Starting phenix.real_space_refine on Thu Sep 18 16:38:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9diu_46919/09_2025/9diu_46919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9diu_46919/09_2025/9diu_46919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9diu_46919/09_2025/9diu_46919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9diu_46919/09_2025/9diu_46919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9diu_46919/09_2025/9diu_46919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9diu_46919/09_2025/9diu_46919.map" } resolution = 4.1 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= 0.000 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 79 5.16 5 C 11444 2.51 5 N 2976 2.21 5 O 3339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 17847 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2302, 17735 Classifications: {'peptide': 2302} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 62, 'TRANS': 2239} Chain breaks: 23 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 915 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 758 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ASN:plan1': 17, 'ARG:plan': 15, 'GLU:plan': 45, 'GLN:plan1': 10, 'HIS:plan': 4, 'ASP:plan': 25, 'PHE:plan': 9, 'TRP:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 543 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.27, per 1000 atoms: 0.18 Number of scatterers: 17847 At special positions: 0 Unit cell: (107.88, 150.8, 155.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 9 15.00 O 3339 8.00 N 2976 7.00 C 11444 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: 1.57 Conformation dependent library (CDL) restraints added in 643.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 14 sheets defined 63.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 1370 through 1380 Processing helix chain 'A' and resid 1397 through 1406 removed outlier: 3.731A pdb=" N LEU A1401 " --> pdb=" O GLU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1460 removed outlier: 4.295A pdb=" N ASP A1454 " --> pdb=" O PHE A1450 " (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 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1561 through 1566 removed outlier: 3.990A pdb=" N PHE A1566 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.507A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1641 removed outlier: 3.577A pdb=" N VAL A1640 " --> pdb=" O GLU A1637 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A1641 " --> pdb=" O VAL A1638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1637 through 1641' Processing helix chain 'A' and resid 1644 through 1666 removed outlier: 3.938A pdb=" N THR A1666 " --> pdb=" O LYS A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1689 removed outlier: 3.821A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1716 Processing helix chain 'A' and resid 1720 through 1729 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.144A 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 removed outlier: 3.820A pdb=" N LEU A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1853 removed outlier: 3.557A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1937 removed outlier: 3.507A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1960 removed outlier: 3.777A pdb=" N CYS A1960 " --> pdb=" O LEU A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1988 removed outlier: 4.247A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 3.662A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2006 removed outlier: 3.661A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A2003 " --> pdb=" O LYS A1999 " (cutoff:3.500A) Proline residue: A2004 - end of helix 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 removed outlier: 3.531A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2146 removed outlier: 3.924A 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 2171 removed outlier: 3.967A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A2168 " --> pdb=" O GLU A2164 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2210 removed outlier: 4.092A pdb=" N THR A2208 " --> pdb=" O PRO A2204 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.684A pdb=" N LEU A2237 " --> pdb=" O SER A2233 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2257 removed outlier: 3.645A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.035A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2298 Processing helix chain 'A' and resid 2299 through 2302 removed outlier: 3.849A 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 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 2382 through 2387 removed outlier: 3.605A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 4.216A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2513 removed outlier: 3.758A pdb=" N LEU A2504 " --> pdb=" O GLN