Starting phenix.real_space_refine on Sun Feb 25 02:12:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/02_2024/8dyu_27782_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/02_2024/8dyu_27782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/02_2024/8dyu_27782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/02_2024/8dyu_27782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/02_2024/8dyu_27782_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/02_2024/8dyu_27782_trim_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.025 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 S 142 5.16 5 C 15665 2.51 5 N 4260 2.21 5 O 4534 1.98 5 H 23568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1683": "OE1" <-> "OE2" Residue "A TYR 1845": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1870": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1897": "OE1" <-> "OE2" Residue "A GLU 1934": "OE1" <-> "OE2" Residue "A ASP 2077": "OD1" <-> "OD2" Residue "A GLU 2205": "OE1" <-> "OE2" Residue "A GLU 2438": "OE1" <-> "OE2" Residue "A TYR 2582": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2606": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2616": "OE1" <-> "OE2" Residue "A ASP 2670": "OD1" <-> "OD2" Residue "A GLU 2819": "OE1" <-> "OE2" Residue "A GLU 2841": "OE1" <-> "OE2" Residue "A PHE 2972": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3048": "OE1" <-> "OE2" Residue "A GLU 3108": "OE1" <-> "OE2" Residue "A GLU 3771": "OE1" <-> "OE2" Residue "A GLU 3776": "OE1" <-> "OE2" Residue "A GLU 3842": "OE1" <-> "OE2" Residue "A PHE 3996": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 4050": "OD1" <-> "OD2" Residue "A GLU 4129": "OE1" <-> "OE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48178 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 38760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2562, 38760 Classifications: {'peptide': 2562} Link IDs: {'PCIS': 2, 'PTRANS': 119, 'TRANS': 2440} Chain breaks: 19 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1142 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 29, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 31, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 574 Chain: "B" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4721 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4585 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 21.54, per 1000 atoms: 0.45 Number of scatterers: 48178 At special positions: 0 Unit cell: (105.56, 147.32, 190.24, 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 142 16.00 P 9 15.00 O 4534 8.00 N 4260 7.00 C 15665 6.00 H 23568 1.00 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 - 3.50 Amino acid : False - 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: 40.87 Conformation dependent library (CDL) restraints added in 4.8 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 31 sheets defined 43.7% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.87 Creating SS restraints... Processing helix chain 'A' and resid 1653 through 1655 No H-bonds generated for 'chain 'A' and resid 1653 through 1655' Processing helix chain 'A' and resid 1705 through 1724 removed outlier: 3.669A pdb=" N MET A1709 " --> pdb=" O VAL A1705 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1747 through 1767 removed outlier: 3.528A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1757 " --> pdb=" O SER A1753 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP A1758 " --> pdb=" O ALA A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1795 Processing helix chain 'A' and resid 1802 through 1827 removed outlier: 3.786A pdb=" N LYS A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1839 No H-bonds generated for 'chain 'A' and resid 1836 through 1839' Processing helix chain 'A' and resid 1883 through 1897 removed outlier: 3.679A pdb=" N MET A1892 " --> pdb=" O CYS A1888 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1923 Processing helix chain 'A' and resid 1938 through 1951 removed outlier: 3.672A pdb=" N VAL A1951 " --> pdb=" O GLY A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1986 removed outlier: 3.553A pdb=" N SER A1969 " --> pdb=" O GLU A1965 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A1979 " --> pdb=" O VAL A1975 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1981 " --> pdb=" O CYS A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2030 through 2035 removed outlier: 3.760A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A2035 " --> pdb=" O ASN A2031 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2030 through 2035' Processing helix chain 'A' and resid 2046 through 2057 removed outlier: 3.805A pdb=" N MET A2053 " --> pdb=" O ILE A2049 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A2054 " --> pdb=" O ALA A2050 " (cutoff:3.500A) Processing helix chain 'A' and resid 2062 through 2079 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2090 through 2110 Processing helix chain 'A' and resid 2133 through 2144 removed outlier: 3.533A pdb=" N LEU A2137 " --> pdb=" O GLU A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2146 through 2148 No H-bonds generated for 'chain 'A' and resid 2146 through 2148' Processing helix chain 'A' and resid 2154 through 2164 Processing helix chain 'A' and resid 2176 through 2186 Processing helix chain 'A' and resid 2201 through 2216 removed outlier: 3.611A pdb=" N ILE A2216 " --> pdb=" O GLN A2212 " (cutoff:3.500A) Processing helix chain 'A' and resid 2230 through 2244 Processing helix chain 'A' and resid 2261 through 2265 Processing helix chain 'A' and resid 2279 through 2289 Processing helix chain 'A' and resid 2294 through 2296 No H-bonds generated for 'chain 'A' and resid 2294 through 2296' Processing helix chain 'A' and resid 2309 through 2315 removed outlier: 3.671A pdb=" N GLU A2313 " --> pdb=" O PRO A2309 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN A2314 " --> pdb=" O GLU A2310 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2309 through 2315' Processing helix chain 'A' and resid 2353 through 2356 No H-bonds generated for 'chain 'A' and resid 2353 through 2356' Processing helix chain 'A' and resid 2371 through 2384 Processing helix chain 'A' and resid 2411 through 2426 Proline residue: A2425 - end of helix Processing helix chain 'A' and resid 2433 through 2440 Processing helix chain 'A' and resid 2451 through 2475 removed outlier: 3.836A pdb=" N LEU A2458 " --> pdb=" O CYS A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2502 removed outlier: 3.735A pdb=" N ARG A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2521 Processing helix chain 'A' and resid 2534 through 2536 No H-bonds generated for 'chain 'A' and resid 2534 through 2536' Processing helix chain 'A' and resid 2548 through 2550 No H-bonds generated for 'chain 'A' and resid 2548 through 2550' Processing helix chain 'A' and resid 2572 through 2586 Processing helix chain 'A' and resid 