A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2272 No H-bonds generated for 'chain 'A' and resid 2270 through 2272' 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 2381 through 2385 removed outlier: 3.663A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2409 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 4.162A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.818A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 4.405A 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: 6.418A pdb=" N GLU A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) removed outlier: 5.739A 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: 3.830A 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 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2766 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.692A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.715A 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 2904 Processing helix chain 'A' and resid 2905 through 2912 Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.567A 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 3298 Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.626A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 removed outlier: 3.703A pdb=" N PHE A3334 " --> pdb=" O TYR A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3398 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 4.212A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.825A 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 3513 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: 3.577A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 3.587A 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: 4.185A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3728 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3756 through 3767 removed outlier: 4.398A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3836 Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 3.699A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A3861 " --> pdb=" O LYS A3857 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.975A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.728A 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 4001 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.870A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.112A pdb=" N SER C 405 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1575 removed outlier: 3.656A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A1575 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 5.960A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (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 2098 through 2104 removed outlier: 7.970A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (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 2358 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.135A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2464 Processing sheet with id=AB2, first strand: chain 'A' and resid 2514 through 2517 removed outlier: 3.566A pdb=" N PHE A2515 " --> pdb=" O VAL A2524 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.535A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.207A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.488A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 4.426A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3813 through 3815 removed outlier: 4.049A pdb=" N LYS A3872 " --> pdb=" O GLY A3837 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.657A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.341A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N MET B 479 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 466 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 481 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B 464 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 483 " --> pdb=" O ASN B 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 158 through 163 removed outlier: 3.853A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 174 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 201 through 208 removed outlier: 4.742A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 226 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.860A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 279 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR B 292 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 281 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.540A pdb=" N ARG B 320 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 328 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 340 through 345 removed outlier: 3.557A pdb=" N LYS B 342 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER B 377 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 411 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 386 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N CYS B 409 