Starting phenix.real_space_refine on Thu Sep 18 16:23:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkd_46953/09_2025/9dkd_46953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkd_46953/09_2025/9dkd_46953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dkd_46953/09_2025/9dkd_46953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkd_46953/09_2025/9dkd_46953.map" model { file = "/net/cci-nas-00/data/ceres_data/9dkd_46953/09_2025/9dkd_46953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkd_46953/09_2025/9dkd_46953.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 79 5.16 5 C 11468 2.51 5 N 2997 2.21 5 O 3347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17901 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2313, 17788 Classifications: {'peptide': 2313} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 62, 'TRANS': 2250} Chain breaks: 23 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 973 Unresolved non-hydrogen angles: 1204 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'ASN:plan1': 18, 'ARG:plan': 15, 'PHE:plan': 12, 'GLU:plan': 47, 'GLN:plan1': 10, 'HIS:plan': 3, 'ASP:plan': 25, 'TRP:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 565 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: 3.79, per 1000 atoms: 0.21 Number of scatterers: 17901 At special positions: 0 Unit cell: (114.681, 157.353, 154.686, 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 79 16.00 P 9 15.00 Mg 1 11.99 O 3347 8.00 N 2997 7.00 C 11468 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: 1.60 Conformation dependent library (CDL) restraints added in 915.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4408 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 14 sheets defined 63.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 1370 through 1380 Processing helix chain 'A' and resid 1397 through 1406 removed outlier: 3.721A pdb=" N LEU A1401 " --> pdb=" O GLU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1459 removed outlier: 4.739A pdb=" N ASP A1454 " --> pdb=" O PHE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1467 removed outlier: 4.250A pdb=" N GLN A1466 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1492 Processing helix chain 'A' and resid 1506 through 1534 Processing helix chain 'A' and resid 1536 through 1540 removed outlier: 3.776A 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 1561 through 1567 Processing helix chain 'A' and resid 1603 through 1632 Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.956A 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: 3.763A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.551A pdb=" N ASN A1717 " --> pdb=" O GLY A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1730 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.920A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1849 through 1853 removed outlier: 3.801A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1874 removed outlier: 3.553A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1874 " --> pdb=" O ASN A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 Processing helix chain 'A' and resid 1942 through 1960 Processing helix chain 'A' and resid 1969 through 1985 removed outlier: 3.635A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix Processing helix chain 'A' and resid 1990 through 2002 removed outlier: 3.621A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2008 through 2022 Processing helix chain 'A' and resid 2032 through 2046 Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2143 through 2146 removed outlier: 3.856A pdb=" N LYS A2146 " --> pdb=" O GLY A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2143 through 2146' Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2205 through 2210 removed outlier: 3.720A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.535A pdb=" N LYS A2225 " --> pdb=" O SER A2221 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2256 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.133A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 Processing helix chain 'A' and resid 2299 through 2302 removed outlier: 3.507A pdb=" N PHE A2302 " --> pdb=" O ARG A2299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2299 through 2302' Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2347 removed outlier: 3.779A pdb=" N GLY A2347 " --> pdb=" O ASN A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2374 No H-bonds generated for 'chain 'A' and resid 2372 through 2374' Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.706A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2381 through 2385' Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2432 Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 4.040A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2513 removed outlier: 3.623A pdb=" N LEU A2504 " --> pdb=" O GLN A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 