Starting phenix.real_space_refine on Fri Sep 19 04:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnb_47033/09_2025/9dnb_47033.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnb_47033/09_2025/9dnb_47033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dnb_47033/09_2025/9dnb_47033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnb_47033/09_2025/9dnb_47033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dnb_47033/09_2025/9dnb_47033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnb_47033/09_2025/9dnb_47033.map" } resolution = 3.0 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= 0.033 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 96 5.16 5 C 14672 2.51 5 N 3918 2.21 5 O 4267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s 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: 22963 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2332, 18183 Classifications: {'peptide': 2332} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 64, 'TRANS': 2267} Chain breaks: 13 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 848 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLU:plan': 38, 'GLN:plan1': 7, 'ASN:plan1': 11, 'TRP:plan': 1, 'PHE:plan': 8, 'TYR:plan': 3, 'ASP:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 389 Chain: "B" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 1994 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 827 Unresolved non-hydrogen angles: 1066 Unresolved non-hydrogen dihedrals: 710 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'TRP:plan': 9, 'ARG:plan': 15, 'ASN:plan1': 12, 'GLU:plan': 7, 'ASP:plan': 19, 'TYR:plan': 5, 'GLN:plan1': 9, 'HIS:plan': 9, 'PHE:plan': 10} Unresolved non-hydrogen planarities: 453 Chain: "C" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 5, 'PHE:plan': 1, 'ASP:plan': 7, 'GLN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.67, per 1000 atoms: 0.20 Number of scatterers: 22963 At special positions: 0 Unit cell: (100.457, 139.573, 188.468, 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 96 16.00 P 9 15.00 Mg 1 11.99 O 4267 8.00 N 3918 7.00 C 14672 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: 1.84 Conformation dependent library (CDL) restraints added in 940.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5754 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 32 sheets defined 49.6% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 1433 through 1461 Processing helix chain 'A' and resid 1471 through 1494 Processing helix chain 'A' and resid 1511 through 1521 removed outlier: 3.933A pdb=" N SER A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1534 Processing helix chain 'A' and resid 1535 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1557 through 1560 Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.864A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.749A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1666 removed outlier: 3.500A pdb=" N THR A1666 " --> pdb=" O LYS A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 3.889A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1730 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.243A 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 1850 through 1853 removed outlier: 3.565A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1850 through 1853' Processing helix chain 'A' and resid 1854 through 1875 removed outlier: 3.575A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.568A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1981 Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.978A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2008 through 2022 removed outlier: 3.565A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 4.153A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2096 removed outlier: 3.701A pdb=" N THR A2086 " --> pdb=" O ALA A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2129 through 2140 removed outlier: 3.623A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2209 removed outlier: 3.849A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2237 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.105A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A2270 " --> pdb=" O PHE A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2299 removed outlier: 3.507A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2300 through 2302 No H-bonds generated for 'chain 'A' and resid 2300 through 2302' Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2345 Processing helix chain 'A' and resid 2382 through 2386 removed outlier: 3.803A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2382 through 2386' Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 4.150A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2458 removed outlier: 3.545A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 Processing helix chain 'A' and resid 2547 through 2553 removed outlier: 4.276A pdb=" N HIS A2553 " --> pdb=" O ARG A2549 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2581 through 2587 removed outlier: 6.525A pdb=" N GLU A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.855A 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 removed outlier: 3.599A pdb=" N LEU A2712 " --> pdb=" O ASN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2766 through 2778 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.600A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.774A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A2837 " --> pdb=" O THR A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2844 Processing helix chain 'A' and resid 2846 through 2864 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2904 Processing helix chain 'A' and resid 2905 through 2911 Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.639A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 Processing helix chain 'A' and resid 3290 through 3299 Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.515A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.604A pdb=" N PHE A3356 " --> pdb=" O LEU A3352 " (cutoff:3.500A) 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: 4.067A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3462 through 3467 Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.601A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 3.716A pdb=" N GLY A3643 " --> pdb=" O TRP A3640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.665A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3728 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.418A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3835 Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 3.620A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.532A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.803A 