2601 through 2610 Processing helix chain 'A' and resid 2628 through 2638 Processing helix chain 'A' and resid 2678 through 2689 removed outlier: 3.562A pdb=" N HIS A2689 " --> pdb=" O GLN A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2725 through 2728 No H-bonds generated for 'chain 'A' and resid 2725 through 2728' Processing helix chain 'A' and resid 2741 through 2755 removed outlier: 3.711A pdb=" N THR A2745 " --> pdb=" O PRO A2741 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) Processing helix chain 'A' and resid 2760 through 2781 removed outlier: 4.736A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A2766 " --> pdb=" O ARG A2763 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU A2767 " --> pdb=" O THR A2764 " (cutoff:3.500A) Proline residue: A2768 - end of helix removed outlier: 3.797A pdb=" N ALA A2771 " --> pdb=" O PRO A2768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A2773 " --> pdb=" O THR A2770 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A2774 " --> pdb=" O ALA A2771 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A2777 " --> pdb=" O VAL A2774 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A2780 " --> pdb=" O TYR A2777 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A2781 " --> pdb=" O THR A2778 " (cutoff:3.500A) Processing helix chain 'A' and resid 2797 through 2810 Processing helix chain 'A' and resid 2818 through 2832 Processing helix chain 'A' and resid 2840 through 2857 Processing helix chain 'A' and resid 2886 through 2903 Processing helix chain 'A' and resid 2914 through 2927 Processing helix chain 'A' and resid 2945 through 2953 removed outlier: 3.716A pdb=" N MET A2953 " --> pdb=" O PHE A2949 " (cutoff:3.500A) Processing helix chain 'A' and resid 2969 through 2984 Processing helix chain 'A' and resid 3004 through 3014 removed outlier: 3.711A pdb=" N MET A3008 " --> pdb=" O PHE A3004 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 3.560A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3047 through 3061 Processing helix chain 'A' and resid 3072 through 3081 Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3099 through 3109 Processing helix chain 'A' and resid 3139 through 3164 removed outlier: 3.521A pdb=" N HIS A3151 " --> pdb=" O CYS A3147 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3173 through 3213 Processing helix chain 'A' and resid 3474 through 3481 Processing helix chain 'A' and resid 3483 through 3493 Processing helix chain 'A' and resid 3496 through 3501 Processing helix chain 'A' and resid 3503 through 3516 Processing helix chain 'A' and resid 3522 through 3538 Processing helix chain 'A' and resid 3549 through 3553 removed outlier: 3.626A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3549 through 3553' Processing helix chain 'A' and resid 3556 through 3565 Processing helix chain 'A' and resid 3571 through 3581 Processing helix chain 'A' and resid 3595 through 3603 Processing helix chain 'A' and resid 3605 through 3607 No H-bonds generated for 'chain 'A' and resid 3605 through 3607' Processing helix chain 'A' and resid 3619 through 3629 removed outlier: 4.429A pdb=" N GLU A3624 " --> pdb=" O ARG A3620 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A3625 " --> pdb=" O LYS A3621 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A3629 " --> pdb=" O SER A3625 " (cutoff:3.500A) Processing helix chain 'A' and resid 3638 through 3640 No H-bonds generated for 'chain 'A' and resid 3638 through 3640' Processing helix chain 'A' and resid 3643 through 3650 Proline residue: A3647 - end of helix removed outlier: 3.527A pdb=" N ASN A3650 " --> pdb=" O PRO A3647 " (cutoff:3.500A) Processing helix chain 'A' and resid 3690 through 3693 No H-bonds generated for 'chain 'A' and resid 3690 through 3693' Processing helix chain 'A' and resid 3705 through 3720 removed outlier: 3.815A pdb=" N GLN A3711 " --> pdb=" O SER A3707 " (cutoff:3.500A) Processing helix chain 'A' and resid 3722 through 3754 removed outlier: 3.654A pdb=" N LEU A3753 " --> pdb=" O LEU A3749 " (cutoff:3.500A) Processing helix chain 'A' and resid 3765 through 3798 removed outlier: 3.548A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A3774 " --> pdb=" O LEU A3770 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A3778 " --> pdb=" O LYS A3774 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU A3779 " --> pdb=" O ARG A3775 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A3780 " --> pdb=" O GLU A3776 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR A3781 " --> pdb=" O ALA A3777 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A3782 " --> pdb=" O ALA A3778 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU A3795 " --> pdb=" O MET A3791 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR A3796 " --> pdb=" O GLN A3792 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A3797 " --> pdb=" O GLU A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3802 through 3822 removed outlier: 3.956A pdb=" N LEU A3818 " --> pdb=" O THR A3814 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS A3819 " --> pdb=" O MET A3815 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN A3820 " --> pdb=" O GLU A3816 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE A3821 " --> pdb=" O SER A3817 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3842 removed outlier: 3.760A pdb=" N TYR A3836 " --> pdb=" O PHE A3832 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A3841 " --> pdb=" O HIS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3874 removed outlier: 3.842A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A3865 " --> pdb=" O LYS A3861 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A3871 " --> pdb=" O ALA A3867 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3891 removed outlier: 4.465A pdb=" N ILE A3881 " --> pdb=" O GLN A3878 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A3883 " --> pdb=" O HIS A3880 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A3884 " --> pdb=" O ILE A3881 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A3885 " --> pdb=" O THR A3882 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A3890 " --> pdb=" O LEU A3887 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A3891 " --> pdb=" O ALA A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3905 No H-bonds generated for 'chain 'A' and resid 3902 through 3905' Processing helix chain 'A' and resid 3907 through 3910 No H-bonds generated for 'chain 'A' and resid 3907 through 3910' Processing helix chain 'A' and resid 3929 through 3940 removed outlier: 3.665A pdb=" N ALA A3934 " --> pdb=" O GLU A3930 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3945 through 3948 removed outlier: 3.645A pdb=" N ILE A3948 " --> pdb=" O LYS A3945 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3945 through 3948' Processing helix chain 'A' and resid 3950 through 3953 No H-bonds generated for 'chain 'A' and resid 3950 through 