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 420 through 426 removed outlier: 4.360A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 433 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 452 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N CYS B 441 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.605A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 484 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 481 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.668A pdb=" N LEU C 194 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.984A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 237 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 242 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.543A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 281 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.518A pdb=" N SER C 302 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 314 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.802A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.578A pdb=" N SER C 432 " --> pdb=" O ARG C 440 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3744 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: 6.39 Time building geometry restraints manager: 2.43 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: 7608 1.34 - 1.46: 5061 1.46 - 1.58: 11438 1.58 - 1.70: 12 1.70 - 1.82: 166 Bond restraints: 24285 Sorted by residual: bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.65e+00 bond pdb=" CB ASP B 465 " pdb=" CG ASP B 465 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.90e+00 bond pdb=" C VAL A3946 " pdb=" N PRO A3947 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" CG MET A2428 " pdb=" SD MET A2428 " ideal model delta sigma weight residual 1.803 1.775 0.028 2.50e-02 1.60e+03 1.24e+00 ... (remaining 24280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 32226 1.65 - 3.30: 602 3.30 - 4.96: 87 4.96 - 6.61: 38 6.61 - 8.26: 6 Bond angle restraints: 32959 Sorted by residual: angle pdb=" C LYS A2809 " pdb=" N GLU A2810 " pdb=" CA GLU A2810 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" N LEU A2491 " pdb=" CA LEU A2491 " pdb=" C LEU A2491 " ideal model delta sigma weight residual 109.81 116.46 -6.65 2.21e+00 2.05e-01 9.06e+00 angle pdb=" N MET A2938 " pdb=" CA MET A2938 " pdb=" C MET A2938 " ideal model delta sigma weight residual 114.04 110.40 3.64 1.24e+00 6.50e-01 8.63e+00 angle pdb=" CA TRP A2084 " pdb=" CB TRP A2084 " pdb=" CG TRP A2084 " ideal model delta sigma weight residual 113.60 119.16 -5.56 1.90e+00 2.77e-01 8.56e+00 angle pdb=" CG1 ILE A2689 " pdb=" CB ILE A2689 " pdb=" CG2 ILE A2689 " ideal model delta sigma weight residual 110.70 102.52 8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 32954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 14141 34.03 - 68.06: 283 68.06 - 102.08: 26 102.08 - 136.11: 0 136.11 - 170.14: 1 Dihedral angle restraints: 14451 sinusoidal: 5608 harmonic: 8843 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 -98.31 -170.14 1 2.00e+01 2.50e-03 4.76e+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 91.55 163.46 -71.91 1 2.00e+01 2.50e-03 1.65e+01 dihedral pdb=" C4' ADP A4103 " pdb=" C5' ADP A4103 " pdb=" O5' ADP A4103 " pdb=" PA ADP A4103 " ideal model delta sinusoidal sigma weight residual 180.00 114.05 65.95 1 2.00e+01 2.50e-03 1.42e+01 ... (remaining 14448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2687 0.041 - 0.082: 797 0.082 - 0.124: 256 0.124 - 0.165: 41 0.165 - 0.206: 5 Chirality restraints: 3786 Sorted by residual: chirality pdb=" CB ILE A2689 " pdb=" CA ILE A2689 " pdb=" CG1 ILE A2689 " pdb=" CG2 ILE A2689 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+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 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR A2518 " pdb=" N THR A2518 " pdb=" C THR A2518 " pdb=" CB THR A2518 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 3783 not shown) Planarity restraints: 4134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A3704 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C CYS A3704 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A3704 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A3705 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A3459 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A3460 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A3460 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A3460 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A2619 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " -0.027 5.00e-02 4.00e+02 ... (remaining 4131 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 190 2.56 - 3.14: 17885 3.14 - 3.73: 37808 3.73 - 4.31: 51215 4.31 - 4.90: 87542 Nonbonded interactions: 194640 Sorted by model distance: nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 1.975 2.170 nonbonded pdb=" OD2 ASP A1848 " pdb="MG MG A4105 " model vdw 2.025 2.170 