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 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.846A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.721A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.266A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1880 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 8.008A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 removed outlier: 3.546A pdb=" N GLU A2124 " --> pdb=" O LEU A2119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2358 through 2360 removed outlier: 3.535A pdb=" N SER A2367 " --> pdb=" O VAL A2360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.187A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB2, first strand: chain 'A' and resid 2514 through 2517 Processing sheet with id=AB3, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB4, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 5.852A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.398A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 4.455A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3813 through 3815 removed outlier: 3.894A pdb=" N LYS A3872 " --> pdb=" O GLY A3837 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.791A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.433A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 481 " --> pdb=" O ASP B 465 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 463 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 158 through 163 removed outlier: 6.875A pdb=" N ALA B 173 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 161 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE B 171 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 163 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE B 169 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 192 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 201 through 208 removed outlier: 6.805A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B 236 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 226 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.702A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 279 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR B 292 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 281 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.654A pdb=" N ARG B 320 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 340 through 345 removed outlier: 3.632A pdb=" N LYS B 342 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 382 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR B 412 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 384 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 420 through 426 removed outlier: 4.151A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 434 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 452 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS B 441 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.765A pdb=" N CYS C 150 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET C 480 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 481 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 465 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.724A pdb=" N LEU C 194 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.773A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP C 236 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 222 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 256 through 258 removed outlier: 6.848A pdb=" N CYS C 273 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 261 through 264 removed outlier: 7.695A pdb=" N ILE C 281 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 290 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.587A pdb=" N SER C 314 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 331 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 340 through 346 removed outlier: 4.822A pdb=" N TYR C 372 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 411 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.853A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 432 " --> pdb=" O ARG C 440 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 2.46 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: 7432 1.34 - 1.46: 3798 1.46 - 1.58: 12034 1.58 - 1.69: 14 1.69 - 1.81: 149 Bond restraints: 23427 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 2.78e+00 bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" CG LEU A2038 " pdb=" CD1 LEU A2038 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CA ASN C 210 " pdb=" CB ASN C 210 " ideal model delta sigma weight residual 1.536 1.557 -0.021 2.08e-02 2.31e+03 1.06e+00 bond pdb=" C PHE A3608 " pdb=" N PRO A3609 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.28e-02 6.10e+03 1.01e+00 ... (remaining 23422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 31379 1.77 - 3.54: 384 3.54 - 5.30: 63 5.30 - 7.07: 18 7.07 - 8.84: 1 Bond angle restraints: 31845 Sorted by residual: angle pdb=" N ILE A3462 " pdb=" CA ILE A3462 " pdb=" C ILE A3462 " ideal model delta sigma weight residual 111.91 108.10 3.81 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N GLU A3331 " pdb=" CA GLU A3331 " pdb=" CB GLU A3331 " ideal model delta sigma weight residual 110.16 114.81 -4.65 1.48e+00 4.57e-01 9.86e+00 angle pdb=" CG1 ILE A2689 " pdb=" CB ILE A2689 " pdb=" CG2 ILE A2689 " ideal model delta sigma weight residual 110.70 101.86 8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" N SER A3847 " pdb=" CA SER A3847 " pdb=" C SER A3847 " ideal model delta sigma weight residual 110.44 107.17 3.27 1.20e+00 6.94e-01 7.40e+00 angle pdb=" CA TRP A2084 " pdb=" CB TRP A2084 " pdb=" CG TRP A2084 " ideal model delta sigma weight residual 113.60 118.49 -4.89 1.90e+00 2.77e-01 6.63e+00 ... (remaining 31840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 13692 34.76 - 69.52: 211 69.52 - 104.28: 25 104.28 - 139.05: 0 139.05 - 173.81: 1 Dihedral angle restraints: 13929 sinusoidal: 5094 harmonic: 8835 Sorted by residual: dihedral pdb=" C2' ADP A4104 " pdb=" C1' ADP A4104 " pdb=" N9 ADP A4104 " pdb=" C4 ADP A4104 " ideal model delta sinusoidal sigma weight residual 91.55 -82.26 173.81 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA MET A1963 " pdb=" C MET A1963 " pdb=" N ASN A1964 " pdb=" CA ASN A1964 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 176.14 -84.59 1 2.00e+01 2.50e-03 2.17e+01 ... (remaining 13926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2825 0.045 - 0.090: 651 0.090 - 0.135: 226 0.135 - 0.181: 5 0.181 - 0.226: 2 Chirality restraints: 3709 Sorted by residual: chirality pdb=" CB ILE A2689 " pdb=" CA ILE A2689 " pdb=" CG1 ILE A2689 " pdb=" CG2 ILE A2689 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A2222 " pdb=" CA ILE A2222 " pdb=" CG1 