3953' Processing helix chain 'A' and resid 3957 through 3961 Processing helix chain 'A' and resid 3982 through 3996 Processing helix chain 'A' and resid 3998 through 4012 removed outlier: 4.679A pdb=" N LEU A4002 " --> pdb=" O ASP A3999 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A4003 " --> pdb=" O ARG A4000 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A4004 " --> pdb=" O LEU A4001 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A4009 " --> pdb=" O HIS A4006 " (cutoff:3.500A) Processing helix chain 'A' and resid 4027 through 4033 Processing helix chain 'A' and resid 4052 through 4062 removed outlier: 3.687A pdb=" N GLU A4056 " --> pdb=" O SER A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4090 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4103 through 4114 removed outlier: 3.537A pdb=" N GLU A4110 " --> pdb=" O LEU A4106 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A4111 " --> pdb=" O MET A4107 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4141 Processing helix chain 'A' and resid 4153 through 4163 removed outlier: 3.728A pdb=" N MET A4157 " --> pdb=" O VAL A4153 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A4158 " --> pdb=" O LYS A4154 " (cutoff:3.500A) Processing helix chain 'A' and resid 4166 through 4169 No H-bonds generated for 'chain 'A' and resid 4166 through 4169' Processing helix chain 'A' and resid 4175 through 4195 removed outlier: 3.613A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4209 through 4226 Processing helix chain 'A' and resid 4240 through 4249 Processing helix chain 'A' and resid 4259 through 4272 Processing helix chain 'A' and resid 4275 through 4278 Processing helix chain 'A' and resid 4304 through 4311 removed outlier: 4.132A pdb=" N TRP A4308 " --> pdb=" O GLU A4304 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A4309 " --> pdb=" O PHE A4305 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A4310 " --> pdb=" O VAL A4306 " (cutoff:3.500A) Processing helix chain 'A' and resid 4318 through 4320 No H-bonds generated for 'chain 'A' and resid 4318 through 4320' Processing helix chain 'A' and resid 4325 through 4346 removed outlier: 3.728A pdb=" N VAL A4330 " --> pdb=" O ALA A4327 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A4332 " --> pdb=" O ARG A4329 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A4333 " --> pdb=" O VAL A4330 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A4337 " --> pdb=" O THR A4334 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A4340 " --> pdb=" O VAL A4337 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A4341 " --> pdb=" O ASP A4338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A4342 " --> pdb=" O MET A4339 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A4343 " --> pdb=" O ILE A4340 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A4345 " --> pdb=" O LYS A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4389 Processing helix chain 'A' and resid 4391 through 4394 No H-bonds generated for 'chain 'A' and resid 4391 through 4394' Processing helix chain 'A' and resid 4408 through 4439 removed outlier: 3.672A pdb=" N PHE A4412 " --> pdb=" O PRO A4408 " (cutoff:3.500A) Processing helix chain 'A' and resid 4449 through 4457 Processing helix chain 'A' and resid 4475 through 4497 removed outlier: 3.707A pdb=" N GLU A4484 " --> pdb=" O SER A4480 " (cutoff:3.500A) Processing helix chain 'A' and resid 4503 through 4505 No H-bonds generated for 'chain 'A' and resid 4503 through 4505' Processing helix chain 'A' and resid 4517 through 4532 Processing helix chain 'A' and resid 4633 through 4638 removed outlier: 3.917A pdb=" N ARG A4638 " --> pdb=" O PHE A4635 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.282A pdb=" N SER B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B 293 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.451A pdb=" N SER C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 295 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1844 through 1846 Processing sheet with id= B, first strand: chain 'A' and resid 2036 through 2040 removed outlier: 6.656A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A1902 " --> pdb=" O ILE A2014 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2360 through 2364 removed outlier: 6.106A pdb=" N ILE A2341 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET A2222 " --> pdb=" O ILE A2341 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A2343 " --> pdb=" O MET A2222 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLY A2224 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A2345 " --> pdb=" O GLY A2224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A2340 " --> pdb=" O GLN A2299 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id= E, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id= F, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id= G, first strand: chain 'A' and resid 2732 through 2734 removed outlier: 6.707A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 3.611A pdb=" N ARG A2642 " --> pdb=" O VAL A2649 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 3090 through 3092 removed outlier: 6.622A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 3587 through 3591 removed outlier: 6.633A pdb=" N THR A3697 " --> pdb=" O LEU A3588 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A3590 " --> pdb=" O THR A3697 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A3699 " --> pdb=" O ILE A3590 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 3610 through 3613 Processing sheet with id= L, first strand: chain 'A' and resid 3661 through 3663 Processing sheet with id= M, first strand: chain 'A' and resid 4143 through 4147 Processing sheet with id= N, first strand: chain 'A' and resid 4542 through 4544 Processing sheet with id= O, first strand: chain 'A' and resid 4564 through 4566 Processing sheet with id= P, first strand: chain 'A' and resid 4605 through 4609 removed outlier: 4.111A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.224A pdb=" N GLU B 408 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 102 through 104 Processing sheet with id= S, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.597A pdb=" N ALA B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 114 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 124 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.977A pdb=" N CYS B 168 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 156 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 166 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE B 158 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 164 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP B 178 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS B 184 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 195 through 200 removed outlier: 6.904A pdb=" N ALA B 210 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 198 