nonbonded pdb=" OH TYR A2115 " pdb=" O TYR A2162 " model vdw 2.211 3.040 nonbonded pdb=" O GLY A1988 " pdb=" OG1 THR A1993 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A2977 " pdb=" O SER A2988 " model vdw 2.225 3.040 ... (remaining 194635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 139 through 154 or (resid 155 and (name N or name CA or na \ me C or name O or name CB )) or resid 156 through 183 or (resid 184 and (name N \ or name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (nam \ e N or name CA or name C or name O or name CB )) or resid 187 or (resid 188 thro \ ugh 189 and (name N or name CA or name C or name O or name CB )) or resid 190 th \ rough 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) \ or resid 209 through 211 or (resid 212 through 213 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 238 or (resid 239 and (name N \ or name CA or name C or name O or name CB )) or resid 240 through 243 or (resid \ 244 and (name N or name CA or name C or name O or name CB )) or resid 245 throug \ h 262 or (resid 263 through 267 and (name N or name CA or name C or name O or na \ me CB )) or resid 268 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB )) or resid 291 through 307 or (resid 308 and (name N or n \ ame CA or name C or name O or name CB )) or resid 309 through 362 or (resid 363 \ and (name N or name CA or name C or name O or name CB )) or resid 364 through 36 \ 5 or (resid 366 and (name N or name CA or name C or name O or name CB )) or resi \ d 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or \ resid 369 through 388 or (resid 389 and (name N or name CA or name C or name O o \ r name CB )) or resid 390 or (resid 391 through 397 and (name N or name CA or na \ me C or name O or name CB )) or resid 398 through 407 or (resid 408 and (name N \ or name CA or name C or name O or name CB )) or resid 409 or (resid 410 and (nam \ e N or name CA or name C or name O or name CB )) or resid 411 through 466 or (re \ sid 467 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 470 or (resid 471 through 473 and (name N or name CA or name C \ or name O or name CB )) or resid 474 or (resid 475 and (name N or name CA or na \ me C or name O or name CB )) or resid 476 through 494)) selection = (chain 'C' and (resid 139 through 350 or resid 355 through 400 or resid 405 thro \ ugh 454 or (resid 455 and (name N or name CA or name C or name O or name CB )) o \ r resid 456 through 493 or (resid 494 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2) \ ))) } 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.041 24285 Z= 0.140 Angle : 0.579 8.262 32959 Z= 0.295 Chirality : 0.044 0.206 3786 Planarity : 0.004 0.057 4134 Dihedral : 14.431 170.140 8695 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.32 (0.15), residues: 2975 helix: 1.15 (0.13), residues: 1383 sheet: -0.07 (0.25), residues: 466 loop : -0.76 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3655 TYR 0.018 0.001 TYR C 219 PHE 0.029 0.001 PHE A1575 TRP 0.028 0.001 TRP B 288 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00319 (24285) covalent geometry : angle 0.57935 (32959) hydrogen bonds : bond 0.15740 ( 1274) hydrogen bonds : angle 6.21098 ( 3744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6159 (m-80) cc_final: 0.5364 (t80) REVERT: A 1557 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8150 (tp-100) REVERT: A 2015 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7536 (mmtt) REVERT: A 2146 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7609 (tmtt) REVERT: A 2942 ASP cc_start: 0.7871 (p0) cc_final: 0.7320 (t70) REVERT: A 3469 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 3702 MET cc_start: 0.8393 (mtt) cc_final: 0.7995 (mtm) REVERT: A 3814 ILE cc_start: 0.8810 (mt) cc_final: 0.8602 (mt) REVERT: A 4048 ILE cc_start: 0.8204 (tp) cc_final: 0.7967 (tp) REVERT: A 4071 LEU cc_start: 0.7825 (mt) cc_final: 0.7586 (pp) REVERT: B 309 TYR cc_start: 0.6509 (m-80) cc_final: 0.5848 (m-80) REVERT: B 342 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7560 (mmtp) REVERT: C 260 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8172 (mmmt) REVERT: C 281 ILE cc_start: 0.6511 (mt) cc_final: 0.6155 (mt) REVERT: C 478 GLN cc_start: 0.6502 (mt0) cc_final: 0.5684 (pt0) REVERT: C 486 ASP cc_start: 0.7380 (t0) cc_final: 0.7093 (t0) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1389 time to fit residues: 70.6957 Evaluate side-chains 241 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2459 HIS A2521 ASN A3018 ASN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3680 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115964 restraints weight = 40389.167| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.34 r_work: 0.3455 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24285 Z= 0.119 Angle : 0.521 7.722 32959 Z= 0.267 Chirality : 0.042 0.188 3786 Planarity : 0.004 0.061 4134 Dihedral : 6.010 172.643 3277 