ILE A2222 " pdb=" CG2 ILE A2222 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 3706 not shown) Planarity restraints: 4027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3459 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO A3460 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A3460 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A3460 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A2619 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2159 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A2160 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A2160 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2160 " 0.025 5.00e-02 4.00e+02 ... (remaining 4024 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 221 2.62 - 3.19: 19379 3.19 - 3.76: 36641 3.76 - 4.33: 48855 4.33 - 4.90: 82545 Nonbonded interactions: 187641 Sorted by model distance: nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.051 2.170 nonbonded pdb=" OH TYR A2115 " pdb=" O TYR A2162 " model vdw 2.210 3.040 nonbonded pdb=" NE2 HIS A3624 " pdb=" OD2 ASP A3709 " model vdw 2.212 3.120 nonbonded pdb=" NH2 ARG A3512 " pdb=" O2A ADP A4103 " model vdw 2.234 3.120 nonbonded pdb=" O TYR A1643 " pdb=" NZ LYS A1697 " model vdw 2.267 3.120 ... (remaining 187636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 139 through 183 or (resid 184 and (name N or name CA or na \ me C or name O or name CB )) or resid 185 or (resid 186 through 189 and (name N \ or name CA or name C or name O or name CB )) or resid 190 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throug \ h 213 or resid 218 through 227 or (resid 228 through 231 and (name N or name CA \ or name C or name O or name CB )) or resid 232 through 238 or (resid 239 through \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 or (r \ esid 242 and (name N or name CA or name C or name O or name CB )) or resid 243 o \ r (resid 244 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 45 through 474 or (resid 475 through 480 and (name N or name CA or name C or nam \ e O or name CB )) or resid 481 through 494)) selection = (chain 'C' and ((resid 139 through 143 and (name N or name CA or name C or name \ O or name CB )) or resid 144 or (resid 145 through 147 and (name N or name CA or \ name C or name O or name CB )) or resid 148 through 149 or (resid 150 through 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 or (res \ id 159 through 160 and (name N or name CA or name C or name O or name CB )) or r \ esid 161 or (resid 162 through 163 and (name N or name CA or name C or name O or \ name CB )) or resid 164 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 186 or (resid 187 through 189 a \ nd (name N or name CA or name C or name O or name CB )) or resid 190 through 198 \ or (resid 199 through 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 204 or (resid 205 and (name N or name CA or name C or n \ ame O or name CB )) or resid 206 or (resid 207 through 208 and (name N or name C \ A or name C or name O or name CB )) or resid 209 through 226 or (resid 227 throu \ gh 231 and (name N or name CA or name C or name O or name CB )) or resid 232 thr \ ough 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) \ or resid 251 through 252 or (resid 253 through 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 or (resid 257 through 258 and (name N o \ r name CA or name C or name O or name CB )) or resid 259 or (resid 260 and (name \ N or name CA or name C or name O or name CB )) or resid 261 or (resid 262 throu \ gh 268 and (name N or name CA or name C or name O or name CB )) or resid 269 thr \ ough 272 or (resid 273 and (name N or name CA or name C or name O or name CB )) \ or resid 274 or (resid 275 through 280 and (name N or name CA or name C or name \ O or name CB )) or resid 281 through 282 or (resid 283 and (name N or name CA or \ name C or name O or name CB )) or resid 284 through 290 or (resid 291 through 3 \ 06 and (name N or name CA or name C or name O or name CB )) or (resid 307 throug \ h 312 and (name N or name CA or name C or name O or name CB )) or resid 313 or ( \ resid 314 through 326 and (name N or name CA or name C or name O or name CB )) o \ r resid 327 or (resid 328 and (name N or name CA or name C or name O or name CB \ )) or resid 329 or (resid 330 through 332 and (name N or name CA or name C or na \ me O or name CB )) or resid 333 or (resid 334 and (name N or name CA or name C o \ r name O or name CB )) or resid 335 or (resid 336 through 350 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 355 through 359 and (name N or \ name CA or name C or name O or name CB )) or resid 360 or (resid 361 through 368 \ and (name N or name CA or name C or name O or name CB )) or resid 369 or (resid \ 370 through 387 and (name N or name CA or name C or name O or name CB )) or res \ id 388 through 397 or (resid 398 through 400 and (name N or name CA or name C or \ name O or name CB )) or (resid 405 through 414 and (name N or name CA or name C \ or name O or name CB )) or resid 415 or (resid 416 through 426 and (name N or n \ ame CA or name C or name O or name CB )) or resid 427 or (resid 428 through 446 \ and (name N or name CA or name C or name O or name CB )) or resid 447 or (resid \ 448 through 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 or (resid 460 through 480 and (name N or name CA or name C or name O or na \ me CB )) or resid 481 or (resid 482 and (name N or name CA or name C or name O o \ r name CB )) or resid 483 through 484 or (resid 485 through 488 and (name N or n \ ame CA or name C or name O or name CB )) or resid 489 or (resid 490 and (name N \ or name CA or name C or name O or name CB )) or resid 491 or (resid 492 through \ 494 and (name N or name CA or name C or name O or name CB )))) } 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: 0.010 Normalize map: mean=0, sd=1: 4.020 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.950 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.002 0.039 23427 Z= 0.114 Angle : 0.521 8.841 31845 Z= 0.275 Chirality : 0.042 0.226 3709 Planarity : 0.004 0.061 4027 Dihedral : 13.694 173.806 8175 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 0.85 (0.15), residues: 2974 helix: 1.54 (0.14), residues: 1414 sheet: 0.57 (0.26), residues: 439 loop : -0.66 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2771 TYR 0.021 0.001 TYR A2234 PHE 0.019 0.001 PHE A2972 TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00232 (23427) covalent geometry : angle 0.52136 (31845) hydrogen bonds : bond 0.14585 ( 1274) hydrogen bonds : angle 5.90628 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 1718 CYS cc_start: 0.8270 (t) cc_final: 0.8007 (t) REVERT: A 1856 LYS cc_start: 0.8394 (mttm) cc_final: 0.8133 (mtmm) REVERT: A 2488 