A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.909A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2586 removed outlier: 3.623A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.939A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 4.167A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2751 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2792 through 2810 Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 4.191A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2860 Processing helix chain 'A' and resid 2870 through 2883 Processing helix chain 'A' and resid 2899 through 2905 Processing helix chain 'A' and resid 2905 through 2912 removed outlier: 4.299A pdb=" N ARG A2911 " --> pdb=" O ALA A2907 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A2912 " --> pdb=" O LEU A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 removed outlier: 4.110A pdb=" N ASP A2934 " --> pdb=" O ASN A2930 " (cutoff:3.500A) 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: 4.590A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 3.890A 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 3372 through 3381 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3423 Processing helix chain 'A' and resid 3436 through 3447 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 Processing helix chain 'A' and resid 3593 through 3605 Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 3.604A pdb=" N TYR A3618 " --> pdb=" O LEU A3614 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3639 removed outlier: 3.717A pdb=" N GLY A3636 " --> pdb=" O LEU A3632 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A3637 " --> pdb=" O GLU A3633 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3659 Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 4.009A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.515A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3742 through 3754 removed outlier: 3.892A pdb=" N TYR A3746 " --> pdb=" O ASP A3742 " (cutoff:3.500A) 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 3807 Processing helix chain 'A' and resid 3818 through 3836 Processing helix chain 'A' and resid 3847 through 3860 removed outlier: 4.330A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.719A pdb=" N LEU A3889 " --> pdb=" O PRO A3885 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3885 through 3891' Processing helix chain 'A' and resid 3902 through 3914 removed outlier: 3.627A pdb=" N THR A3906 " --> pdb=" O GLY A3902 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 4.024A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.847A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 removed outlier: 3.755A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 4.362A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.746A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.720A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (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 1896 through 1898 Processing sheet with id=AA4, first strand: chain 'A' and resid 1818 through 1819 removed outlier: 6.228A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA6, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.603A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP A2155 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A2104 " --> pdb=" O ASP A2155 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A2191 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A2152 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2357 through 2360 removed outlier: 3.518A pdb=" N THR A2358 " --> pdb=" O SER A2369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 5.750A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB1, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.790A pdb=" N SER A2697 " --> pdb=" O LYS A2705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2780 through 2781 removed outlier: 6.300A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A2888 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N MET A2757 " --> pdb=" O TRP A2916 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY A2918 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A2759 " --> pdb=" O GLY A2918 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3406 through 3408 removed outlier: 6.028A pdb=" N LEU A3407 " --> pdb=" O SER A3498 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 3470 through 3471 Processing sheet with id=AB5, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 5.887A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 3186 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: 4.00 Time building geometry restraints manager: 1.96 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: 5704 1.34 - 1.46: 4271 1.46 - 1.58: 8085 1.58 - 1.70: 12 1.70 - 1.82: 123 Bond restraints: 18195 Sorted by residual: bond pdb=" C VAL A3946 " pdb=" N PRO