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 208 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 200 " --> pdb=" O HIS B 206 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N HIS B 206 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 270 through 272 Processing sheet with id= W, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.751A pdb=" N GLY B 314 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE B 282 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 312 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TRP B 284 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE B 310 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 341 through 346 removed outlier: 6.531A pdb=" N CYS B 356 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 344 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 354 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 357 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP B 366 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS B 372 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.190A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 396 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 398 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 385 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.666A pdb=" N ARG C 144 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.033A pdb=" N CYS C 168 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE C 156 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA C 166 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE C 158 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU C 164 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 186 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 195 through 200 removed outlier: 7.009A pdb=" N ALA C 210 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 198 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 208 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 200 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS C 206 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 228 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 270 through 272 removed outlier: 3.702A pdb=" N ALA C 270 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 239 " --> pdb=" O CYS C 252 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 310 through 314 removed outlier: 6.617A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 341 through 346 removed outlier: 6.844A pdb=" N CYS C 356 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL C 344 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU C 354 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 357 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP C 366 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N CYS C 372 " --> pdb=" O ASP C 366 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3012 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: 25.03 Time building geometry restraints manager: 41.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 23514 1.04 - 1.24: 2060 1.24 - 1.43: 8746 1.43 - 1.63: 14181 1.63 - 1.83: 228 Bond restraints: 48729 Sorted by residual: bond pdb=" C VAL B 278 " pdb=" O VAL B 278 " ideal model delta sigma weight residual 1.236 1.135 0.101 1.19e-02 7.06e+03 7.18e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" CA SER C 399 " pdb=" CB SER C 399 " ideal model delta sigma weight residual 1.533 1.470 0.063 1.60e-02 3.91e+03 1.55e+01 bond pdb=" N VAL C 383 " pdb=" CA VAL C 383 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.15e-02 7.56e+03 1.16e+01 ... (remaining 48724 not shown) Histogram of bond angle deviations from ideal: 97.05 - 105.60: 653 105.60 - 114.15: 58247 114.15 - 122.70: 22529 122.70 - 131.25: 6327 131.25 - 139.81: 98 Bond angle restraints: 87854 Sorted by residual: angle pdb=" CA THR B 112 " pdb=" C THR B 112 " pdb=" O THR B 112 " ideal model delta sigma weight residual 119.67 110.07 9.60 1.15e+00 7.56e-01 6.97e+01 angle pdb=" CA THR C 384 " pdb=" C THR C 384 " pdb=" O THR C 384 " ideal model delta sigma weight residual 120.90 112.49 8.41 1.03e+00 9.43e-01 6.66e+01 angle pdb=" C THR B 319 " pdb=" CA THR B 319 " pdb=" CB THR B 319 " ideal model delta sigma weight residual 110.62 98.88 11.74 1.51e+00 4.39e-01 6.04e+01 angle pdb=" CA VAL B 278 " pdb=" C VAL B 278 " pdb=" O VAL B 278 " ideal model delta sigma weight residual 120.78 112.20 8.58 1.25e+00 6.40e-01 4.72e+01 angle pdb=" N LYS B 318 " pdb=" CA LYS B 318 " pdb=" C LYS B 318 " ideal model delta sigma weight residual 113.23 105.34 7.89 1.22e+00 6.72e-01 4.18e+01 ... (remaining 87849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 22476 35.38 - 70.75: 599 70.75 - 106.13: 32 106.13 - 141.51: 2 141.51 - 176.88: 1 Dihedral angle restraints: 23110 sinusoidal: 12213 harmonic: 10897 Sorted by residual: dihedral pdb=" O2A ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PA ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 116.88 -176.88 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A4704 " pdb=" O5' ADP A4704 " pdb=" PA ADP A4704 " pdb=" O2A ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 70.59 -130.59 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " pdb=" PA ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 -171.77 111.77 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 23107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3549 0.079 - 0.157: 349 0.157 - 0.236: 17 0.236 - 0.315: 5 0.315 - 0.394: 1 Chirality restraints: 3921 Sorted by residual: chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB VAL B 278 " pdb=" CA VAL B 278 " pdb=" CG1 VAL B 278 " pdb=" CG2 VAL B 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' ATP A4702 " pdb=" C1' ATP A4702 " pdb=" C3' ATP A4702 " pdb=" O2' ATP A4702 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3918 not shown) Planarity restraints: 7367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 377 " 0.183 2.00e-02 2.50e+03 2.01e-01 6.03e+02 pdb=" CG ASN C 377 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN C 377 " -0.171 2.00e-02 2.50e+03 pdb=" ND2 ASN C 377 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 377 " -0.292 2.00e-02 2.50e+03 pdb="HD22 ASN C 377 " 0.304 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A3754 " 0.166 2.00e-02 2.50e+03 1.83e-01 5.03e+02 pdb=" CG ASN A3754 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A3754 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN A3754 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A3754 " 0.278 2.00e-02 2.50e+03 pdb="HD22 ASN A3754 " -0.268 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A3772 " 0.108 2.00e-02 2.50e+03 1.17e-01 2.04e+02 pdb=" CG ASN A3772 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A3772 " -0.107 2.00e-02 2.50e+03 pdb=" ND2 ASN A3772 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A3772 " 0.171 2.00e-02 2.50e+03 pdb="HD22 ASN A3772 " -0.171 