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.59 % Allowed : 7.49 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2975 helix: 1.78 (0.14), residues: 1401 sheet: -0.11 (0.24), residues: 492 loop : -0.66 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3512 TYR 0.025 0.001 TYR A3824 PHE 0.013 0.001 PHE C 293 TRP 0.019 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00264 (24285) covalent geometry : angle 0.52077 (32959) hydrogen bonds : bond 0.03874 ( 1274) hydrogen bonds : angle 4.51143 ( 3744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 268 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6181 (m-80) cc_final: 0.5360 (t80) REVERT: A 1557 GLN cc_start: 0.8456 (tp-100) cc_final: 0.7913 (tp-100) REVERT: A 2015 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7612 (mmtt) REVERT: A 2146 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7674 (tmtt) REVERT: A 2851 LYS cc_start: 0.8619 (pttm) cc_final: 0.8353 (pttp) REVERT: A 2861 ARG cc_start: 0.8511 (mpp80) cc_final: 0.7357 (mpp80) REVERT: A 2942 ASP cc_start: 0.7894 (p0) cc_final: 0.7316 (t70) REVERT: A 3469 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 3484 HIS cc_start: 0.7735 (p-80) cc_final: 0.7289 (p-80) REVERT: A 3702 MET cc_start: 0.8575 (mtt) cc_final: 0.8232 (mtm) REVERT: A 4048 ILE cc_start: 0.8190 (tp) cc_final: 0.7968 (tp) REVERT: A 4071 LEU cc_start: 0.7923 (mt) cc_final: 0.7669 (pp) REVERT: C 260 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8376 (mmmt) REVERT: C 486 ASP cc_start: 0.7645 (t0) cc_final: 0.7390 (t0) outliers start: 15 outliers final: 12 residues processed: 276 average time/residue: 0.1437 time to fit residues: 64.8509 Evaluate side-chains 237 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 3018 ASN Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3448 SER Chi-restraints excluded: chain A residue 3549 ILE Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 184 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3680 GLN ** B 296 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 = 0.3854 r_free = 0.3854 target = 0.137756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113017 restraints weight = 40101.891| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.46 r_work: 0.3402 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24285 Z= 0.157 Angle : 0.535 7.753 32959 Z= 0.272 Chirality : 0.043 0.174 3786 Planarity : 0.004 0.049 4134 Dihedral : 6.066 174.308 3277 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 9.54 % Favored : 89.01 % 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: 0.94 (0.16), residues: 2975 helix: 1.91 (0.14), residues: 1403 sheet: -0.26 (0.24), residues: 492 loop : -0.62 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3512 TYR 0.021 0.001 TYR A3824 PHE 0.015 0.001 PHE A2972 TRP 0.020 0.001 TRP A2084 HIS 0.007 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00368 (24285) covalent geometry : angle 0.53535 (32959) hydrogen bonds : bond 0.03807 ( 1274) hydrogen bonds : angle 4.31135 ( 3744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6189 (m-80) cc_final: 0.5299 (t80) REVERT: A 1557 GLN cc_start: 0.8423 (tp-100) cc_final: 0.7893 (tp-100) REVERT: A 2832 ASN cc_start: 0.8556 (t0) cc_final: 0.8353 (t0) REVERT: A 2851 LYS cc_start: 0.8590 (pttm) cc_final: 0.8311 (pttp) REVERT: A 2861 ARG cc_start: 0.8556 (mpp80) cc_final: 0.7502 (mpp80) REVERT: A 2942 ASP cc_start: 0.7906 (p0) cc_final: 0.7391 (t70) REVERT: A 3469 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7068 (mm-30) REVERT: A 3702 MET cc_start: 0.8430 (mtt) cc_final: 0.8022 (mtm) REVERT: A 3873 MET cc_start: 0.8494 (tpp) cc_final: 0.7934 (tpp) REVERT: A 4048 ILE cc_start: 0.8314 (tp) cc_final: 0.8079 (tt) REVERT: A 4071 LEU cc_start: 0.7847 (mt) cc_final: 0.7573 (pp) REVERT: B 424 SER cc_start: 0.8203 (t) cc_final: 0.7963 (m) REVERT: C 260 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8280 (mmmt) REVERT: C 422 ASP cc_start: 0.7424 (t70) cc_final: 0.7072 (t0) REVERT: C 486 ASP cc_start: 0.7465 (t0) cc_final: 0.7188 (t0) outliers start: 37 outliers final: 26 residues processed: 255 average time/residue: 0.1425 time to fit residues: 60.2005 Evaluate side-chains 245 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2490 ASN Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2896 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3448 SER Chi-restraints excluded: chain A residue 3549 ILE Chi-restraints excluded: chain A residue 3597 ILE Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 479 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 183 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1851 ASN A4036 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS C 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.136057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111297 restraints weight = 40293.314| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.46 r_work: 0.3376 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24285 