A3947 " ideal model delta sigma weight residual 1.336 1.362 -0.026 9.80e-03 1.04e+04 6.89e+00 bond pdb=" CB ARG A2044 " pdb=" CG ARG A2044 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CA ASN A2099 " pdb=" CB ASN A2099 " ideal model delta sigma weight residual 1.532 1.555 -0.024 1.74e-02 3.30e+03 1.84e+00 bond pdb=" CB ASN A2099 " pdb=" CG ASN A2099 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CB GLU A3536 " pdb=" CG GLU A3536 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 ... (remaining 18190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 24123 2.02 - 4.03: 431 4.03 - 6.05: 103 6.05 - 8.06: 26 8.06 - 10.08: 7 Bond angle restraints: 24690 Sorted by residual: angle pdb=" C SER A3630 " pdb=" N MET A3631 " pdb=" CA MET A3631 " ideal model delta sigma weight residual 121.14 114.37 6.77 1.75e+00 3.27e-01 1.50e+01 angle pdb=" N VAL A3769 " pdb=" CA VAL A3769 " pdb=" C VAL A3769 " ideal model delta sigma weight residual 113.53 109.79 3.74 9.80e-01 1.04e+00 1.45e+01 angle pdb=" C THR A2083 " pdb=" N TRP A2084 " pdb=" CA TRP A2084 " ideal model delta sigma weight residual 120.68 114.68 6.00 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CA TRP A2084 " pdb=" CB TRP A2084 " pdb=" CG TRP A2084 " ideal model delta sigma weight residual 113.60 120.24 -6.64 1.90e+00 2.77e-01 1.22e+01 angle pdb=" N MET A2938 " pdb=" CA MET A2938 " pdb=" C MET A2938 " ideal model delta sigma weight residual 114.56 110.27 4.29 1.27e+00 6.20e-01 1.14e+01 ... (remaining 24685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 10109 23.82 - 47.65: 659 47.65 - 71.47: 51 71.47 - 95.29: 16 95.29 - 119.12: 1 Dihedral angle restraints: 10836 sinusoidal: 4099 harmonic: 6737 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 -149.34 -119.12 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" CA MET A2756 " pdb=" C MET A2756 " pdb=" N MET A2757 " pdb=" CA MET A2757 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN A2931 " pdb=" C ASN A2931 " pdb=" N MET A2932 " pdb=" CA MET A2932 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 10833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2386 0.058 - 0.116: 437 0.116 - 0.174: 45 0.174 - 0.232: 8 0.232 - 0.290: 2 Chirality restraints: 2878 Sorted by residual: 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 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE A2544 " pdb=" CA ILE A2544 " pdb=" CG1 ILE A2544 " pdb=" CG2 ILE A2544 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE A1476 " pdb=" N PHE A1476 " pdb=" C PHE A1476 " pdb=" CB PHE A1476 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2875 not shown) Planarity restraints: 3091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2209 " 0.209 9.50e-02 1.11e+02 9.39e-02 5.63e+00 pdb=" NE ARG A2209 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A2209 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A2209 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A2209 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A2619 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1772 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A1773 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1773 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1773 " 0.029 5.00e-02 4.00e+02 ... (remaining 3088 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4121 2.79 - 3.31: 17601 3.31 - 3.84: 31032 3.84 - 4.37: 33402 4.37 - 4.90: 56906 Nonbonded interactions: 143062 Sorted by model distance: nonbonded pdb=" OG SER A1559 " pdb=" OG SER A1571 " model vdw 2.257 3.040 nonbonded pdb=" O LYS A1686 " pdb=" OG SER A1690 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A3400 " pdb=" O ALA A3403 " model vdw 2.279 3.040 nonbonded pdb=" O THR A2631 " pdb=" OG1 THR A2635 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN A2409 " pdb=" OH TYR A2438 " model vdw 2.311 3.040 ... (remaining 143057 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.890 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 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 0.044 18195 Z= 0.147 Angle : 0.716 10.081 24690 Z= 0.363 Chirality : 0.045 0.290 2878 Planarity : 0.005 0.094 3091 Dihedral : 14.950 119.115 6450 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.17), residues: 2254 helix: 0.61 (0.14), residues: 1347 sheet: 0.12 (0.44), residues: 171 loop : -1.28 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3514 TYR 0.026 0.001 TYR A1538 PHE 0.016 0.001 PHE A2992 TRP 0.026 0.001 TRP A2775 HIS 0.003 0.001 HIS A3948 Details of bonding type rmsd covalent geometry : bond 0.00288 (18195) covalent geometry : angle 0.71569 (24690) hydrogen bonds : bond 0.12190 ( 1079) hydrogen bonds : angle 5.82967 ( 3186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8535 (pmm) cc_final: 0.8108 (pmm) REVERT: A 2428 MET cc_start: 0.8683 (tmm) cc_final: 0.8352 (tmm) REVERT: A 2742 ILE cc_start: 0.8121 (pt) cc_final: 0.7912 (pt) REVERT: A 2977 TYR cc_start: 0.7335 (m-80) cc_final: 0.6992 (m-80) REVERT: A 2992 PHE cc_start: 0.8724 (t80) cc_final: 0.8398 (t80) REVERT: A 3316 THR cc_start: 0.6820 (m) cc_final: 0.6597 (p) REVERT: A 3414 MET cc_start: 0.7985 (mtp) cc_final: 0.7580 (mtp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1225 time to fit residues: 33.9372 Evaluate side-chains 126 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3761 ASN A3948 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.104653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084625 restraints weight = 89779.