2.00e-02 2.50e+03 ... (remaining 7364 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1148 2.13 - 2.75: 85241 2.75 - 3.37: 136312 3.37 - 3.98: 169801 3.98 - 4.60: 267979 Nonbonded interactions: 660481 Sorted by model distance: nonbonded pdb=" HG SER B 313 " pdb=" HE1 TRP B 323 " model vdw 1.516 2.100 nonbonded pdb=" OE1 GLU A3720 " pdb=" HH TYR A3801 " model vdw 1.604 1.850 nonbonded pdb=" OD1 ASP C 213 " pdb=" HG1 THR C 215 " model vdw 1.615 1.850 nonbonded pdb=" O LEU A1873 " pdb="HE22 GLN A1876 " model vdw 1.624 1.850 nonbonded pdb=" HG SER C 313 " pdb=" HE1 TRP C 323 " model vdw 1.630 2.100 ... (remaining 660476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 91 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 102 through 107 or (re \ sid 108 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or res \ id 109 through 162 or (resid 163 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 164 through 179 or (resid 180 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 181 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 270 through 272 or (resid 273 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 274 throu \ gh 286 or (resid 287 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 288 through 294 or (resid 295 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 296 or (resid 2 \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 308 through 350 or (resid 351 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 352 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 371 through 410)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.700 Extract box with map and model: 11.760 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 156.280 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 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 : 0.005 0.110 25161 Z= 0.309 Angle : 0.868 11.738 34237 Z= 0.489 Chirality : 0.048 0.394 3921 Planarity : 0.006 0.112 4362 Dihedral : 14.186 176.883 8989 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.23 % Allowed : 0.74 % Favored : 99.02 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3122 helix: 0.61 (0.14), residues: 1360 sheet: -0.53 (0.23), residues: 494 loop : -0.67 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1758 HIS 0.023 0.002 HIS C 193 PHE 0.026 0.002 PHE B 310 TYR 0.050 0.002 TYR A1889 ARG 0.016 0.001 ARG A1943 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 707 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 701 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1836 PHE cc_start: 0.6002 (t80) cc_final: 0.5743 (t80) REVERT: A 1897 GLU cc_start: 0.6359 (tp30) cc_final: 0.5932 (tp30) REVERT: A 1929 VAL cc_start: 0.8627 (t) cc_final: 0.8365 (p) REVERT: A 2034 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7944 (ttmm) REVERT: A 2088 PHE cc_start: 0.7751 (m-10) cc_final: 0.7504 (m-10) REVERT: A 2097 LEU cc_start: 0.8485 (mt) cc_final: 0.8245 (mt) REVERT: A 2221 MET cc_start: 0.7065 (ttt) cc_final: 0.6579 (ttt) REVERT: A 2222 MET cc_start: 0.8204 (mtt) cc_final: 0.7890 (mpp) REVERT: A 2361 MET cc_start: 0.6190 (ttm) cc_final: 0.5925 (ttm) REVERT: A 2493 TYR cc_start: 0.7820 (t80) cc_final: 0.7539 (t80) REVERT: A 2823 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7384 (tpt170) REVERT: A 2852 THR cc_start: 0.8422 (p) cc_final: 0.8157 (t) REVERT: A 2910 VAL cc_start: 0.7950 (p) cc_final: 0.7551 (m) REVERT: A 2924 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7921 (mtp-110) REVERT: A 3205 LEU cc_start: 0.8479 (mt) cc_final: 0.8202 (tt) REVERT: A 3747 LYS cc_start: 0.8662 (tttt) cc_final: 0.8432 (tppt) REVERT: A 4493 SER cc_start: 0.9008 (t) cc_final: 0.8508 (p) REVERT: B 141 ASP cc_start: 0.7662 (m-30) cc_final: 0.7230 (m-30) REVERT: B 254 ASN cc_start: 0.7380 (m110) cc_final: 0.7156 (m110) REVERT: B 356 CYS cc_start: 0.6729 (p) cc_final: 0.6366 (p) REVERT: C 387 ASP cc_start: 0.7619 (t70) cc_final: 0.7197 (t70) outliers start: 6 outliers final: 1 residues processed: 704 average time/residue: 0.8623 time to fit residues: 924.4144 Evaluate side-chains 445 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1856 GLN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2468 ASN ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3063 HIS A3104 GLN A3155 HIS A3711 GLN A4006 HIS B 402 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25161 Z= 0.293 Angle : 0.636 6.560 34237 Z= 0.334 Chirality : 0.041 0.174 3921 Planarity : 0.005 0.084 4362 Dihedral : 7.611 174.144 3461 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.84 % Allowed : 10.05 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3122 helix: 0.85 (0.14), residues: 1364 sheet: -0.43 (0.23), residues: 506 loop : -0.77 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1758 HIS 0.006 0.001 HIS A2791 PHE 0.025 0.002 PHE A3054 TYR 0.029 0.002 TYR A2748 ARG 0.006 0.001 ARG A4140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 489 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 442 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1836 PHE cc_start: 0.6423 (t80) cc_final: 0.6184 (t80) REVERT: A 1929 VAL cc_start: 0.8715 (t) cc_final: 0.8384 (p) REVERT: A 2034 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8142 (ttmm) REVERT: A 2088 PHE cc_start: 0.8075 (m-10) cc_final: 0.7771 (m-10) REVERT: A 2222 MET cc_start: 0.8161 (mtt) cc_final: 0.7487 (mpp) REVERT: A 2823 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7465 (tpt170) REVERT: A 2849 ASN cc_start: 0.8242 (m110) cc_final: 0.7695 (m110) REVERT: A 3094 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 3115 LEU cc_start: 0.6985 (mt) cc_final: 0.6753 (mt) REVERT: A 3176 TYR cc_start: 0.7653 (t80) cc_final: 0.7449 (t80) REVERT: A 3579 MET cc_start: 0.7706 (mmp) cc_final: 0.6886 (mmp) REVERT: A 3735 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: A 3747 LYS cc_start: 0.8704 (tttt) cc_final: 0.8399 (tppt) REVERT: A 4004 MET cc_start: 0.6461 (tpt) cc_final: 0.5920 (tpt) REVERT: A 4211 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6829 (m-30) REVERT: A 4493 SER cc_start: 0.9043 (t) cc_final: 0.8498 (p) REVERT: B 141 ASP cc_start: 0.7565 (m-30) cc_final: 0.7222 (m-30) outliers start: 47 outliers final: 38 residues processed: 468 average time/residue: 0.8217 time to fit residues: 607.7488 Evaluate side-chains 441 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 400 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2304 ASP Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2868 SER Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4483 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 289 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 256 optimal weight: 0.2980 chunk 285 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1856 GLN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN ** A4566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25161 Z= 0.158 Angle : 0.546 6.386 34237 Z= 0.277 Chirality : 0.040 