3.541A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2606 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.983A 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 2657 through 2659 No H-bonds generated for 'chain 'A' and resid 2657 through 2659' 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 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2810 Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.816A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2844 removed outlier: 3.858A pdb=" N LEU A2843 " --> pdb=" O ILE A2840 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A2844 " --> pdb=" O PRO A2841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2840 through 2844' Processing helix chain 'A' and resid 2846 through 2860 Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2899 through 2905 removed outlier: 3.847A pdb=" N ILE A2903 " --> pdb=" O SER A2899 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A2904 " --> pdb=" O SER A2900 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2961 through 2980 Processing helix chain 'A' and resid 2989 through 3025 Processing helix chain 'A' and resid 3299 through 3334 removed outlier: 4.666A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3357 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 3.850A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3447 Processing helix chain 'A' and resid 3454 through 3458 Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3537 Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 3.633A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3593 through 3605 Processing helix chain 'A' and resid 3607 through 3618 Processing helix chain 'A' and resid 3619 through 3639 removed outlier: 3.538A pdb=" N GLY A3636 " --> pdb=" O LEU A3632 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A3637 " --> pdb=" O GLU A3633 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.896A 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 3708 Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.787A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3742 through 3752 Processing helix chain 'A' and resid 3755 through 3768 Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3808 Processing helix chain 'A' and resid 3818 through 3836 Processing helix chain 'A' and resid 3847 through 3860 removed outlier: 4.362A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.727A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3914 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.709A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 removed outlier: 3.595A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 3.644A pdb=" N GLU A4041 " --> pdb=" O SER A4037 " (cutoff:3.500A) Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.531A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1571 through 1574 removed outlier: 4.129A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.800A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A1582 " --> pdb=" O LEU A1590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1734 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.574A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2103 removed outlier: 6.737A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A2195 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A2070 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A2196 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A2072 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA7, first strand: chain 'A' and resid 2438 through 2440 removed outlier: 6.007A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 2438 through 2440 removed outlier: 6.007A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 2462 through 2465 removed outlier: 3.585A pdb=" N PHE A2515 " --> pdb=" O VAL A2524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB2, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.393A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3426 through 3429 removed outlier: 6.495A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3478 through 3481 Processing sheet with id=AB5, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 3.675A pdb=" N LYS A3812 " --> pdb=" O TRP A3838 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A3840 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A3786 " --> pdb=" O MET A3873 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3225 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: 4.29 Time building geometry restraints manager: 2.09 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: 5717 1.34 - 1.46: 3269 1.46 - 1.58: 9131 1.58 - 1.70: 11 1.70 - 1.81: 123 Bond restraints: 18251 Sorted by residual: bond pdb=" C LEU A2491 " pdb=" N PRO A2492 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.79e+00 bond pdb=" CD GLU A4005 " pdb=" OE1 GLU A4005 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.90e+00 bond pdb=" CG GLU A4005 " pdb=" CD GLU A4005 