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086116 restraints weight = 64743.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.086694 restraints weight = 43196.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087011 restraints weight = 40651.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.087021 restraints weight = 34225.669| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18195 Z= 0.170 Angle : 0.591 8.406 24690 Z= 0.306 Chirality : 0.040 0.160 2878 Planarity : 0.004 0.054 3091 Dihedral : 6.112 119.514 2498 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % 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: 0.54 (0.18), residues: 2254 helix: 1.25 (0.14), residues: 1359 sheet: 0.03 (0.42), residues: 173 loop : -1.23 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2507 TYR 0.020 0.001 TYR A1705 PHE 0.016 0.001 PHE A3767 TRP 0.017 0.001 TRP A2084 HIS 0.006 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00364 (18195) covalent geometry : angle 0.59051 (24690) hydrogen bonds : bond 0.04112 ( 1079) hydrogen bonds : angle 4.75551 ( 3186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2592 PHE cc_start: 0.7705 (m-80) cc_final: 0.7420 (m-80) REVERT: A 2742 ILE cc_start: 0.8267 (pt) cc_final: 0.8055 (pt) REVERT: A 2835 LEU cc_start: 0.8273 (mt) cc_final: 0.7873 (tp) REVERT: A 2992 PHE cc_start: 0.8690 (t80) cc_final: 0.8374 (t80) REVERT: A 3414 MET cc_start: 0.8379 (mtp) cc_final: 0.7955 (mtp) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1480 time to fit residues: 36.0366 Evaluate side-chains 126 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 104 optimal weight: 0.1980 chunk 128 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.0020 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.107888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.089166 restraints weight = 92449.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.089308 restraints weight = 71398.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.090355 restraints weight = 57524.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.090883 restraints weight = 42342.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.090814 restraints weight = 38708.377| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18195 Z= 0.125 Angle : 0.553 7.293 24690 Z= 0.282 Chirality : 0.039 0.150 2878 Planarity : 0.003 0.048 3091 Dihedral : 6.029 119.698 2498 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2254 helix: 1.50 (0.14), residues: 1359 sheet: -0.04 (0.42), residues: 172 loop : -1.13 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1725 TYR 0.018 0.001 TYR A1538 PHE 0.020 0.001 PHE A1476 TRP 0.017 0.001 TRP A2084 HIS 0.003 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00264 (18195) covalent geometry : angle 0.55316 (24690) hydrogen bonds : bond 0.03809 ( 1079) hydrogen bonds : angle 4.52733 ( 3186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1456 TYR cc_start: 0.7823 (t80) cc_final: 0.7522 (t80) REVERT: A 1580 THR cc_start: 0.7885 (t) cc_final: 0.7666 (m) REVERT: A 2546 MET cc_start: 0.6544 (tpp) cc_final: 0.6309 (tpp) REVERT: A 2742 ILE cc_start: 0.8188 (pt) cc_final: 0.7986 (pt) REVERT: A 2835 LEU cc_start: 0.8223 (mt) cc_final: 0.7911 (tt) REVERT: A 2992 PHE cc_start: 0.8622 (t80) cc_final: 0.8303 (t80) REVERT: A 3414 MET cc_start: 0.8425 (mtp) cc_final: 0.8017 (mtp) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1552 time to fit residues: 39.5439 Evaluate side-chains 126 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 126 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 136 optimal weight: 0.0170 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3761 ASN A3948 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.104603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085986 restraints weight = 91255.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.085810 restraints weight = 63797.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.086806 restraints weight = 55616.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087355 restraints weight = 41624.