0.185 3921 Planarity : 0.004 0.072 4362 Dihedral : 6.979 179.643 3457 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.37 % Allowed : 11.49 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3122 helix: 1.31 (0.14), residues: 1349 sheet: -0.30 (0.23), residues: 502 loop : -0.63 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4387 HIS 0.022 0.001 HIS A3155 PHE 0.019 0.001 PHE A3678 TYR 0.019 0.001 TYR A1889 ARG 0.004 0.000 ARG A2358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 428 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.8943 (m) cc_final: 0.8564 (p) REVERT: A 1929 VAL cc_start: 0.8642 (t) cc_final: 0.8327 (p) REVERT: A 2034 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8077 (ttmm) REVERT: A 2222 MET cc_start: 0.8206 (mtt) cc_final: 0.7582 (mpp) REVERT: A 2658 TRP cc_start: 0.6696 (m100) cc_final: 0.6302 (m-10) REVERT: A 2823 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7263 (tpt170) REVERT: A 3068 MET cc_start: 0.6348 (mmp) cc_final: 0.5965 (mmp) REVERT: A 3094 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7261 (t80) REVERT: A 3579 MET cc_start: 0.7799 (mmp) cc_final: 0.6859 (mmp) REVERT: A 3735 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: A 3747 LYS cc_start: 0.8678 (tttt) cc_final: 0.8401 (tppt) REVERT: A 4004 MET cc_start: 0.6404 (tpt) cc_final: 0.6001 (tpt) REVERT: A 4157 MET cc_start: 0.7473 (mpp) cc_final: 0.7028 (mpp) REVERT: A 4493 SER cc_start: 0.8964 (t) cc_final: 0.8456 (p) REVERT: B 141 ASP cc_start: 0.7540 (m-30) cc_final: 0.7230 (m-30) REVERT: B 254 ASN cc_start: 0.7754 (m110) cc_final: 0.7338 (m-40) REVERT: B 339 ASN cc_start: 0.7549 (t0) cc_final: 0.7242 (m110) REVERT: B 365 TRP cc_start: 0.7909 (m100) cc_final: 0.7621 (m100) REVERT: C 405 LYS cc_start: 0.8034 (mttm) cc_final: 0.7376 (mttt) outliers start: 35 outliers final: 23 residues processed: 449 average time/residue: 0.8433 time to fit residues: 601.8988 Evaluate side-chains 427 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 402 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2498 ILE Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 273 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A4174 ASN ** A4566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25161 Z= 0.223 Angle : 0.558 6.597 34237 Z= 0.287 Chirality : 0.039 0.160 3921 Planarity : 0.004 0.059 4362 Dihedral : 6.760 170.676 3457 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.76 % Allowed : 12.28 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3122 helix: 1.32 (0.14), residues: 1357 sheet: -0.40 (0.23), residues: 507 loop : -0.73 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4387 HIS 0.006 0.001 HIS A2218 PHE 0.020 0.001 PHE A3054 TYR 0.015 0.001 TYR A1889 ARG 0.002 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 457 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 412 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5143 (tpt) cc_final: 0.4942 (tpt) REVERT: A 1759 SER cc_start: 0.8967 (m) cc_final: 0.8615 (p) REVERT: A 1836 PHE cc_start: 0.6503 (t80) cc_final: 0.6175 (t80) REVERT: A 1846 PHE cc_start: 0.7646 (t80) cc_final: 0.7295 (t80) REVERT: A 1921 HIS cc_start: 0.6330 (t70) cc_final: 0.6118 (t-170) REVERT: A 1929 VAL cc_start: 0.8689 (t) cc_final: 0.8358 (p) REVERT: A 2034 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8226 (ttmm) REVERT: A 2222 MET cc_start: 0.8188 (mtt) cc_final: 0.7421 (mpp) REVERT: A 2343 PHE cc_start: 0.7926 (m-10) cc_final: 0.7669 (m-10) REVERT: A 2412 MET cc_start: 0.7362 (mmm) cc_final: 0.7059 (mmt) REVERT: A 2658 TRP cc_start: 0.6843 (m100) cc_final: 0.6389 (m-10) REVERT: A 2823 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7333 (tpt170) REVERT: A 2849 ASN cc_start: 0.8029 (m110) cc_final: 0.7677 (m110) REVERT: A 3094 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7115 (t80) REVERT: A 3735 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 3747 LYS cc_start: 0.8736 (tttt) cc_final: 0.8433 (tppt) REVERT: A 4004 MET cc_start: 0.6496 (tpt) cc_final: 0.6052 (tpt) REVERT: A 4100 HIS cc_start: 0.5701 (p-80) cc_final: 0.4156 (p-80) REVERT: A 4157 MET cc_start: 0.7626 (mpp) cc_final: 0.7141 (mpp) REVERT: A 4493 SER cc_start: 0.8978 (t) cc_final: 0.8490 (p) REVERT: B 141 ASP cc_start: 0.7680 (m-30) cc_final: 0.7333 (m-30) REVERT: B 254 ASN cc_start: 0.7826 (m110) cc_final: 0.7434 (m-40) REVERT: B 339 ASN cc_start: 0.7699 (t0) cc_final: 0.7308 (m110) REVERT: C 217 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7545 (tppt) REVERT: C 405 LYS cc_start: 0.8062 (mttm) cc_final: 0.7215 (mtmm) outliers start: 45 outliers final: 36 residues processed: 444 average time/residue: 0.8774 time to fit residues: 621.5794 Evaluate side-chains 429 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 391 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2868 SER Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4174 ASN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4483 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 0.7980 chunk 173 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 274 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A4174 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25161 Z= 0.195 Angle : 0.538 6.067 34237 Z= 0.276 Chirality : 0.039 0.151 3921 Planarity : 0.004 0.065 4362 Dihedral : 6.520 159.385 3457 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.92 % Allowed : 13.25 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3122 helix: 1.38 (0.14), residues: 1357 sheet: -0.38 (0.23), residues: 507 loop : -0.70 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4387 HIS 0.025 0.001 HIS A3155 PHE 0.019 0.001 PHE A3054 TYR 0.012 0.001 TYR A1889 ARG 0.007 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 407 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5227 (tpt) cc_final: 0.5016 (tpt) REVERT: A 1759 SER cc_start: 0.8890 (m) cc_final: 0.8534 (p) REVERT: A 1804 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7449 (ttm170) REVERT: A 1836 PHE cc_start: 0.6445 (t80) cc_final: 0.6134 (t80) REVERT: A 1846 PHE cc_start: 0.7730 (t80) cc_final: 0.7311 (t80) REVERT: A 1929 VAL cc_start: 0.8684 (t) cc_final: 0.8359 (p) REVERT: A 2034 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8208 (ttmm) REVERT: A 2222 MET cc_start: 0.8176 (mtt) cc_final: 0.7377 (mpp) REVERT: A 2230 LYS cc_start: 0.8040 (mttp) cc_final: 0.7819 (mttp) REVERT: A 2343 PHE cc_start: 0.7915 (m-10) cc_final: 0.7606 (m-10) REVERT: A 2412 MET cc_start: 0.7427 (mmm) cc_final: 0.7129 (mmt) REVERT: A 2658 TRP cc_start: 0.6790 (m100) cc_final: 0.6452 (m-10) REVERT: A 2823 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7081 (tpt170) REVERT: A 2849 ASN cc_start: 0.8024 (m110) cc_final: 0.7631 (m110) REVERT: A 3094 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6843 (t80) REVERT: A 3176 TYR cc_start: 0.7250 (t80) cc_final: 0.6863 (t80) REVERT: A 3198 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 