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7524 (tp30) REVERT: A 2829 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 2991 TYR cc_start: 0.7942 (m-80) cc_final: 0.7588 (m-80) REVERT: A 3008 GLN cc_start: 0.7499 (mm110) cc_final: 0.7215 (tm-30) REVERT: A 3476 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6823 (ttp-110) REVERT: A 3535 THR cc_start: 0.8647 (m) cc_final: 0.8216 (p) REVERT: A 3541 MET cc_start: 0.7117 (tpp) cc_final: 0.6812 (tpp) REVERT: A 3638 PHE cc_start: 0.7679 (m-80) cc_final: 0.7249 (t80) REVERT: A 4053 ILE cc_start: 0.7724 (mt) cc_final: 0.7223 (pp) REVERT: B 171 PHE cc_start: 0.6292 (m-80) cc_final: 0.6015 (m-80) REVERT: B 186 ASN cc_start: 0.4982 (m110) cc_final: 0.4594 (OUTLIER) REVERT: B 197 HIS cc_start: 0.5912 (m-70) cc_final: 0.5504 (m-70) REVERT: B 203 SER cc_start: 0.6934 (m) cc_final: 0.6662 (m) REVERT: B 226 SER cc_start: 0.6759 (p) cc_final: 0.6373 (p) REVERT: B 238 SER cc_start: 0.7918 (p) cc_final: 0.7676 (p) REVERT: B 242 LYS cc_start: 0.7041 (pttm) cc_final: 0.6688 (pttm) REVERT: C 230 GLN cc_start: 0.6614 (pt0) cc_final: 0.6145 (mt0) REVERT: C 309 TYR cc_start: 0.6567 (m-80) cc_final: 0.6296 (m-80) outliers start: 0 outliers final: 2 residues processed: 337 average time/residue: 0.4931 time to fit residues: 194.2448 Evaluate side-chains 241 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2689 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 GLN A2270 ASN A2340 GLN A2459 HIS A2854 ASN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 HIS C 490 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137208 restraints weight = 30668.926| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.43 r_work: 0.3548 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23427 Z= 0.138 Angle : 0.526 7.788 31845 Z= 0.271 Chirality : 0.043 0.168 3709 Planarity : 0.004 0.055 4027 Dihedral : 6.247 173.584 3257 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.82 % Allowed : 8.50 % Favored : 89.68 % 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: 1.09 (0.15), residues: 2974 helix: 1.90 (0.14), residues: 1421 sheet: 0.48 (0.25), residues: 454 loop : -0.74 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2191 TYR 0.021 0.001 TYR A3683 PHE 0.014 0.001 PHE A2972 TRP 0.019 0.001 TRP A2084 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00322 (23427) covalent geometry : angle 0.52580 (31845) hydrogen bonds : bond 0.03805 ( 1274) hydrogen bonds : angle 4.47168 ( 3738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7857 (ttp80) REVERT: A 1718 CYS cc_start: 0.8417 (t) cc_final: 0.8150 (t) REVERT: A 1856 LYS cc_start: 0.8397 (mttm) cc_final: 0.7942 (mtmm) REVERT: A 2386 MET cc_start: 0.9251 (mmm) cc_final: 0.9048 (mmp) REVERT: A 2428 MET cc_start: 0.8061 (ttt) cc_final: 0.7813 (tmm) REVERT: A 2520 GLU cc_start: 0.8555 (pm20) cc_final: 0.8340 (pm20) REVERT: A 2829 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 3008 GLN cc_start: 0.7454 (mm110) cc_final: 0.7041 (tm-30) REVERT: A 3448 SER cc_start: 0.8714 (t) cc_final: 0.8420 (p) REVERT: A 3476 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6747 (ttp-110) REVERT: A 3535 THR cc_start: 0.8511 (m) cc_final: 0.8140 (p) REVERT: A 3541 MET cc_start: 0.6842 (tpp) cc_final: 0.6544 (tpp) REVERT: A 3638 PHE cc_start: 0.7697 (m-80) cc_final: 0.7271 (t80) REVERT: A 3715 TYR cc_start: 0.6909 (t80) cc_final: 0.6469 (t80) REVERT: A 3744 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6687 (mm) REVERT: A 3846 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: A 4051 ASN cc_start: 0.7035 (m-40) cc_final: 0.6251 (t0) REVERT: B 171 PHE cc_start: 0.6200 (m-80) cc_final: 0.5942 (m-80) REVERT: B 179 LEU cc_start: 0.7206 (tt) cc_final: 0.7004 (tm) REVERT: B 186 ASN cc_start: 0.4763 (m110) cc_final: 0.4397 (OUTLIER) REVERT: B 195 GLN cc_start: 0.5319 (tp40) cc_final: 0.5055 (tp-100) REVERT: B 203 SER cc_start: 0.7110 (m) cc_final: 0.6786 (m) REVERT: B 226 SER cc_start: 0.7120 (p) cc_final: 0.6811 (p) REVERT: B 234 PHE cc_start: 0.7407 (m-80) cc_final: 0.6422 (m-80) REVERT: B 242 LYS cc_start: 0.6867 (pttm) cc_final: 0.6417 (pttm) REVERT: B 249 LEU cc_start: 0.6510 (mt) cc_final: 0.6305 (mt) REVERT: C 230 GLN cc_start: 0.6680 (pt0) cc_final: 0.6094 (mt0) REVERT: C 309 TYR cc_start: 0.6589 (m-80) cc_final: 0.6304 (m-80) outliers start: 42 outliers final: 15 residues processed: 288 average time/residue: 0.4624 time to fit residues: 158.3253 Evaluate side-chains 248 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 2118 MET Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2824 GLU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 342 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 250 optimal weight: 30.0000 chunk 158 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 252 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2500 GLN A2959 GLN A2971 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137362 restraints weight = 30695.074| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.06 r_work: 0.3568 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23427 Z= 0.109 Angle : 0.487 8.466 31845 Z= 0.249 Chirality : 0.042 0.205 3709 Planarity : 0.003 0.054 4027 Dihedral : 6.104 174.824 3255 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.56 % Allowed : 11.19 % Favored : 87.25 % 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: 1.24 (0.15), residues: 2974 helix: 2.09 (0.14), residues: 1426 sheet: 0.33 (0.25), residues: 460 loop : -0.67 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2191 TYR 0.018 0.001 TYR A2234 PHE 0.014 0.001 PHE A2972 TRP 0.026 0.001 TRP B 288 HIS 0.005 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00243 (23427) covalent geometry : angle 0.48722 (31845) hydrogen bonds : bond 0.03473 ( 1274) hydrogen bonds : angle 4.20861 ( 3738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7851 (ttp80) REVERT: A 1718 CYS cc_start: 0.8432 (t) cc_final: 0.8175 (t) REVERT: A 1856 LYS cc_start: 0.8367 (mttm) cc_final: 0.7903 (mtmm) REVERT: A 2386 MET cc_start: 0.9300 (mmm) cc_final: 0.9073 (mmp) REVERT: A 2428 MET cc_start: 0.8023 (ttt) cc_final: 0.7745 (tmm) REVERT: A 2829 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 3008 GLN cc_start: 0.7485 (mm110) cc_final: 0.7025 (tm-30) REVERT: A 3330 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: A 3448 SER cc_start: 0.8723 (t) cc_final: 0.8450 (p) REVERT: A 3476 ARG cc_start: 0.7011 (ttp-170) cc_final: 0.6762 (ttp-110) REVERT: A 3535 THR cc_start: 0.8512 (m) cc_final: 0.8139 (p) REVERT: A 3541 MET cc_start: 0.6880 (tpp) cc_final: 0.6636 (tpp) REVERT: A 3638 PHE cc_start: 0.7674 (m-80) cc_final: 0.7297 (t80) REVERT: A 3715 TYR cc_start: 0.7013 (t80) cc_final: 0.6538 (t80) REVERT: A 3744 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6603 (mm) REVERT: A 3782 GLU cc_start: 0.7310 (tp30) cc_final: 0.7100 (tp30) REVERT: A 4051 ASN cc_start: 0.6934 (m-40) cc_final: 0.6301 (t0) REVERT: B 171 PHE cc_start: 0.6256 (m-80) cc_final: 0.6009 (m-80) REVERT: B 186 ASN cc_start: 0.4733 (m110) cc_final: 0.4503 (t0) REVERT: B 195 GLN cc_start: 0.5240 (tp40) cc_final: 0.5006 (tp-100) REVERT: B 203 SER cc_start: 0.7263 (m) cc_final: 0.6920 (m) REVERT: B 242 LYS cc_start: 0.6920 (pttm) cc_final: 0.6646 (ptpp) REVERT: B 249 LEU cc_start: 0.6701 (mt) cc_final: 0.6476 (mt) REVERT: B 286 ASN cc_start: 0.7372 (t0) cc_final: 0.7072 (t160) REVERT: C 230 GLN cc_start: 0.6607 (pt0) cc_final: 0.6071 (mt0) REVERT: C 309 TYR cc_start: 0.6561 (m-80) cc_final: 0.6256 (m-80) outliers start: 36 outliers final: 13 residues processed: 276 average time/residue: 0.4405 time to fit residues: 145.6366 Evaluate side-chains 247 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 2118 MET Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2824 GLU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 337 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 174 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 235 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS A1867 GLN A2270 ASN ** A2490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2500 GLN A2959 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138177 restraints weight = 30571.366| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.97 r_work: 0.3573 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23427 Z= 0.102 Angle : 0.476 8.898 31845 Z= 0.242 Chirality : 0.041 0.195 3709 Planarity : 0.003 0.049 4027 Dihedral : 6.024 175.261 3255 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.82 % Allowed : 12.40 % Favored : 85.78 % 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: 1.37 (0.16), residues: 2974 helix: 2.23 (0.14), residues: 1426 sheet: 0.37 (0.25), residues: 459 loop : -0.64 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2191 TYR 0.021 0.001 TYR A3683 PHE 0.015 0.001 PHE A2940 TRP 0.020 0.001 TRP A2084 HIS 0.008 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00230 (23427) covalent geometry : angle 0.47568 (31845) hydrogen bonds : bond 0.03250 ( 1274) hydrogen bonds : angle 4.03440 ( 3738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7848 (ttp80) REVERT: A 1718 CYS cc_start: 0.8528 (t) cc_final: 0.8257 (t) REVERT: A 1856 LYS cc_start: 0.8368 (mttm) cc_final: 0.7821 (mtmt) REVERT: A 1993 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7361 (t) REVERT: A 2386 MET cc_start: 0.9361 (mmm) cc_final: 0.9093 (mmp) REVERT: A 2428 MET cc_start: 0.8006 (ttt) cc_final: 0.7795 (tmm) REVERT: A 3008 GLN cc_start: 0.7491 (mm110) cc_final: 0.7024 (tm-30) REVERT: A 3330 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: A 3448 SER cc_start: 0.8756 (t) cc_final: 0.8493 (p) REVERT: A 3476 ARG cc_start: 0.6996 (ttp-170) cc_final: 0.6719 (ttp-110) REVERT: A 3535 THR cc_start: 0.8514 (m) cc_final: 0.8145 (p) REVERT: A 3541 MET cc_start: 0.6892 (tpp) cc_final: 0.6646 (tpp) REVERT: A 3715 TYR cc_start: 0.7048 (t80) cc_final: 0.6544 (t80) REVERT: A 3744 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6613 (mm) REVERT: A 3782 GLU cc_start: 0.7427 (tp30) cc_final: 0.7200 (tp30) REVERT: A 3791 GLU cc_start: 0.7388 (pm20) cc_final: 0.7150 (mp0) REVERT: A 4051 ASN cc_start: 0.6902 (m-40) cc_final: 0.6329 (t0) REVERT: B 183 ASP cc_start: 0.5034 (t0) cc_final: 0.4815 (t0) REVERT: B 186 ASN cc_start: 0.4871 (m110) cc_final: 0.4588 (t0) REVERT: B 203 SER cc_start: 0.7294 (m) cc_final: 0.6955 (m) REVERT: B 242 LYS cc_start: 0.6930 (pttm) cc_final: 0.6632 (ptpp) REVERT: B 286 ASN cc_start: 0.7270 (t0) cc_final: 0.6963 (t0) REVERT: C 230 GLN cc_start: 0.6617 (pt0) cc_final: 0.6100 (mt0) REVERT: C 309 TYR cc_start: 0.6628 (m-80) cc_final: 0.6360 (m-80) outliers start: 42 outliers final: 20 residues processed: 283 average time/residue: 0.4537 time to fit residues: 153.2500 Evaluate side-chains 258 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2701 SER Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2824 GLU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 285 optimal weight: 4.9990 chunk 213 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN A2959 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133973 restraints weight = 30685.585| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.96 r_work: 0.3509 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23427 Z= 0.184 Angle : 0.549 8.356 31845 Z= 0.280 Chirality : 0.044 0.177 3709 Planarity : 0.004 0.049 4027 Dihedral : 6.294 172.216 3255 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.39 % Allowed : 13.40 % Favored : 84.22 % 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 (0.15), residues: 2974 helix: 1.99 (0.14), residues: 1424 sheet: 0.22 (0.25), residues: 464 loop : -0.71 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2771 TYR 0.022 0.002 TYR A3683 PHE 0.022 0.002 PHE A2550 TRP 0.024 0.002 TRP A3306 HIS 0.012 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00446 (23427) covalent geometry : angle 0.54902 (31845) hydrogen bonds : bond 0.03826 ( 1274) hydrogen bonds : angle 4.13500 ( 3738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.7829 (ttp80) REVERT: A 1718 CYS cc_start: 0.8578 (t) cc_final: 0.8294 (t) REVERT: A 1856 LYS cc_start: 0.8486 (mttm) cc_final: 0.8048 (mtmm) REVERT: A 2164 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7581 (mm-30) REVERT: A 2428 MET cc_start: 0.8118 (ttt) cc_final: 0.7802 (tmm) REVERT: A 2491 LEU cc_start: 0.8214 (mm) cc_final: 0.7975 (mt) REVERT: A 2792 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7693 (tt) REVERT: A 2829 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6854 (tm-30) REVERT: A 2971 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.8000 (m170) REVERT: A 3007 TYR cc_start: 0.7101 (t80) cc_final: 0.6706 (t80) REVERT: A 3008 GLN cc_start: 0.7563 (mm110) cc_final: 0.7123 (tm-30) REVERT: A 3448 SER cc_start: 0.8772 (t) cc_final: 0.8561 (p) REVERT: A 3512 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6747 (mtm-85) REVERT: A 3535 THR cc_start: 0.8542 (m) cc_final: 0.8182 (p) REVERT: A 3541 MET cc_start: 0.6851 (tpp) cc_final: 0.6595 (tpp) REVERT: A 3709 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7354 (t0) REVERT: A 3715 TYR cc_start: 0.7107 (t80) cc_final: 0.6526 (t80) REVERT: A 3744 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6630 (mm) REVERT: A 3745 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.7006 (mmp-170) REVERT: A 3893 ASP cc_start: 0.8662 (m-30) cc_final: 0.8456 (m-30) REVERT: A 4051 ASN cc_start: 0.6946 (m-40) cc_final: 0.6343 (t0) REVERT: B 183 ASP cc_start: 0.5237 (t0) cc_final: 0.4911 (t0) REVERT: B 186 ASN cc_start: 0.5125 (m110) cc_final: 0.4719 (t0) REVERT: B 197 HIS cc_start: 0.5444 (OUTLIER) cc_final: 