Z= 0.169 Angle : 0.543 8.057 32959 Z= 0.276 Chirality : 0.043 0.173 3786 Planarity : 0.004 0.051 4134 Dihedral : 6.077 176.383 3277 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.58 % Allowed : 11.23 % Favored : 87.19 % 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: 0.83 (0.16), residues: 2975 helix: 1.90 (0.14), residues: 1402 sheet: -0.48 (0.24), residues: 502 loop : -0.69 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3512 TYR 0.017 0.001 TYR A2571 PHE 0.017 0.001 PHE A2972 TRP 0.021 0.001 TRP A2084 HIS 0.009 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00403 (24285) covalent geometry : angle 0.54343 (32959) hydrogen bonds : bond 0.03805 ( 1274) hydrogen bonds : angle 4.24895 ( 3744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6184 (m-80) cc_final: 0.5308 (t80) REVERT: A 1557 GLN cc_start: 0.8500 (tp-100) cc_final: 0.7740 (tp-100) REVERT: A 2487 ASP cc_start: 0.8173 (t0) cc_final: 0.7086 (t0) REVERT: A 2488 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8057 (mp0) REVERT: A 2851 LYS cc_start: 0.8467 (pttm) cc_final: 0.8219 (pttp) REVERT: A 2942 ASP cc_start: 0.7910 (p0) cc_final: 0.7327 (t0) REVERT: A 3428 LEU cc_start: 0.7990 (mt) cc_final: 0.7675 (tt) REVERT: A 3680 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6529 (mp-120) REVERT: A 3702 MET cc_start: 0.8456 (mtt) cc_final: 0.8046 (mtm) REVERT: A 3873 MET cc_start: 0.8607 (tpp) cc_final: 0.8233 (tpp) REVERT: A 4048 ILE cc_start: 0.8327 (tp) cc_final: 0.8086 (tt) REVERT: A 4071 LEU cc_start: 0.7766 (mt) cc_final: 0.7487 (pp) REVERT: B 282 TRP cc_start: 0.8205 (OUTLIER) cc_final: 0.7979 (m100) REVERT: C 219 TYR cc_start: 0.6805 (p90) cc_final: 0.6430 (p90) REVERT: C 235 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7332 (tptp) REVERT: C 260 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8240 (mmmt) REVERT: C 422 ASP cc_start: 0.7367 (t70) cc_final: 0.7071 (t0) REVERT: C 486 ASP cc_start: 0.7408 (t0) cc_final: 0.7134 (t0) outliers start: 40 outliers final: 30 residues processed: 261 average time/residue: 0.1442 time to fit residues: 62.4872 Evaluate side-chains 251 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2140 ASP Chi-restraints excluded: chain A residue 2218 ASP Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2896 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3404 VAL Chi-restraints excluded: chain A residue 3448 SER Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3549 ILE Chi-restraints excluded: chain A residue 3597 ILE Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 5 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 282 optimal weight: 0.7980 chunk 117 optimal weight: 0.0040 chunk 79 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1557 GLN B 296 HIS B 336 HIS ** 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 = 0.3862 r_free = 0.3862 target = 0.137026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113635 restraints weight = 40259.510| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.32 r_work: 0.3429 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24285 Z= 0.104 Angle : 0.494 7.858 32959 Z= 0.250 Chirality : 0.041 0.194 3786 Planarity : 0.003 0.050 4134 Dihedral : 5.931 175.469 3277 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.34 % Allowed : 12.49 % Favored : 86.17 % 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: 1.09 (0.16), residues: 2975 helix: 2.10 (0.14), residues: 1404 sheet: -0.21 (0.24), residues: 475 loop : -0.64 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3512 TYR 0.019 0.001 TYR A2571 PHE 0.015 0.001 PHE A2972 TRP 0.024 0.001 TRP A2084 HIS 0.004 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00233 (24285) covalent geometry : angle 0.49440 (32959) hydrogen bonds : bond 0.03403 ( 1274) hydrogen bonds : angle 4.07729 ( 3744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6113 (m-80) cc_final: 0.5271 (t80) REVERT: A 1557 GLN cc_start: 0.8493 (tp40) cc_final: 0.8086 (tp-100) REVERT: A 1630 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8099 (mp) REVERT: A 2851 LYS cc_start: 0.8577 (pttm) cc_final: 0.8321 (pttp) REVERT: A 2861 ARG cc_start: 0.8594 (mpp80) cc_final: 0.7623 (mpp80) REVERT: A 2942 ASP cc_start: 0.7816 (p0) cc_final: 0.7306 (t0) REVERT: A 3428 LEU cc_start: 0.7915 (mt) cc_final: 0.7702 (tt) REVERT: A 3591 LYS cc_start: 0.6361 (tptp) cc_final: 0.6042 (ptpp) REVERT: A 3680 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: A 3702 MET cc_start: 0.8701 (mtt) cc_final: 0.8361 (mtm) REVERT: A 4048 ILE cc_start: 0.8292 (tp) cc_final: 0.8060 (tt) REVERT: A 4071 LEU cc_start: 0.7926 (mt) cc_final: 0.7649 (tt) REVERT: C 260 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8373 (mmmt) REVERT: C 486 ASP cc_start: 0.7569 (t0) cc_final: 0.7335 (t0) outliers start: 34 outliers final: 22 residues processed: 272 average time/residue: 0.1415 time to fit residues: 63.4551 Evaluate side-chains 249 