3579 MET cc_start: 0.8064 (mmp) cc_final: 0.6694 (mmp) REVERT: A 3735 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: A 3747 LYS cc_start: 0.8705 (tttt) cc_final: 0.8433 (tppt) REVERT: A 4004 MET cc_start: 0.6426 (tpt) cc_final: 0.6027 (tpt) REVERT: A 4115 SER cc_start: 0.8254 (m) cc_final: 0.7516 (p) REVERT: A 4493 SER cc_start: 0.8985 (t) cc_final: 0.8507 (p) REVERT: B 141 ASP cc_start: 0.7680 (m-30) cc_final: 0.7336 (m-30) REVERT: B 254 ASN cc_start: 0.7814 (m110) cc_final: 0.7438 (m-40) REVERT: B 339 ASN cc_start: 0.7696 (t0) cc_final: 0.7275 (m110) REVERT: C 405 LYS cc_start: 0.7963 (mttm) cc_final: 0.7161 (mtmm) outliers start: 49 outliers final: 42 residues processed: 443 average time/residue: 0.8313 time to fit residues: 587.5598 Evaluate side-chains 431 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 387 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2947 SER Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4174 ASN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4483 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 25161 Z= 0.285 Angle : 0.593 7.042 34237 Z= 0.310 Chirality : 0.040 0.223 3921 Planarity : 0.004 0.062 4362 Dihedral : 6.528 137.792 3457 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.46 % Allowed : 13.29 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3122 helix: 1.11 (0.14), residues: 1344 sheet: -0.47 (0.23), residues: 505 loop : -0.94 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A4387 HIS 0.012 0.002 HIS A2689 PHE 0.021 0.002 PHE A3054 TYR 0.032 0.002 TYR A1889 ARG 0.005 0.000 ARG A3937 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 454 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 391 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5406 (tpt) cc_final: 0.5184 (tpt) REVERT: A 1759 SER cc_start: 0.8924 (m) cc_final: 0.8565 (p) REVERT: A 1929 VAL cc_start: 0.8716 (t) cc_final: 0.8366 (p) REVERT: A 2034 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8335 (ttmm) REVERT: A 2412 MET cc_start: 0.7583 (mmm) cc_final: 0.7294 (mmt) REVERT: A 2849 ASN cc_start: 0.7945 (m110) cc_final: 0.7575 (m110) REVERT: A 3094 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6855 (t80) REVERT: A 3198 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 3579 MET cc_start: 0.8218 (mmp) cc_final: 0.7260 (mmp) REVERT: A 3735 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: A 3747 LYS cc_start: 0.8772 (tttt) cc_final: 0.8470 (tppt) REVERT: A 4004 MET cc_start: 0.6563 (tpt) cc_final: 0.6140 (tpt) REVERT: A 4115 SER cc_start: 0.8279 (m) cc_final: 0.7597 (p) REVERT: A 4493 SER cc_start: 0.8978 (t) cc_final: 0.8495 (p) REVERT: B 141 ASP cc_start: 0.7624 (m-30) cc_final: 0.7250 (m-30) REVERT: B 254 ASN cc_start: 0.7775 (m110) cc_final: 0.7514 (m-40) REVERT: C 405 LYS cc_start: 0.8040 (mttm) cc_final: 0.7450 (mttt) outliers start: 63 outliers final: 54 residues processed: 437 average time/residue: 0.8253 time to fit residues: 575.6875 Evaluate side-chains 426 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 370 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4174 ASN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4483 SER Chi-restraints excluded: chain A residue 4486 ILE Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 304 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 140 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4174 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25161 Z= 0.221 Angle : 0.561 9.627 34237 Z= 0.289 Chirality : 0.040 0.147 3921 Planarity : 0.004 0.066 4362 Dihedral : 6.248 115.307 3457 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.35 % Allowed : 13.76 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3122 helix: 1.18 (0.14), residues: 1351 sheet: -0.46 (0.23), residues: 500 loop : -0.87 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4387 HIS 0.007 0.001 HIS C 193 PHE 0.021 0.001 PHE A3054 TYR 0.015 0.001 TYR A2496 ARG 0.004 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 393 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.8934 (m) cc_final: 0.8578 (p) REVERT: A 1873 LEU cc_start: 0.7982 (mm) cc_final: 0.7761 (mm) REVERT: A 1921 HIS cc_start: 0.6117 (t70) cc_final: 0.5826 (t70) REVERT: A 1929 VAL cc_start: 0.8681 (t) cc_final: 0.8341 (p) REVERT: A 2034 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8319 (ttmm) REVERT: A 2849 ASN cc_start: 0.8078 (m110) cc_final: 0.7648 (m110) REVERT: A 3094 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6714 (t80) REVERT: A 3176 TYR cc_start: 0.7331 (t80) cc_final: 0.6803 (t80) REVERT: A 3198 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 3579 MET cc_start: 0.8256 (mmp) cc_final: 0.6952 (mmp) REVERT: A 3735 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: A 3747 LYS cc_start: 0.8745 (tttt) cc_final: 0.8446 (tppt) REVERT: A 4004 MET cc_start: 0.6501 (tpt) cc_final: 0.6065 (tpt) REVERT: A 4115 SER cc_start: 0.8261 (m) cc_final: 0.7574 (p) REVERT: A 4493 SER cc_start: 0.8970 (t) cc_final: 0.8489 (p) REVERT: B 141 ASP cc_start: 0.7597 (m-30) cc_final: 0.7274 (m-30) REVERT: B 254 ASN cc_start: 0.7774 (m110) cc_final: 0.7492 (m-40) REVERT: B 269 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7368 (mmmt) REVERT: C 203 ASN cc_start: 0.7616 (p0) cc_final: 0.6913 (p0) REVERT: C 405 LYS cc_start: 0.8030 (mttm) cc_final: 0.7438 (mttt) outliers start: 60 outliers final: 49 residues processed: 435 average time/residue: 0.8163 time to fit residues: 562.4976 Evaluate side-chains 435 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 384 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4174 ASN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4483 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25161 Z= 0.263 Angle : 0.582 9.500 34237 Z= 0.302 Chirality : 0.040 0.145 3921 Planarity : 0.004 0.065 4362 Dihedral : 6.127 87.073 3457 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.35 % Allowed : 14.66 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3122 helix: 1.10 (0.14), residues: 1339 sheet: -0.54 (0.23), residues: 501 loop : -0.94 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A4387 HIS 0.007 0.001 HIS C 193 PHE 0.021 0.002 PHE A3054 TYR 0.016 0.002 TYR A2496 ARG 0.004 0.000 ARG A3682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 438 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 378 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.8913 (m) cc_final: 0.8565 (p) REVERT: A 1929 VAL cc_start: 0.8683 (t) cc_final: 0.8342 (p) REVERT: A 2034 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8359 (ttmm) REVERT: A 2849 ASN cc_start: 0.7996 (m110) cc_final: 0.7608 (m110) REVERT: A 3094 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 3176 TYR cc_start: 0.7462 (t80) cc_final: 0.6872 (t80) REVERT: A 3198 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7602 (tm-30) REVERT: A 3579 MET cc_start: 0.8327 (mmp) cc_final: 0.7025 (mmp) REVERT: A 3735 