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" CB GLU A2374 " pdb=" CG GLU A2374 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CG LEU A1813 " pdb=" CD1 LEU A1813 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 ... (remaining 18246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 24204 1.85 - 3.71: 449 3.71 - 5.56: 75 5.56 - 7.42: 32 7.42 - 9.27: 6 Bond angle restraints: 24766 Sorted by residual: angle pdb=" C LEU A4004 " pdb=" N GLU A4005 " pdb=" CA GLU A4005 " ideal model delta sigma weight residual 121.58 112.31 9.27 1.95e+00 2.63e-01 2.26e+01 angle pdb=" C LEU A3945 " pdb=" N VAL A3946 " pdb=" CA VAL A3946 " ideal model delta sigma weight residual 120.33 123.91 -3.58 8.00e-01 1.56e+00 2.01e+01 angle pdb=" N GLU A4005 " pdb=" CA GLU A4005 " pdb=" CB GLU A4005 " ideal model delta sigma weight residual 110.41 116.98 -6.57 1.68e+00 3.54e-01 1.53e+01 angle pdb=" CA GLU A4005 " pdb=" CB GLU A4005 " pdb=" CG GLU A4005 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" N GLN A1449 " pdb=" CA GLN A1449 " pdb=" CB GLN A1449 " ideal model delta sigma weight residual 110.30 115.33 -5.03 1.54e+00 4.22e-01 1.07e+01 ... (remaining 24761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 10327 26.76 - 53.51: 478 53.51 - 80.27: 50 80.27 - 107.03: 6 107.03 - 133.79: 1 Dihedral angle restraints: 10862 sinusoidal: 4092 harmonic: 6770 Sorted by residual: dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 -134.67 -133.79 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" CA VAL A2440 " pdb=" C VAL A2440 " pdb=" N VAL A2441 " pdb=" CA VAL A2441 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LEU A2432 " pdb=" C LEU A2432 " pdb=" N ARG A2433 " pdb=" CA ARG A2433 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 10859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2666 0.081 - 0.162: 206 0.162 - 0.243: 6 0.243 - 0.324: 1 0.324 - 0.405: 1 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CB ILE A2150 " pdb=" CA ILE A2150 " pdb=" CG1 ILE A2150 " pdb=" CG2 ILE A2150 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CB ILE A2822 " pdb=" CA ILE A2822 " pdb=" CG1 ILE A2822 " pdb=" CG2 ILE A2822 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL A1639 " pdb=" CA VAL A1639 " pdb=" CG1 VAL A1639 " pdb=" CG2 VAL A1639 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2877 not shown) Planarity restraints: 3104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A2619 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A4005 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" CD GLU A4005 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU A4005 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A4005 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2003 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A2004 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A2004 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2004 " 0.028 5.00e-02 4.00e+02 ... (remaining 3101 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 214 2.64 - 3.20: 15865 3.20 - 3.77: 28658 3.77 - 4.33: 36861 4.33 - 4.90: 61836 Nonbonded interactions: 143434 Sorted by model distance: nonbonded pdb=" OD2 ASP A2487 " pdb="MG MG A4105 " model vdw 2.072 2.170 nonbonded pdb=" OE2 GLU A1661 " pdb=" OH TYR A1735 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A1966 " pdb=" OD2 ASP A2010 " model vdw 2.237 3.040 nonbonded pdb=" O LYS A1686 " pdb=" OG SER A1690 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A3954 " pdb=" OD2 ASP A4003 " model vdw 2.253 3.040 ... (remaining 143429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18251 Z= 0.150 Angle : 0.656 9.270 24766 Z= 0.338 Chirality : 0.044 0.405 2880 Planarity : 0.004 0.062 3104 Dihedral : 15.107 133.787 6454 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: 0.12 (0.17), residues: 2265 helix: 0.96 (0.14), residues: 1341 sheet: -0.76 (0.36), residues: 226 loop : -1.25 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2638 TYR 0.022 0.002 TYR A3679 PHE 0.029 0.002 PHE A3508 TRP 0.028 0.002 TRP A2084 HIS 0.010 0.001 HIS A1554 Details of bonding type rmsd covalent geometry : bond 0.00327 (18251) covalent geometry : angle 0.65593 (24766) hydrogen bonds : bond 0.12502 ( 1090) hydrogen bonds : angle 5.84695 ( 3225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2842 ASP cc_start: 0.6673 (p0) cc_final: 0.5116 (t0) REVERT: A 3398 MET cc_start: 0.6239 (tpp) cc_final: 0.5829 (tmm) REVERT: A 3696 MET cc_start: 0.6408 (mtp) cc_final: 0.5557 (tpp) REVERT: A 3798 PHE cc_start: 0.7304 (p90) cc_final: 0.7008 (p90) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1144 time to fit residues: 37.4521 Evaluate side-chains 165 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 GLN A1891 HIS A2971 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.198047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.167430 restraints weight = 26737.653| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.08 