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087430 restraints weight = 34020.467| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18195 Z= 0.197 Angle : 0.633 9.612 24690 Z= 0.324 Chirality : 0.042 0.206 2878 Planarity : 0.004 0.065 3091 Dihedral : 6.136 121.868 2498 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2254 helix: 1.35 (0.14), residues: 1359 sheet: -0.25 (0.41), residues: 182 loop : -1.16 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A3792 TYR 0.025 0.002 TYR A1538 PHE 0.029 0.002 PHE A1779 TRP 0.018 0.001 TRP A2084 HIS 0.005 0.001 HIS A2530 Details of bonding type rmsd covalent geometry : bond 0.00430 (18195) covalent geometry : angle 0.63285 (24690) hydrogen bonds : bond 0.04094 ( 1079) hydrogen bonds : angle 4.66763 ( 3186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2299 ARG cc_start: 0.6740 (ttt180) cc_final: 0.6469 (ttt180) REVERT: A 2546 MET cc_start: 0.6410 (tpp) cc_final: 0.6201 (tpp) REVERT: A 2580 LYS cc_start: 0.8960 (mmpt) cc_final: 0.8597 (mmmt) REVERT: A 2742 ILE cc_start: 0.8223 (pt) cc_final: 0.8012 (pt) REVERT: A 2835 LEU cc_start: 0.8294 (mt) cc_final: 0.7940 (tt) REVERT: A 2992 PHE cc_start: 0.8592 (t80) cc_final: 0.8308 (t80) REVERT: A 3414 MET cc_start: 0.8381 (mtp) cc_final: 0.8016 (mtp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1517 time to fit residues: 36.1859 Evaluate side-chains 125 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 169 optimal weight: 0.0030 chunk 37 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.107954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.089438 restraints weight = 92191.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.089998 restraints weight = 70880.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.091309 restraints weight = 50044.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.091312 restraints weight = 39922.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.091634 restraints weight = 35861.976| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18195 Z= 0.116 Angle : 0.558 7.148 24690 Z= 0.283 Chirality : 0.040 0.152 2878 Planarity : 0.003 0.046 3091 Dihedral : 5.953 118.209 2498 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.18), residues: 2254 helix: 1.57 (0.14), residues: 1361 sheet: -0.11 (0.42), residues: 172 loop : -1.01 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3468 TYR 0.029 0.001 TYR A1538 PHE 0.021 0.001 PHE A3653 TRP 0.020 0.001 TRP A2084 HIS 0.003 0.001 HIS A2453 Details of bonding type rmsd covalent geometry : bond 0.00245 (18195) covalent geometry : angle 0.55785 (24690) hydrogen bonds : bond 0.03716 ( 1079) hydrogen bonds : angle 4.42125 ( 3186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1779 PHE cc_start: 0.7331 (m-80) cc_final: 0.7100 (m-80) REVERT: A 2835 LEU cc_start: 0.8258 (mt) cc_final: 0.7847 (tt) REVERT: A 2992 PHE cc_start: 0.8642 (t80) cc_final: 0.8401 (t80) REVERT: A 3414 MET cc_start: 0.8351 (mtp) cc_final: 0.7928 (mtp) REVERT: A 3440 LEU cc_start: 0.9308 (mt) cc_final: 0.9089 (pp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1439 time to fit residues: 37.1080 Evaluate side-chains 124 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.105138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.084301 restraints weight = 89292.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.086099 restraints weight = 56013.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087333 restraints weight = 40204.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.088067 restraints weight = 32142.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.088728 restraints weight = 27762.465| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18195 Z= 0.122 Angle : 0.560 8.103 24690 Z= 0.283 Chirality : 0.040 0.159 2878 Planarity : 0.003 0.049 3091 Dihedral : 5.762 105.686 2498 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.99 (0.18), residues: 2254 helix: 1.66 (0.14), residues: 1357 sheet: -0.13 (0.42), residues: 172 loop : -1.04 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1725 TYR 0.025 0.001 TYR A1538 PHE 0.012 0.001 PHE A2194 TRP 0.019 0.001 TRP A2084 HIS 0.003 0.001 HIS A2453 Details of bonding type rmsd covalent geometry : bond 0.00263 (18195) covalent geometry : angle 0.55973 (24690) hydrogen bonds : bond 0.03635 ( 1079) hydrogen bonds : angle 4.36339 ( 3186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.7788 (tpp) cc_final: 0.7414 (tpp) REVERT: A 2835 LEU cc_start: 0.8319 (mt) cc_final: 0.7842 (tt) REVERT: A 2977 TYR cc_start: 0.7940 (m-80) cc_final: 0.7701 (m-80) REVERT: A 2992 PHE cc_start: 0.8708 (t80) cc_final: 0.8468 (t80) REVERT: A 3414 MET cc_start: 0.8331 (mtp) cc_final: 0.7927 (mtp) REVERT: A 3440 LEU cc_start: 0.9326 (mt) cc_final: 0.9110 (pp) REVERT: A 3846 MET cc_start: 0.7211 (tpp) cc_final: 0.6959 (mmp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1286 time to fit residues: 33.0879 Evaluate side-chains 123 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 85 optimal weight: 0.2980 chunk 130 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3948 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.107640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.088172 restraints weight = 92103.