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 99 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3624 HIS B 336 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.139510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114698 restraints weight = 39952.448| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.49 r_work: 0.3422 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24285 Z= 0.102 Angle : 0.495 7.729 32959 Z= 0.249 Chirality : 0.041 0.160 3786 Planarity : 0.003 0.053 4134 Dihedral : 5.864 174.731 3277 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.62 % Allowed : 13.12 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.16), residues: 2975 helix: 2.21 (0.14), residues: 1403 sheet: -0.27 (0.24), residues: 490 loop : -0.56 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3512 TYR 0.017 0.001 TYR A2571 PHE 0.018 0.001 PHE A1575 TRP 0.021 0.001 TRP A2084 HIS 0.005 0.001 HIS A3624 Details of bonding type rmsd covalent geometry : bond 0.00230 (24285) covalent geometry : angle 0.49454 (32959) hydrogen bonds : bond 0.03296 ( 1274) hydrogen bonds : angle 3.99180 ( 3744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6101 (m-80) cc_final: 0.5205 (t80) REVERT: A 1557 GLN cc_start: 0.8337 (tp40) cc_final: 0.7783 (tp-100) REVERT: A 1630 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 2851 LYS cc_start: 0.8523 (pttm) cc_final: 0.8236 (pttp) REVERT: A 2942 ASP cc_start: 0.7777 (p0) cc_final: 0.7316 (t0) REVERT: A 3428 LEU cc_start: 0.7852 (mt) cc_final: 0.7596 (tt) REVERT: A 3591 LYS cc_start: 0.6362 (tptp) cc_final: 0.6044 (ptpp) REVERT: A 3680 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6387 (mp-120) REVERT: A 3702 MET cc_start: 0.8480 (mtt) cc_final: 0.8084 (mtm) REVERT: A 3828 GLU cc_start: 0.7553 (tp30) cc_final: 0.7345 (mm-30) REVERT: A 3873 MET cc_start: 0.8647 (tpp) cc_final: 0.8189 (tpp) REVERT: A 4048 ILE cc_start: 0.8285 (tp) cc_final: 0.8055 (tt) REVERT: A 4071 LEU cc_start: 0.7752 (mt) cc_final: 0.7480 (pp) REVERT: C 260 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8243 (mmmt) REVERT: C 486 ASP cc_start: 0.7406 (t0) cc_final: 0.7161 (t0) outliers start: 41 outliers final: 28 residues processed: 263 average time/residue: 0.1369 time to fit residues: 59.9177 Evaluate side-chains 259 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2490 ASN Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2896 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3889 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 224 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 174 optimal weight: 0.0980 chunk 245 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3914 GLN B 336 HIS ** 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 = 0.3885 r_free = 0.3885 target = 0.140199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115908 restraints weight = 39637.576| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.44 r_work: 0.3446 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24285 Z= 0.094 Angle : 0.481 7.499 32959 Z= 0.242 Chirality : 0.041 0.162 3786 Planarity : 0.003 0.043 4134 Dihedral : 5.779 173.499 3277 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.46 % Allowed : 13.51 % Favored : 85.03 % 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: 1.28 (0.16), residues: 2975 helix: 2.27 (0.14), residues: 1404 sheet: -0.21 (0.24), residues: 495 loop : -0.52 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3512 TYR 0.022 0.001 TYR C 219 PHE 0.019 0.001 PHE A2550 TRP 0.022 0.001 TRP A2084 HIS 0.003 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00204 (24285) covalent geometry : angle 0.48060 (32959) hydrogen bonds : bond 0.03158 ( 1274) hydrogen bonds : angle 3.91918 ( 3744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6049 (m-80) cc_final: 0.5212 (t80) REVERT: A 1557 GLN cc_start: 0.8287 (tp40) cc_final: 0.7945 (tp-100) REVERT: A 1630 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 1970 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (tt) REVERT: A 2222 ILE cc_start: 0.7685 (mm) cc_final: 0.7406 (mm) REVERT: A 2487 ASP cc_start: 0.7704 (t0) cc_final: 0.7218 (t0) REVERT: A 2488 GLU cc_start: 0.8025 (mp0) cc_final: 0.7553 (mp0) REVERT: A 2851 LYS cc_start: 0.8477 (pttm) cc_final: 0.8190 (pttp) REVERT: A 2861 ARG cc_start: 0.8561 (mpp80) cc_final: 0.7596 (mpp80) REVERT: A 2942 ASP cc_start: 0.7784 (p0) cc_final: 0.7305 (t0) REVERT: A 3428 LEU cc_start: 0.7861 (mt) cc_final: 0.7588 (tt) REVERT: A 3591 LYS cc_start: 0.6250 (tptp) cc_final: 0.6034 (pttt) REVERT: A 3680 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: A 3702 MET cc_start: 0.8409 (mtt) cc_final: 0.8034 (mtm) REVERT: A 3828 GLU cc_start: 0.7574 (tp30) cc_final: 0.7331 (mm-30) REVERT: A 3873 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8001 (tpp) REVERT: A 4005 GLU cc_start: 0.8280 (tp30) cc_final: 0.7851 (tp30) REVERT: A 4071 LEU cc_start: 0.7669 (mt) cc_final: 0.7419 (tt) REVERT: C 242 LYS cc_start: 0.6939 (tptt) cc_final: 0.6422 (tttm) REVERT: C 260 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8192 (mmmt) REVERT: C 486 ASP cc_start: 0.7423 (t0) cc_final: 0.7209 (t0) outliers start: 37 outliers final: 26 residues processed: 271 average time/residue: 0.1366 time to fit residues: 61.3652 Evaluate side-chains 264 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3873 MET Chi-restraints excluded: chain A residue 3889 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 282 TRP Chi-restraints excluded: chain C residue 479 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 201 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 HIS ** 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 = 0.3870 r_free = 0.3870 target = 0.139075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114705 restraints weight = 39768.420| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.45 r_work: 0.3427 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24285 Z= 0.110 Angle : 0.495 7.910 32959 Z= 0.249 Chirality : 0.041 0.161 3786 Planarity : 0.003 0.043 4134 Dihedral : 5.789 173.495 3277 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.42 % Allowed : 14.11 % Favored : 84.48 % 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: 1.29 (0.16), residues: 2975 helix: 2.27 (0.14), residues: 1403 sheet: -0.17 (0.24), residues: 491 loop : -0.50 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3512 TYR 0.018 0.001 TYR C 219 PHE 0.016 0.001 PHE A1575 TRP 0.040 0.001 TRP A3762 HIS 0.005 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00254 (24285) covalent geometry : angle 0.49545 (32959) hydrogen bonds : bond 0.03241 ( 1274) hydrogen bonds : angle 3.91342 ( 3744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6057 (m-80) cc_final: 0.5215 (t80) REVERT: A 1630 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 2222 ILE cc_start: 0.7805 (mm) cc_final: 0.7519 (mm) REVERT: A 2487 ASP cc_start: 0.7695 (t0) cc_final: 0.7117 (t0) REVERT: A 2488 GLU cc_start: 0.8083 (mp0) cc_final: 0.7665 (mp0) REVERT: A 2851 LYS cc_start: 0.8527 (pttm) cc_final: 0.8250 (pttp) REVERT: A 2942 ASP cc_start: 0.7781 (p0) cc_final: 0.7331 (t0) REVERT: A 3680 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6525 (mp-120) REVERT: A 3702 MET cc_start: 0.8515 (mtt) cc_final: 0.8150 (mtm) REVERT: A 3873 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8045 (tpp) REVERT: A 4005 GLU cc_start: 0.8280 (tp30) cc_final: 0.7859 (tp30) REVERT: A 4071 LEU cc_start: 0.7734 (mt) cc_final: 0.7467 (tt) REVERT: C 242 LYS cc_start: 0.7003 (tptt) cc_final: 0.6518 (tttm) REVERT: C 260 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8289 (mmmt) REVERT: C 486 ASP cc_start: 0.7368 (t0) cc_final: 0.7128 (t0) outliers start: 36 outliers final: 27 residues processed: 265 average time/residue: 0.1399 time to fit residues: 61.7889 Evaluate side-chains 260 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2490 ASN Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2896 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3873 MET Chi-restraints excluded: chain A residue 3889 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 148 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 257 optimal weight: 0.0020 chunk 66 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS ** 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 = 0.3896 r_free = 0.3896 target = 0.141137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116657 restraints weight = 39775.147| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.47 r_work: 0.3451 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24285 Z= 0.092 Angle : 0.484 9.448 32959 Z= 0.243 Chirality : 0.041 0.165 3786 Planarity : 0.003 0.043 4134 Dihedral : 5.703 172.090 3277 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.30 % Allowed : 14.14 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.16), residues: 2975 helix: 2.33 (0.14), residues: 1401 sheet: -0.08 (0.24), residues: 486 loop : -0.50 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3512 TYR 0.018 0.001 TYR C 219 PHE 0.023 0.001 PHE A2550 TRP 0.026 0.001 TRP A3762 HIS 0.002 0.000 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00199 (24285) covalent geometry : angle 0.48423 (32959) hydrogen bonds : bond 0.03093 ( 1274) hydrogen bonds : angle 3.85746 ( 3744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6030 (m-80) cc_final: 0.5157 (t80) REVERT: A 1557 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7684 (tp-100) REVERT: A 2222 ILE cc_start: 0.7681 (mm) cc_final: 0.7399 (mm) REVERT: A 2487 ASP cc_start: 0.7678 (t0) cc_final: 0.7082 (t0) REVERT: A 2488 GLU cc_start: 0.8056 (mp0) cc_final: 0.7634 (mp0) REVERT: A 2851 LYS cc_start: 0.8507 (pttm) cc_final: 0.8243 (pttp) REVERT: A 2942 ASP cc_start: 0.7697 (p0) cc_final: 0.7332 (t0) REVERT: A 2980 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.6165 (mmp) REVERT: A 3428 LEU cc_start: 0.7767 (mt) cc_final: 0.7467 (tt) REVERT: A 