r_work: 0.3901 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18251 Z= 0.222 Angle : 0.617 8.030 24766 Z= 0.319 Chirality : 0.043 0.195 2880 Planarity : 0.004 0.051 3104 Dihedral : 7.038 137.175 2511 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.87 % Allowed : 8.60 % Favored : 90.53 % 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: 0.39 (0.17), residues: 2265 helix: 1.20 (0.14), residues: 1372 sheet: -0.87 (0.37), residues: 213 loop : -1.24 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2624 TYR 0.022 0.002 TYR A2571 PHE 0.033 0.002 PHE A1820 TRP 0.025 0.002 TRP A2084 HIS 0.007 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00526 (18251) covalent geometry : angle 0.61742 (24766) hydrogen bonds : bond 0.04369 ( 1090) hydrogen bonds : angle 4.59941 ( 3225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1673 TRP cc_start: 0.7361 (t60) cc_final: 0.7121 (t60) REVERT: A 1788 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: A 2316 LEU cc_start: 0.6487 (tp) cc_final: 0.6074 (tp) REVERT: A 2544 ILE cc_start: 0.6832 (mt) cc_final: 0.6622 (mt) REVERT: A 2842 ASP cc_start: 0.7085 (p0) cc_final: 0.5388 (t0) REVERT: A 3696 MET cc_start: 0.6737 (mtp) cc_final: 0.5781 (tpp) REVERT: A 3873 MET cc_start: 0.7669 (ptm) cc_final: 0.7301 (ptt) outliers start: 16 outliers final: 8 residues processed: 192 average time/residue: 0.1221 time to fit residues: 36.7350 Evaluate side-chains 173 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 4051 ASN Chi-restraints excluded: chain A residue 4053 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 218 optimal weight: 0.5980 chunk 224 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A2490 ASN A2741 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.201463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.172796 restraints weight = 27162.702| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.96 r_work: 0.3993 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18251 Z= 0.118 Angle : 0.510 9.355 24766 Z= 0.261 Chirality : 0.039 0.169 2880 Planarity : 0.003 0.044 3104 Dihedral : 6.780 135.640 2511 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.81 % Allowed : 11.58 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2265 helix: 1.65 (0.14), residues: 1371 sheet: -0.78 (0.37), residues: 206 loop : -1.09 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2624 TYR 0.015 0.001 TYR A2571 PHE 0.023 0.001 PHE A1820 TRP 0.032 0.001 TRP A2301 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00259 (18251) covalent geometry : angle 0.51037 (24766) hydrogen bonds : bond 0.03650 ( 1090) hydrogen bonds : angle 4.21549 ( 3225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2166 MET cc_start: 0.6001 (tpp) cc_final: 0.5766 (tpt) REVERT: A 2316 LEU cc_start: 0.6400 (tp) cc_final: 0.5975 (tp) REVERT: A 2831 MET cc_start: 0.6541 (mpp) cc_final: 0.6129 (mtm) REVERT: A 2842 ASP cc_start: 0.7015 (p0) cc_final: 0.5377 (t0) REVERT: A 3696 MET cc_start: 0.6554 (mtp) cc_final: 0.5702 (tpp) REVERT: A 3698 MET cc_start: 0.6738 (tmm) cc_final: 0.6180 (ttp) REVERT: A 3798 PHE cc_start: 0.6813 (p90) cc_final: 0.6526 (p90) REVERT: A 4076 LEU cc_start: 0.7852 (mp) cc_final: 0.7622 (mp) outliers start: 15 outliers final: 8 residues processed: 192 average time/residue: 0.1219 time to fit residues: 36.3278 Evaluate side-chains 176 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2097 HIS Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 3856 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 21 optimal weight: 1.9990 chunk 150 optimal weight: 0.0370 chunk 79 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A3685 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.200656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.172187 restraints weight = 27036.059| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.90 r_work: 0.3983 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18251 Z= 0.128 Angle : 0.518 8.868 24766 Z= 0.264 Chirality : 0.039 0.175 2880 Planarity : 0.003 0.045 3104 Dihedral : 6.710 134.134 2511 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.68 % Allowed : 12.50 % Favored : 85.82 % 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: 1.05 (0.18), residues: 2265 helix: 1.79 (0.14), residues: 1368 sheet: -0.76 (0.37), residues: 206 loop : -1.05 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1583 TYR 0.015 0.001 TYR A2571 PHE 0.031 0.001 PHE A1476 TRP 0.023 0.001 TRP A2084 HIS 0.004 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00292 (18251) covalent geometry : angle 0.51778 (24766) hydrogen bonds : bond 0.03589 ( 1090) hydrogen bonds : angle 4.12682 ( 3225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1788 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: A 2316 LEU cc_start: 0.6413 (tp) cc_final: 0.6008 (tp) REVERT: A 2544 ILE cc_start: 0.6729 (mt) cc_final: 0.6518 (mt) REVERT: A 2831 MET cc_start: 0.6502 (mpp) cc_final: 0.6000 (mtm) REVERT: A 2842 ASP cc_start: 0.7041 (p0) cc_final: 0.5434 (t0) REVERT: A 3696 MET cc_start: 0.6603 (mtp) cc_final: 0.5899 (tpp) REVERT: A 3698 MET cc_start: 0.6793 (tmm) cc_final: 0.6545 (tmm) REVERT: A 3798 PHE cc_start: 0.6710 (p90) cc_final: 0.6463 (p90) outliers start: 31 outliers final: 17 residues processed: 196 average time/residue: 0.1119 time to fit residues: 34.8773 Evaluate side-chains 186 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1574 PHE Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2097 HIS Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain A residue 3943 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 36 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 209 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A3685 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.201280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.172756 restraints weight = 26941.219| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.91 r_work: 0.3990 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18251 Z= 0.115 Angle : 0.508 12.562 24766 Z= 0.256 Chirality : 0.039 0.162 2880 Planarity : 0.003 0.043 3104 Dihedral : 6.600 132.670 2511 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.62 % Allowed : 13.31 % Favored : 85.06 % 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: 1.23 (0.18), residues: 2265 helix: 1.94 (0.14), residues: 1368 sheet: -0.66 (0.37), residues: 206 loop : -1.00 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2624 TYR 0.014 0.001 TYR A2571 PHE 0.017 0.001 PHE A3763 TRP 0.023 0.001 TRP A1452 HIS 0.003 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00255 (18251) covalent geometry : angle 0.50767 (24766) hydrogen bonds : bond 0.03430 ( 1090) hydrogen bonds : angle 4.02471 ( 3225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1788 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: A 2316 LEU cc_start: 0.6394 (tp) cc_final: 0.5994 (tp) REVERT: A 2544 ILE cc_start: 0.6785 (mt) cc_final: 0.6578 (mt) REVERT: A 2831 MET cc_start: 0.6495 (mpp) cc_final: 0.5908 (mtm) REVERT: A 3696 MET cc_start: 0.6527 (mtp) cc_final: 0.5768 (tpp) REVERT: A 3698 MET cc_start: 0.6711 (tmm) cc_final: 0.6444 (tmm) outliers start: 30 outliers final: 20 residues processed: 199 average time/residue: 0.1212 time to fit residues: 37.7231 Evaluate side-chains 187 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1574 PHE Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2097 HIS Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 4 optimal weight: 9.9990 chunk 97 optimal weight: 0.0270 chunk 56 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 116 optimal weight: 0.2980 chunk 225 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A2536 ASN A2971 HIS A3685 GLN A3975 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.202322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.172643 restraints weight = 26787.504| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.85 r_work: 0.4007 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18251 Z= 0.105 Angle : 0.512 17.069 24766 Z= 0.255 Chirality : 0.039 0.251 2880 Planarity : 0.003 0.043 3104 Dihedral : 6.499 130.882 2511 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.84 % Allowed : 13.74 % Favored : 84.42 % 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: 1.35 (0.18), residues: 2265 helix: 2.02 (0.14), residues: 1376 sheet: -0.58 (0.37), residues: 206 loop : -0.95 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1583 TYR 0.013 0.001 TYR A2571 PHE 0.036 0.001 PHE A3798 TRP 0.025 0.001 TRP A2301 HIS 0.004 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00227 (18251) covalent geometry : angle 0.51163 (24766) hydrogen bonds : bond 0.03335 ( 1090) hydrogen bonds : angle 3.96766 ( 3225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1727 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7770 (tt) REVERT: A 1788 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: A 2316 LEU cc_start: 0.6338 (tp) cc_final: 0.5938 (tp) REVERT: A 2544 ILE cc_start: 0.6835 (mt) cc_final: 0.6629 (mt) REVERT: A 3346 LEU cc_start: 0.2281 (OUTLIER) cc_final: 0.2076 (mt) REVERT: A 3696 MET cc_start: 0.6495 (mtp) cc_final: 0.5737 (tpp) outliers start: 34 outliers final: 20 residues processed: 190 average time/residue: 0.1213 time to fit residues: 36.0465 Evaluate side-chains 186 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1538 TYR Chi-restraints excluded: chain A residue 1574 PHE Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2097 HIS Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2735 HIS Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain A residue 3943 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 149 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2068 GLN A2201 HIS ** A2753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.194987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.167244 