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089681 restraints weight = 65705.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.089762 restraints weight = 47984.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.090492 restraints weight = 41718.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.090396 restraints weight = 36631.833| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18195 Z= 0.108 Angle : 0.549 6.958 24690 Z= 0.276 Chirality : 0.039 0.187 2878 Planarity : 0.003 0.044 3091 Dihedral : 5.639 105.308 2498 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 1.12 (0.18), residues: 2254 helix: 1.73 (0.14), residues: 1364 sheet: -0.10 (0.41), residues: 172 loop : -0.96 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1725 TYR 0.024 0.001 TYR A1538 PHE 0.028 0.001 PHE A1779 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS A2453 Details of bonding type rmsd covalent geometry : bond 0.00228 (18195) covalent geometry : angle 0.54889 (24690) hydrogen bonds : bond 0.03495 ( 1079) hydrogen bonds : angle 4.27673 ( 3186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.7865 (tpp) cc_final: 0.7457 (tpp) REVERT: A 1580 THR cc_start: 0.8143 (t) cc_final: 0.7862 (t) REVERT: A 1595 LYS cc_start: 0.7209 (mmpt) cc_final: 0.6969 (mmmt) REVERT: A 2835 LEU cc_start: 0.8328 (mt) cc_final: 0.7929 (tt) REVERT: A 2977 TYR cc_start: 0.7844 (m-80) cc_final: 0.7573 (m-80) REVERT: A 2996 LEU cc_start: 0.7130 (pp) cc_final: 0.6774 (tt) REVERT: A 3414 MET cc_start: 0.8442 (mtp) cc_final: 0.8003 (mtp) REVERT: A 3440 LEU cc_start: 0.9339 (mt) cc_final: 0.9119 (pp) REVERT: A 3846 MET cc_start: 0.6773 (tpp) cc_final: 0.6538 (mmp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1388 time to fit residues: 37.9018 Evaluate side-chains 126 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 151 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 186 optimal weight: 0.7980 chunk 189 optimal weight: 0.0170 chunk 185 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1442 GLN ** A1444 ASN ** 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 = 0.4113 r_free = 0.4113 target = 0.107108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.086142 restraints weight = 89828.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.087948 restraints weight = 55384.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.089220 restraints weight = 39647.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.090045 restraints weight = 31635.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.090675 restraints weight = 27172.305| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18195 Z= 0.108 Angle : 0.560 7.537 24690 Z= 0.282 Chirality : 0.040 0.158 2878 Planarity : 0.003 0.052 3091 Dihedral : 5.544 103.398 2498 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 1.20 (0.18), residues: 2254 helix: 1.77 (0.14), residues: 1365 sheet: -0.03 (0.41), residues: 172 loop : -0.88 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1725 TYR 0.023 0.001 TYR A1538 PHE 0.034 0.001 PHE A2992 TRP 0.020 0.001 TRP A2084 HIS 0.002 0.000 HIS A2453 Details of bonding type rmsd covalent geometry : bond 0.00225 (18195) covalent geometry : angle 0.56015 (24690) hydrogen bonds : bond 0.03446 ( 1079) hydrogen bonds : angle 4.20824 ( 3186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.7897 (tpp) cc_final: 0.7516 (tpp) REVERT: A 1595 LYS cc_start: 0.7267 (mmpt) cc_final: 0.7048 (mmmt) REVERT: A 1655 MET cc_start: 0.8627 (tpp) cc_final: 0.8416 (tpp) REVERT: A 2835 LEU cc_start: 0.8297 (mt) cc_final: 0.7917 (tp) REVERT: A 2977 TYR cc_start: 0.7785 (m-80) cc_final: 0.7508 (m-80) REVERT: A 2996 LEU cc_start: 0.7127 (pp) cc_final: 0.6898 (tt) REVERT: A 3001 LYS cc_start: 0.8958 (tppt) cc_final: 0.8388 (mmtt) REVERT: A 3414 MET cc_start: 0.8413 (mtp) cc_final: 0.7974 (mtp) REVERT: A 3440 LEU cc_start: 0.9344 (mt) cc_final: 0.9104 (pp) REVERT: A 3846 MET cc_start: 0.7276 (tpp) cc_final: 0.6915 (mmp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1323 time to fit residues: 34.8935 Evaluate side-chains 128 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 213 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.104737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084439 restraints weight = 89446.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.086164 restraints weight = 64321.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.087074 restraints weight = 41736.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087346 restraints weight = 35696.