0.4508 (m-70) REVERT: B 203 SER cc_start: 0.7496 (m) cc_final: 0.7131 (m) REVERT: B 242 LYS cc_start: 0.6944 (pttm) cc_final: 0.6641 (pttm) REVERT: B 286 ASN cc_start: 0.7296 (t0) cc_final: 0.7021 (t0) REVERT: C 230 GLN cc_start: 0.6583 (pt0) cc_final: 0.6058 (mt0) outliers start: 55 outliers final: 32 residues processed: 283 average time/residue: 0.4919 time to fit residues: 163.9667 Evaluate side-chains 268 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2066 THR Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2157 ASP Chi-restraints excluded: chain A residue 2206 THR Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2701 SER Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2824 GLU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3417 VAL Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3512 ARG Chi-restraints excluded: chain A residue 3527 THR Chi-restraints excluded: chain A residue 3709 ASP Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3745 ARG Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 54 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1867 GLN A2270 ASN A2500 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3988 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.169229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134018 restraints weight = 30779.196| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.04 r_work: 0.3514 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23427 Z= 0.144 Angle : 0.513 7.908 31845 Z= 0.262 Chirality : 0.042 0.173 3709 Planarity : 0.003 0.052 4027 Dihedral : 6.266 173.821 3255 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.34 % Allowed : 14.22 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.15), residues: 2974 helix: 2.05 (0.14), residues: 1424 sheet: 0.17 (0.25), residues: 464 loop : -0.69 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2191 TYR 0.018 0.001 TYR A3683 PHE 0.015 0.001 PHE A2972 TRP 0.025 0.001 TRP A3306 HIS 0.010 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00342 (23427) covalent geometry : angle 0.51275 (31845) hydrogen bonds : bond 0.03543 ( 1274) hydrogen bonds : angle 4.07035 ( 3738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 248 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7950 (ttp80) REVERT: A 1675 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8050 (tp30) REVERT: A 1718 CYS cc_start: 0.8579 (t) cc_final: 0.8294 (t) REVERT: A 1856 LYS cc_start: 0.8482 (mttm) cc_final: 0.8055 (mtmm) REVERT: A 2164 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7620 (mm-30) REVERT: A 2491 LEU cc_start: 0.8216 (mm) cc_final: 0.7981 (mt) REVERT: A 2792 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7713 (tt) REVERT: A 2971 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.8006 (m170) REVERT: A 3007 TYR cc_start: 0.7108 (t80) cc_final: 0.6821 (t80) REVERT: A 3008 GLN cc_start: 0.7632 (mm110) cc_final: 0.7105 (tm-30) REVERT: A 3512 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6718 (mtm-85) REVERT: A 3535 THR cc_start: 0.8509 (m) cc_final: 0.8144 (p) REVERT: A 3541 MET cc_start: 0.6856 (tpp) cc_final: 0.6628 (tpp) REVERT: A 3709 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7309 (t0) REVERT: A 3715 TYR cc_start: 0.7104 (t80) cc_final: 0.6237 (t80) REVERT: A 3744 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6273 (mm) REVERT: A 3791 GLU cc_start: 0.7506 (pm20) cc_final: 0.7189 (mm-30) REVERT: A 3893 ASP cc_start: 0.8683 (m-30) cc_final: 0.8477 (m-30) REVERT: A 4051 ASN cc_start: 0.6907 (m-40) cc_final: 0.6343 (t0) REVERT: B 183 ASP cc_start: 0.5155 (t0) cc_final: 0.4800 (t0) REVERT: B 186 ASN cc_start: 0.5200 (m110) cc_final: 0.4804 (t0) REVERT: B 203 SER cc_start: 0.7363 (m) cc_final: 0.7021 (m) REVERT: B 235 LYS cc_start: 0.6606 (ttmt) cc_final: 0.6396 (ttpt) REVERT: B 242 LYS cc_start: 0.6919 (pttm) cc_final: 0.6616 (pttm) REVERT: B 282 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.6596 (m100) REVERT: B 286 ASN cc_start: 0.7150 (t0) cc_final: 0.6794 (t0) REVERT: C 201 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 230 GLN cc_start: 0.6625 (pt0) cc_final: 0.6117 (mt0) REVERT: C 281 ILE cc_start: 0.5279 (OUTLIER) cc_final: 0.5022 (pt) outliers start: 54 outliers final: 28 residues processed: 285 average time/residue: 0.4635 time to fit residues: 156.2206 Evaluate side-chains 269 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2206 THR Chi-restraints excluded: chain A residue 2397 THR Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2701 SER Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2824 GLU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3417 VAL Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3512 ARG Chi-restraints excluded: chain A residue 3709 ASP Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 64 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 HIS B 218 ASN C 371 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.169925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134691 restraints weight = 30814.236| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.17 r_work: 0.3531 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23427 Z= 0.127 Angle : 0.505 8.418 31845 Z= 0.258 Chirality : 0.042 0.196 3709 Planarity : 0.003 0.051 4027 Dihedral : 6.211 174.258 3255 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.34 % Allowed : 14.31 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.16), residues: 2974 helix: 2.10 (0.14), residues: 1425 sheet: 0.18 (0.25), residues: 464 loop : -0.66 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2136 TYR 0.020 0.001 TYR A2234 PHE 0.017 0.001 PHE A2940 TRP 0.027 0.001 TRP A3306 HIS 0.011 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00300 (23427) covalent geometry : angle 0.50531 (31845) hydrogen bonds : bond 0.03436 ( 1274) hydrogen bonds : angle 4.01648 ( 3738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.7967 (ttp80) REVERT: A 1675 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7990 (tp30) REVERT: A 1718 CYS cc_start: 0.8562 (t) cc_final: 0.8276 (t) REVERT: A 1856 LYS cc_start: 0.8454 (mttm) cc_final: 0.8056 (mtmm) REVERT: A 2428 MET cc_start: 0.8174 (tmm) cc_final: 0.7582 (tmm) REVERT: A 2519 PRO cc_start: 0.7554 (Cg_exo) cc_final: 0.7333 (Cg_endo) REVERT: A 2792 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 2971 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7960 (m170) REVERT: A 3007 TYR cc_start: 0.7107 (t80) cc_final: 0.6892 (t80) REVERT: A 3008 GLN cc_start: 0.7608 (mm110) cc_final: 0.7101 (tm-30) REVERT: A 3512 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.6581 (mtm-85) REVERT: A 3535 THR cc_start: 0.8488 (m) cc_final: 0.8124 (p) REVERT: A 3541 MET cc_start: 0.6851 (tpp) cc_final: 0.6627 (tpp) REVERT: A 3709 