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: A 3747 LYS cc_start: 0.8770 (tttt) cc_final: 0.8451 (tppt) REVERT: A 4004 MET cc_start: 0.6548 (tpt) cc_final: 0.6143 (tpt) REVERT: A 4115 SER cc_start: 0.8264 (m) cc_final: 0.7586 (p) REVERT: A 4493 SER cc_start: 0.8993 (t) cc_final: 0.8511 (p) REVERT: B 141 ASP cc_start: 0.7560 (m-30) cc_final: 0.7253 (m-30) REVERT: B 254 ASN cc_start: 0.7956 (m110) cc_final: 0.7706 (m-40) REVERT: B 269 LYS cc_start: 0.8080 (mmpt) cc_final: 0.7525 (mmmt) REVERT: C 203 ASN cc_start: 0.7592 (p0) cc_final: 0.6906 (p0) REVERT: C 332 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7398 (ppp) REVERT: C 405 LYS cc_start: 0.8040 (mttm) cc_final: 0.7440 (mttt) outliers start: 60 outliers final: 52 residues processed: 421 average time/residue: 0.8217 time to fit residues: 551.5324 Evaluate side-chains 425 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 370 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2317 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4483 SER Chi-restraints excluded: chain A residue 4486 ILE Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 170 optimal weight: 0.0870 chunk 123 optimal weight: 2.9990 chunk 222 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 282 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2476 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4174 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25161 Z= 0.150 Angle : 0.540 8.993 34237 Z= 0.272 Chirality : 0.040 0.227 3921 Planarity : 0.004 0.070 4362 Dihedral : 5.641 70.420 3457 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.64 % Allowed : 15.21 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3122 helix: 1.57 (0.14), residues: 1348 sheet: -0.34 (0.23), residues: 491 loop : -0.67 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4387 HIS 0.009 0.001 HIS C 193 PHE 0.020 0.001 PHE A3054 TYR 0.017 0.001 TYR A2748 ARG 0.003 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 399 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.9010 (m) cc_final: 0.8657 (p) REVERT: A 1929 VAL cc_start: 0.8611 (t) cc_final: 0.8293 (p) REVERT: A 2034 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8260 (ttmm) REVERT: A 2658 TRP cc_start: 0.6680 (m100) cc_final: 0.6416 (m-10) REVERT: A 2849 ASN cc_start: 0.7931 (m110) cc_final: 0.7556 (m110) REVERT: A 3094 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6474 (t80) REVERT: A 3176 TYR cc_start: 0.7193 (t80) cc_final: 0.6698 (t80) REVERT: A 3198 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 3579 MET cc_start: 0.8291 (mmp) cc_final: 0.7208 (mmp) REVERT: A 3735 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: A 3747 LYS cc_start: 0.8739 (tttt) cc_final: 0.8407 (tppt) REVERT: A 4004 MET cc_start: 0.6480 (tpt) cc_final: 0.6068 (tpt) REVERT: A 4115 SER cc_start: 0.8184 (m) cc_final: 0.7511 (p) REVERT: A 4493 SER cc_start: 0.8976 (t) cc_final: 0.8507 (p) REVERT: B 141 ASP cc_start: 0.7475 (m-30) cc_final: 0.7135 (m-30) REVERT: B 254 ASN cc_start: 0.7596 (m110) cc_final: 0.7326 (m-40) REVERT: C 123 MET cc_start: 0.6849 (ppp) cc_final: 0.6275 (ppp) REVERT: C 203 ASN cc_start: 0.7605 (p0) cc_final: 0.6892 (p0) REVERT: C 332 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7449 (ppp) REVERT: C 405 LYS cc_start: 0.7976 (mttm) cc_final: 0.7383 (mttt) outliers start: 42 outliers final: 35 residues processed: 428 average time/residue: 0.8186 time to fit residues: 560.9162 Evaluate side-chains 418 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 380 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4174 ASN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2476 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 25161 Z= 0.262 Angle : 0.690 59.140 34237 Z= 0.385 Chirality : 0.040 0.207 3921 Planarity : 0.004 0.069 4362 Dihedral : 5.644 70.124 3457 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.64 % Allowed : 15.44 % Favored : 82.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3122 helix: 1.56 (0.14), residues: 1348 sheet: -0.35 (0.23), residues: 491 loop : -0.67 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4222 HIS 0.017 0.001 HIS C 193 PHE 0.039 0.001 PHE A1836 TYR 0.013 0.001 TYR A2748 ARG 0.006 0.000 ARG A2823 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 376 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.8958 (m) cc_final: 0.8622 (p) REVERT: A 1929 VAL cc_start: 0.8631 (t) cc_final: 0.8309 (p) REVERT: A 2034 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8282 (ttmm) REVERT: A 2658 TRP cc_start: 0.6678 (m100) cc_final: 0.6402 (m-10) REVERT: A 2849 ASN cc_start: 0.7889 (m110) cc_final: 0.7505 (m110) REVERT: A 3094 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6481 (t80) REVERT: A 3176 TYR cc_start: 0.7237 (t80) cc_final: 0.6720 (t80) REVERT: A 3198 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 3579 MET cc_start: 0.8277 (mmp) cc_final: 0.7174 (mmp) REVERT: A 3735 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: A 3747 LYS cc_start: 0.8750 (tttt) cc_final: 0.8422 (tppt) REVERT: A 4004 MET cc_start: 0.6524 (tpt) cc_final: 0.6086 (tpt) REVERT: A 4115 SER cc_start: 0.8190 (m) cc_final: 0.7529 (p) REVERT: A 4493 SER cc_start: 0.8984 (t) cc_final: 0.8518 (p) REVERT: B 141 ASP cc_start: 0.7481 (m-30) cc_final: 0.7144 (m-30) REVERT: B 254 ASN cc_start: 0.7620 (m110) cc_final: 0.7357 (m-40) REVERT: C 123 MET cc_start: 0.6870 (ppp) cc_final: 0.6296 (ppp) REVERT: C 203 ASN cc_start: 0.7548 (p0) cc_final: 0.6849 (p0) REVERT: C 332 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7456 (ppp) REVERT: C 405 LYS cc_start: 0.7981 (mttm) cc_final: 0.7392 (mttt) outliers start: 42 outliers final: 37 residues processed: 407 average time/residue: 0.8224 time to fit residues: 534.0463 Evaluate side-chains 416 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 376 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2476 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.129302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.114836 restraints weight = 188085.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.118539 restraints weight = 81118.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.120804 restraints weight = 44034.773| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 25161 Z= 0.262 Angle : 0.690 59.200 34237 Z= 0.385 Chirality : 0.040 0.206 3921 Planarity : 0.004 0.069 4362 Dihedral : 5.644 70.124 3457 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 15.52 % Favored : 82.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3122 helix: 1.56 (0.14), residues: 1348 sheet: -0.35 (0.23), residues: 491 loop : -0.67 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4222 HIS 0.017 0.001 HIS C 193 PHE 0.039 0.001 PHE A1836 TYR 0.013 0.001 TYR A2748 ARG 0.006 0.000 ARG A2823 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11115.98 seconds wall clock time: 197 minutes 53.33 seconds (11873.33 seconds total)