restraints weight = 27066.265| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.06 r_work: 0.3850 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 18251 Z= 0.261 Angle : 0.670 15.332 24766 Z= 0.339 Chirality : 0.044 0.257 2880 Planarity : 0.004 0.040 3104 Dihedral : 7.075 138.959 2511 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.16 % Allowed : 14.07 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2265 helix: 1.51 (0.14), residues: 1368 sheet: -0.90 (0.37), residues: 209 loop : -1.13 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1978 TYR 0.026 0.002 TYR A2571 PHE 0.041 0.002 PHE A1820 TRP 0.027 0.002 TRP A2301 HIS 0.008 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00629 (18251) covalent geometry : angle 0.66995 (24766) hydrogen bonds : bond 0.04337 ( 1090) hydrogen bonds : angle 4.41718 ( 3225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 1727 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7796 (tt) REVERT: A 1788 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: A 2781 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7809 (mm) REVERT: A 2842 ASP cc_start: 0.6969 (p0) cc_final: 0.5701 (t70) REVERT: A 2971 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.6231 (m90) REVERT: A 3346 LEU cc_start: 0.2861 (OUTLIER) cc_final: 0.2578 (mt) outliers start: 40 outliers final: 25 residues processed: 200 average time/residue: 0.1077 time to fit residues: 34.5929 Evaluate side-chains 194 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1574 PHE Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1818 VAL Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2097 HIS Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2735 HIS Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3003 VAL Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 152 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 217 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A3685 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.198978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.170898 restraints weight = 26893.891| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.98 r_work: 0.3934 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18251 Z= 0.131 Angle : 0.557 15.940 24766 Z= 0.279 Chirality : 0.040 0.266 2880 Planarity : 0.003 0.040 3104 Dihedral : 6.871 138.005 2511 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 14.77 % Favored : 83.55 % 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: 1.05 (0.18), residues: 2265 helix: 1.80 (0.14), residues: 1369 sheet: -0.85 (0.37), residues: 206 loop : -1.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2624 TYR 0.017 0.001 TYR A2571 PHE 0.052 0.002 PHE A2909 TRP 0.026 0.001 TRP A2084 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00297 (18251) covalent geometry : angle 0.55667 (24766) hydrogen bonds : bond 0.03668 ( 1090) hydrogen bonds : angle 4.15319 ( 3225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1485 MET cc_start: 0.7794 (ptm) cc_final: 0.7335 (ppp) REVERT: A 1727 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 1788 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: A 2222 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7530 (mp) REVERT: A 2316 LEU cc_start: 0.6970 (tt) cc_final: 0.5831 (tp) REVERT: A 2544 ILE cc_start: 0.6759 (mt) cc_final: 0.6555 (mt) REVERT: A 2831 MET cc_start: 0.6593 (mpp) cc_final: 0.6114 (mtm) REVERT: A 2842 ASP cc_start: 0.6962 (p0) cc_final: 0.5809 (t70) REVERT: A 3346 LEU cc_start: 0.2579 (OUTLIER) cc_final: 0.2370 (mt) REVERT: A 3696 MET cc_start: 0.6758 (mtp) cc_final: 0.5825 (tpp) outliers start: 31 outliers final: 19 residues processed: 191 average time/residue: 0.1150 time to fit residues: 34.9186 Evaluate side-chains 186 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2097 HIS Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2735 HIS Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 52 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A2351 GLN ** A2753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2971 HIS A3685 GLN A3975 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.194918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.164644 restraints weight = 26736.467| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.09 r_work: 0.3850 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18251 Z= 0.247 Angle : 0.667 15.958 24766 Z= 0.336 Chirality : 0.044 0.265 2880 Planarity : 0.004 0.042 3104 Dihedral : 7.117 140.352 2511 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.95 % Allowed : 14.83 % Favored : 83.23 % 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: 0.65 (0.18), residues: 2265 helix: 1.46 (0.14), residues: 1372 sheet: -1.07 (0.37), residues: 208 loop : -1.13 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1583 TYR 0.024 0.002 TYR A2558 PHE 0.026 0.002 PHE A2976 TRP 0.022 0.002 TRP A2301 HIS 0.007 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00594 (18251) covalent geometry : angle 0.66676 (24766) hydrogen bonds : bond 0.04276 ( 1090) hydrogen bonds : angle 4.42586 ( 3225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 1485 MET cc_start: 0.7916 (ptm) cc_final: 0.7401 (ppp) REVERT: A 1727 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7806 (tt) REVERT: A 1788 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: A 2222 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7765 (mp) REVERT: A 2346 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: A 2544 ILE cc_start: 0.6754 (mt) cc_final: 0.6547 (mt) REVERT: A 2831 MET cc_start: 0.6651 (mpp) cc_final: 0.6241 (mtm) REVERT: A 2842 ASP cc_start: 0.7220 (p0) cc_final: 0.6098 (t70) outliers start: 36 outliers final: 24 residues processed: 194 average time/residue: 0.1174 time to fit residues: 35.7016 Evaluate side-chains 190 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1818 VAL Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2735 HIS Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3003 VAL Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain A residue 4076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 194 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS A2971 HIS A3413 HIS A3685 GLN A3975 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.197337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.169103 restraints weight = 26623.898| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.97 r_work: 0.3907 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18251 Z= 0.160 Angle : 0.592 16.270 24766 Z= 0.298 Chirality : 0.041 0.264 2880 Planarity : 0.003 0.041 3104 Dihedral : 6.995 140.323 2511 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.89 % Allowed : 15.15 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2265 helix: 1.61 (0.14), residues: 1374 sheet: -1.02 (0.37), residues: 208 loop : -1.03 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1583 TYR 0.018 0.001 TYR A2571 PHE 0.029 0.002 PHE A1476 TRP 0.026 0.002 TRP A2301 HIS 0.007 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00375 (18251) covalent geometry : angle 0.59215 (24766) hydrogen bonds : bond 0.03855 ( 1090) hydrogen bonds : angle 4.26839 ( 3225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1485 MET cc_start: 0.7836 (ptm) cc_final: 0.7371 (ppp) REVERT: A 1727 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7740 (tt) REVERT: A 1788 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: A 2316 LEU cc_start: 0.7078 (tt) cc_final: 0.5818 (tp) REVERT: A 2346 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5647 (m-80) REVERT: A 2781 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7763 (mm) REVERT: A 2831 MET cc_start: 0.6608 (mpp) cc_final: 0.6183 (mtm) REVERT: A 2842 ASP cc_start: 0.7141 (p0) cc_final: 0.6080 (t70) outliers start: 35 outliers final: 28 residues processed: 187 average time/residue: 0.1233 time to fit residues: 36.7798 Evaluate side-chains 190 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1788 GLN Chi-restraints excluded: chain A residue 1818 VAL Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2063 MET Chi-restraints excluded: chain A residue 2262 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2735 HIS Chi-restraints excluded: chain A residue 2781 ILE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 3003 VAL Chi-restraints excluded: chain A residue 3685 GLN Chi-restraints excluded: chain A residue 3700 MET Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3763 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain A residue 4076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 228 optimal weight: 0.0770 chunk 101 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2971 HIS A3685 GLN A3975 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.197511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167579 restraints weight = 26880.516| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.14 r_work: 0.3892 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.286 18251 Z= 0.179 Angle : 0.781 59.194 24766 Z= 0.427 Chirality : 0.043 0.635 2880 Planarity : 0.003 0.039 3104 Dihedral : 6.994 140.411 2511 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.89 % Allowed : 15.10 % Favored : 83.01 % Cbeta Deviations : 0.05 % 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: 0.87 (0.18), residues: 2265 helix: 1.63 (0.14), residues: 1374 sheet: -1.02 (0.37), residues: 208 loop : -1.01 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1583 TYR 0.018 0.001 TYR A2571 PHE 0.024 0.002 PHE A1476 TRP 0.026 0.001 TRP A2084 HIS 0.007 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00431 (18251) covalent geometry : angle 0.78066 (24766) hydrogen bonds : bond 0.03874 ( 1090) hydrogen bonds : angle 4.28310 ( 3225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3734.38 seconds wall clock time: 64 minutes 55.51 seconds (3895.51 seconds total)