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7295 (t0) REVERT: A 3715 TYR cc_start: 0.7015 (t80) cc_final: 0.6234 (t80) REVERT: A 3744 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6183 (mm) REVERT: A 3893 ASP cc_start: 0.8677 (m-30) cc_final: 0.8469 (m-30) REVERT: A 4051 ASN cc_start: 0.6883 (m-40) cc_final: 0.6317 (t0) REVERT: B 183 ASP cc_start: 0.5203 (t0) cc_final: 0.4791 (t0) REVERT: B 186 ASN cc_start: 0.5301 (m110) cc_final: 0.4842 (t0) REVERT: B 203 SER cc_start: 0.7321 (m) cc_final: 0.6981 (m) REVERT: B 234 PHE cc_start: 0.7192 (m-80) cc_final: 0.6829 (m-80) REVERT: B 242 LYS cc_start: 0.6913 (pttm) cc_final: 0.6609 (pttm) REVERT: B 245 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6663 (tp40) REVERT: B 282 TRP cc_start: 0.6746 (OUTLIER) cc_final: 0.6467 (m100) REVERT: B 286 ASN cc_start: 0.7092 (m-40) cc_final: 0.6747 (t0) REVERT: C 201 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 281 ILE cc_start: 0.5267 (OUTLIER) cc_final: 0.5021 (pt) REVERT: C 370 MET cc_start: 0.6456 (ptp) cc_final: 0.6195 (mtt) REVERT: C 479 MET cc_start: 0.7357 (mmp) cc_final: 0.6903 (mmt) outliers start: 54 outliers final: 26 residues processed: 283 average time/residue: 0.5031 time to fit residues: 168.8757 Evaluate side-chains 267 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2206 THR Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2701 SER Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3417 VAL Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3512 ARG Chi-restraints excluded: chain A residue 3709 ASP Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 36 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 chunk 177 optimal weight: 0.0270 chunk 155 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1788 GLN A2270 ASN ** A2490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.169817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135965 restraints weight = 30475.018| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.96 r_work: 0.3558 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23427 Z= 0.108 Angle : 0.495 8.761 31845 Z= 0.252 Chirality : 0.041 0.174 3709 Planarity : 0.003 0.049 4027 Dihedral : 6.106 175.135 3255 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 15.22 % Favored : 82.78 % 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: 1.29 (0.16), residues: 2974 helix: 2.21 (0.14), residues: 1424 sheet: 0.10 (0.25), residues: 462 loop : -0.62 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2136 TYR 0.023 0.001 TYR A2234 PHE 0.014 0.001 PHE A2972 TRP 0.029 0.001 TRP A3306 HIS 0.009 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00248 (23427) covalent geometry : angle 0.49457 (31845) hydrogen bonds : bond 0.03253 ( 1274) hydrogen bonds : angle 3.95528 ( 3738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.903 Fit side-chains REVERT: A 1583 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7904 (ttp80) REVERT: A 1675 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7980 (tp30) REVERT: A 1718 CYS cc_start: 0.8511 (t) cc_final: 0.8237 (t) REVERT: A 1856 LYS cc_start: 0.8419 (mttm) cc_final: 0.8032 (mtmm) REVERT: A 2428 MET cc_start: 0.8108 (tmm) cc_final: 0.7517 (tmm) REVERT: A 2971 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (m170) REVERT: A 3007 TYR cc_start: 0.7092 (t80) cc_final: 0.6803 (t80) REVERT: A 3008 GLN cc_start: 0.7606 (mm110) cc_final: 0.7108 (tm-30) REVERT: A 3512 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6554 (mtm-85) REVERT: A 3535 THR cc_start: 0.8510 (m) cc_final: 0.8147 (p) REVERT: A 3541 MET cc_start: 0.6885 (tpp) cc_final: 0.6682 (tpp) REVERT: A 3709 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 3715 TYR cc_start: 0.6990 (t80) cc_final: 0.6236 (t80) REVERT: A 3744 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6306 (mm) REVERT: A 3893 ASP cc_start: 0.8645 (m-30) cc_final: 0.8434 (m-30) REVERT: A 4051 ASN cc_start: 0.6866 (m-40) cc_final: 0.6326 (t0) REVERT: B 183 ASP cc_start: 0.5296 (t0) cc_final: 0.4830 (t0) REVERT: B 186 ASN cc_start: 0.5306 (m110) cc_final: 0.4865 (t0) REVERT: B 203 SER cc_start: 0.7326 (m) cc_final: 0.7001 (m) REVERT: B 234 PHE cc_start: 0.7181 (m-80) cc_final: 0.6741 (m-80) REVERT: B 242 LYS cc_start: 0.6909 (pttm) cc_final: 0.6610 (ptpp) REVERT: B 286 ASN cc_start: 0.6918 (m-40) cc_final: 0.6663 (t0) REVERT: C 281 ILE cc_start: 0.5297 (OUTLIER) cc_final: 0.5061 (pt) REVERT: C 342 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7587 (mttt) REVERT: C 479 MET cc_start: 0.7356 (mmp) cc_final: 0.6999 (mmt) outliers start: 46 outliers final: 24 residues processed: 272 average time/residue: 0.4371 time to fit residues: 142.5587 Evaluate side-chains 260 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2157 ASP Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3417 VAL Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3512 ARG Chi-restraints excluded: chain A residue 3709 ASP Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 145 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 265 optimal weight: 40.0000 chunk 96 optimal weight: 1.9990 chunk 168 optimal weight: 0.0270 chunk 226 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3821 ASN A3978 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.171875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137169 restraints weight = 30748.844| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.09 r_work: 0.3553 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23427 Z= 0.105 Angle : 0.496 9.516 31845 Z= 0.252 Chirality : 0.042 0.196 3709 Planarity : 0.003 0.067 4027 Dihedral : 6.038 175.601 3255 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.65 % Allowed : 16.05 % Favored : 82.31 % 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: 1.37 (0.16), residues: 2974 helix: 2.28 (0.14), residues: 1424 sheet: 0.14 (0.25), residues: 462 loop : -0.59 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A2136 TYR 0.024 0.001 TYR A3683 PHE 0.020 0.001 PHE A2940 TRP 0.031 0.001 TRP A3306 HIS 0.005 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00238 (23427) covalent geometry : angle 0.49637 (31845) hydrogen bonds : bond 0.03185 ( 1274) hydrogen bonds : angle 3.90773 ( 3738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7946 (ttp80) REVERT: A 1675 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7990 (tp30) REVERT: A 1718 CYS cc_start: 0.8545 (t) cc_final: 0.8239 (t) REVERT: A 1856 LYS cc_start: 0.8421 (mttm) cc_final: 0.8037 (mtmm) REVERT: A 2428 MET cc_start: 0.8149 (tmm) cc_final: 0.7559 (tmm) REVERT: A 2792 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7633 (tt) REVERT: A 2971 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7931 (m170) REVERT: A 3008 GLN cc_start: 0.7543 (mm110) cc_final: 0.7091 (tm-30) REVERT: A 3512 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6540 (mtm-85) REVERT: A 3535 THR cc_start: 0.8482 (m) cc_final: 0.8115 (p) REVERT: A 3541 MET cc_start: 0.6807 (tpp) cc_final: 0.6599 (tpp) REVERT: A 3709 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7305 (t0) REVERT: A 3715 TYR cc_start: 0.6966 (t80) cc_final: 0.6217 (t80) REVERT: A 3744 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6339 (mm) REVERT: A 4051 ASN cc_start: 0.6874 (m-40) cc_final: 0.6323 (t0) REVERT: B 183 ASP cc_start: 0.5248 (t0) cc_final: 0.4756 (t0) REVERT: B 186 ASN cc_start: 0.5278 (m110) cc_final: 0.4830 (t0) REVERT: B 203 SER cc_start: 0.7322 (m) cc_final: 0.7000 (m) REVERT: B 234 PHE cc_start: 0.7210 (m-80) cc_final: 0.6798 (m-80) REVERT: B 242 LYS cc_start: 0.6930 (pttm) cc_final: 0.6633 (ptpp) REVERT: B 286 ASN cc_start: 0.6825 (m-40) cc_final: 0.6614 (t160) REVERT: C 281 ILE cc_start: 0.5313 (OUTLIER) cc_final: 0.5046 (pt) REVERT: C 479 MET cc_start: 0.7232 (mmp) cc_final: 0.6894 (mmt) outliers start: 38 outliers final: 26 residues processed: 271 average time/residue: 0.4351 time to fit residues: 140.9330 Evaluate side-chains 265 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2157 ASP Chi-restraints excluded: chain A residue 2206 THR Chi-restraints excluded: chain A residue 2397 THR Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3417 VAL Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3512 ARG Chi-restraints excluded: chain A residue 3709 ASP Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 251 optimal weight: 30.0000 chunk 159 optimal weight: 0.0670 chunk 125 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 266 optimal weight: 30.0000 overall best weight: 2.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2270 ASN A2490 ASN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3842 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130175 restraints weight = 30833.793| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.11 r_work: 0.3489 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23427 Z= 0.205 Angle : 0.591 9.150 31845 Z= 0.300 Chirality : 0.045 0.195 3709 Planarity : 0.004 0.044 4027 Dihedral : 6.394 172.380 3255 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.69 % Allowed : 16.31 % Favored : 82.00 % 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: 1.01 (0.15), residues: 2974 helix: 1.95 (0.14), residues: 1425 sheet: 0.03 (0.25), residues: 461 loop : -0.74 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2136 TYR 0.029 0.002 TYR A3683 PHE 0.022 0.002 PHE A2550 TRP 0.037 0.002 TRP A3306 HIS 0.007 0.001 HIS A2735 Details of bonding type rmsd covalent geometry : bond 0.00498 (23427) covalent geometry : angle 0.59115 (31845) hydrogen bonds : bond 0.03922 ( 1274) hydrogen bonds : angle 4.12034 ( 3738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 1583 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.7885 (ttp80) REVERT: A 1675 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7978 (tp30) REVERT: A 1718 CYS cc_start: 0.8589 (t) cc_final: 0.8245 (t) REVERT: A 1856 LYS cc_start: 0.8418 (mttm) cc_final: 0.8001 (mtmm) REVERT: A 2164 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7511 (mm-30) REVERT: A 2428 MET cc_start: 0.8260 (tmm) cc_final: 0.7499 (tmm) REVERT: A 2519 PRO cc_start: 0.7500 (Cg_exo) cc_final: 0.7265 (Cg_endo) REVERT: A 2792 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7720 (tt) REVERT: A 2971 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.8056 (m170) REVERT: A 2991 TYR cc_start: 0.8118 (m-80) cc_final: 0.7645 (m-80) REVERT: A 3007 TYR cc_start: 0.7124 (t80) cc_final: 0.6844 (t80) REVERT: A 3008 GLN cc_start: 0.7541 (mm110) cc_final: 0.7005 (tm-30) REVERT: A 3512 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6868 (mtm-85) REVERT: A 3535 THR cc_start: 0.8459 (m) cc_final: 0.8099 (p) REVERT: A 3541 MET cc_start: 0.6747 (tpp) cc_final: 0.6520 (tpp) REVERT: A 3709 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7305 (t0) REVERT: A 3715 TYR cc_start: 0.7066 (t80) cc_final: 0.6165 (t80) REVERT: A 3744 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6340 (mm) REVERT: A 4051 ASN cc_start: 0.6936 (m-40) cc_final: 0.6327 (t0) REVERT: B 183 ASP cc_start: 0.5211 (t0) cc_final: 0.4768 (t0) REVERT: B 186 ASN cc_start: 0.5340 (m110) cc_final: 0.4858 (t0) REVERT: B 203 SER cc_start: 0.7296 (m) cc_final: 0.6991 (m) REVERT: B 234 PHE cc_start: 0.7180 (m-80) cc_final: 0.6783 (m-80) REVERT: B 242 LYS cc_start: 0.6778 (pttm) cc_final: 0.6477 (ptpp) REVERT: B 286 ASN cc_start: 0.7026 (m-40) cc_final: 0.6803 (t0) REVERT: C 281 ILE cc_start: 0.5437 (OUTLIER) cc_final: 0.5003 (pt) REVERT: C 428 GLN cc_start: 0.7511 (pt0) cc_final: 0.7301 (pt0) REVERT: C 479 MET cc_start: 0.7387 (mmp) cc_final: 0.7164 (mmt) outliers start: 39 outliers final: 25 residues processed: 270 average time/residue: 0.4477 time to fit residues: 142.4205 Evaluate side-chains 263 residues out of total 2765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2110 THR Chi-restraints excluded: chain A residue 2157 ASP Chi-restraints excluded: chain A residue 2206 THR Chi-restraints excluded: chain A residue 2397 THR Chi-restraints excluded: chain A residue 2474 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2701 SER Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2853 LEU Chi-restraints excluded: chain A residue 2971 HIS Chi-restraints excluded: chain A residue 3417 VAL Chi-restraints excluded: chain A residue 3512 ARG Chi-restraints excluded: chain A residue 3709 ASP Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 481 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 296 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2753 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3890 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134294 restraints weight = 30768.801| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.12 r_work: 0.3523 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23427 Z= 0.144 Angle : 0.544 9.453 31845 Z= 0.276 Chirality : 0.043 0.173 3709 Planarity : 0.003 0.049 4027 Dihedral : 6.327 173.878 3255 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.65 % Allowed : 16.83 % Favored : 81.53 % 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: 1.10 (0.15), residues: 2974 helix: 2.05 (0.14), residues: 1422 sheet: 0.02 (0.24), residues: 466 loop : -0.72 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2136 TYR 0.029 0.001 TYR A2234 PHE 0.019 0.001 PHE A2550 TRP 0.032 0.002 TRP A3924 HIS 0.006 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00344 (23427) covalent geometry : angle 0.54368 (31845) hydrogen bonds : bond 0.03539 ( 1274) hydrogen bonds : angle 4.05458 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7566.32 seconds wall clock time: 129 minutes 39.08 seconds (7779.08 seconds total)