3680 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6436 (mp-120) REVERT: A 3702 MET cc_start: 0.8515 (mtt) cc_final: 0.8146 (mtm) REVERT: A 3873 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8041 (tpp) REVERT: A 4005 GLU cc_start: 0.8265 (tp30) cc_final: 0.7865 (tp30) REVERT: A 4071 LEU cc_start: 0.7688 (mt) cc_final: 0.7487 (pp) REVERT: C 242 LYS cc_start: 0.7066 (tptt) cc_final: 0.6632 (tttm) REVERT: C 260 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8265 (mmmt) REVERT: C 299 TRP cc_start: 0.7257 (p-90) cc_final: 0.6398 (p-90) outliers start: 33 outliers final: 24 residues processed: 273 average time/residue: 0.1428 time to fit residues: 63.9856 Evaluate side-chains 261 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2896 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3873 MET Chi-restraints excluded: chain A residue 3889 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 217 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 chunk 253 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2228 HIS B 336 HIS ** 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 = 0.3821 r_free = 0.3821 target = 0.135308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110777 restraints weight = 40277.808| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.45 r_work: 0.3372 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24285 Z= 0.181 Angle : 0.571 9.024 32959 Z= 0.288 Chirality : 0.044 0.180 3786 Planarity : 0.004 0.044 4134 Dihedral : 6.019 174.832 3277 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.30 % Allowed : 14.46 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2975 helix: 2.06 (0.14), residues: 1405 sheet: -0.35 (0.24), residues: 491 loop : -0.61 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2183 TYR 0.015 0.001 TYR C 219 PHE 0.021 0.002 PHE A1534 TRP 0.025 0.001 TRP A3762 HIS 0.009 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00433 (24285) covalent geometry : angle 0.57097 (32959) hydrogen bonds : bond 0.03737 ( 1274) hydrogen bonds : angle 4.05577 ( 3744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 1470 PHE cc_start: 0.6097 (m-80) cc_final: 0.5171 (t80) REVERT: A 1557 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7814 (tp-100) REVERT: A 2222 ILE cc_start: 0.7917 (mm) cc_final: 0.7473 (mm) REVERT: A 2487 ASP cc_start: 0.7862 (t0) cc_final: 0.7220 (t0) REVERT: A 2488 GLU cc_start: 0.8184 (mp0) cc_final: 0.7738 (mp0) REVERT: A 2851 LYS cc_start: 0.8513 (pttm) cc_final: 0.8257 (pttp) REVERT: A 2942 ASP cc_start: 0.7707 (p0) cc_final: 0.7415 (t0) REVERT: A 3428 LEU cc_start: 0.7911 (mt) cc_final: 0.7575 (tt) REVERT: A 3680 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6535 (mp-120) REVERT: A 3692 LYS cc_start: 0.7935 (tttt) cc_final: 0.7726 (ttmt) REVERT: A 3702 MET cc_start: 0.8572 (mtt) cc_final: 0.8201 (mtm) REVERT: A 3873 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8161 (tpp) REVERT: A 4071 LEU cc_start: 0.7750 (mt) cc_final: 0.7482 (pp) REVERT: C 260 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8304 (mmmt) REVERT: C 422 ASP cc_start: 0.7256 (t70) cc_final: 0.6961 (t0) outliers start: 33 outliers final: 25 residues processed: 251 average time/residue: 0.1461 time to fit residues: 60.7215 Evaluate side-chains 243 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2574 TYR Chi-restraints excluded: chain A residue 2686 LEU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2896 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3873 MET Chi-restraints excluded: chain A residue 3889 LEU Chi-restraints excluded: chain A residue 3980 ILE Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 TRP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 282 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 298 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 156 optimal weight: 0.0040 chunk 157 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.138106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113725 restraints weight = 39595.449| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.44 r_work: 0.3417 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24285 Z= 0.107 Angle : 0.516 8.762 32959 Z= 0.260 Chirality : 0.042 0.269 3786 Planarity : 0.003 0.043 4134 Dihedral : 5.914 174.437 3277 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.02 % Allowed : 15.05 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.16), residues: 2975 helix: 2.18 (0.14), residues: 1406 sheet: -0.22 (0.24), residues: 488 loop : -0.52 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3512 TYR 0.018 0.001 TYR A2571 PHE 0.023 0.001 PHE A2550 TRP 0.023 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00242 (24285) covalent geometry : angle 0.51638 (32959) hydrogen bonds : bond 0.03325 ( 1274) hydrogen bonds : angle 3.96794 ( 3744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4687.90 seconds wall clock time: 81 minutes 33.35 seconds (4893.35 seconds total)