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.087434 restraints weight = 31503.612| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18195 Z= 0.165 Angle : 0.619 7.643 24690 Z= 0.313 Chirality : 0.041 0.165 2878 Planarity : 0.004 0.053 3091 Dihedral : 5.700 104.089 2498 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 1.02 (0.18), residues: 2254 helix: 1.64 (0.14), residues: 1365 sheet: -0.27 (0.42), residues: 171 loop : -0.95 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1725 TYR 0.023 0.002 TYR A1705 PHE 0.018 0.001 PHE A3635 TRP 0.017 0.001 TRP A2084 HIS 0.003 0.001 HIS A2755 Details of bonding type rmsd covalent geometry : bond 0.00364 (18195) covalent geometry : angle 0.61909 (24690) hydrogen bonds : bond 0.03766 ( 1079) hydrogen bonds : angle 4.40707 ( 3186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2259 MET cc_start: 0.7739 (mtt) cc_final: 0.6957 (mmt) REVERT: A 2592 PHE cc_start: 0.7766 (m-80) cc_final: 0.7511 (m-80) REVERT: A 2977 TYR cc_start: 0.8002 (m-80) cc_final: 0.7724 (m-80) REVERT: A 2992 PHE cc_start: 0.8704 (t80) cc_final: 0.8411 (t80) REVERT: A 3001 LYS cc_start: 0.8914 (tppt) cc_final: 0.8385 (mmtt) REVERT: A 3414 MET cc_start: 0.8417 (mtp) cc_final: 0.7999 (mtp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1264 time to fit residues: 32.3740 Evaluate side-chains 120 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 156 optimal weight: 40.0000 chunk 112 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 223 optimal weight: 0.0470 chunk 46 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.106297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.085430 restraints weight = 89902.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087023 restraints weight = 56938.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088279 restraints weight = 42086.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.089140 restraints weight = 34004.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.089583 restraints weight = 29393.274| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18195 Z= 0.116 Angle : 0.588 7.897 24690 Z= 0.294 Chirality : 0.040 0.160 2878 Planarity : 0.003 0.047 3091 Dihedral : 5.605 103.257 2498 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 1.11 (0.18), residues: 2254 helix: 1.73 (0.14), residues: 1364 sheet: -0.23 (0.42), residues: 171 loop : -0.92 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1725 TYR 0.024 0.001 TYR A1538 PHE 0.026 0.001 PHE A1476 TRP 0.021 0.001 TRP A2084 HIS 0.004 0.001 HIS A2755 Details of bonding type rmsd covalent geometry : bond 0.00252 (18195) covalent geometry : angle 0.58787 (24690) hydrogen bonds : bond 0.03548 ( 1079) hydrogen bonds : angle 4.26424 ( 3186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 PHE cc_start: 0.6345 (m-80) cc_final: 0.5967 (m-80) REVERT: A 1565 MET cc_start: 0.8318 (pmm) cc_final: 0.8111 (pmm) REVERT: A 1655 MET cc_start: 0.8681 (tpp) cc_final: 0.8477 (tpp) REVERT: A 2592 PHE cc_start: 0.7634 (m-80) cc_final: 0.7427 (m-80) REVERT: A 2742 ILE cc_start: 0.8263 (pt) cc_final: 0.8046 (pt) REVERT: A 2977 TYR cc_start: 0.7939 (m-80) cc_final: 0.7642 (m-80) REVERT: A 2996 LEU cc_start: 0.7201 (pp) cc_final: 0.6780 (tt) REVERT: A 3001 LYS cc_start: 0.8950 (tppt) cc_final: 0.8408 (mmtt) REVERT: A 3414 MET cc_start: 0.8340 (mtp) cc_final: 0.7911 (mtp) REVERT: A 3440 LEU cc_start: 0.9254 (mt) cc_final: 0.9017 (pp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1334 time to fit residues: 33.5670 Evaluate side-chains 120 residues out of total 2099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 195 optimal weight: 0.3980 chunk 168 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.105100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.085256 restraints weight = 91168.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.086646 restraints weight = 68837.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086397 restraints weight = 48603.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086808 restraints weight = 48933.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.086980 restraints weight = 42540.898| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18195 Z= 0.149 Angle : 0.611 7.982 24690 Z= 0.308 Chirality : 0.041 0.157 2878 Planarity : 0.003 0.046 3091 Dihedral : 5.670 104.198 2498 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.01 (0.18), residues: 2254 helix: 1.66 (0.14), residues: 1364 sheet: -0.32 (0.42), residues: 171 loop : -0.98 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1725 TYR 0.026 0.001 TYR A1538 PHE 0.030 0.001 PHE A2992 TRP 0.018 0.001 TRP A2084 HIS 0.003 0.001 HIS A2755 Details of bonding type rmsd covalent geometry : bond 0.00331 (18195) covalent geometry : angle 0.61127 (24690) hydrogen bonds : bond 0.03686 ( 1079) hydrogen bonds : angle 4.37885 ( 3186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.98 seconds wall clock time: 50 minutes 51.10 seconds (3051.10 seconds total)