Starting phenix.real_space_refine on Tue Sep 24 11:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/09_2024/8dzz_27810_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/09_2024/8dzz_27810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/09_2024/8dzz_27810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/09_2024/8dzz_27810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/09_2024/8dzz_27810_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/09_2024/8dzz_27810_neut.cif" } resolution = 4.1 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= 0.003 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 236 5.16 5 C 31738 2.51 5 N 8330 2.21 5 O 9270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 19073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19073 Classifications: {'peptide': 2363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 64, 'TRANS': 2298} Chain breaks: 10 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2773 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Chain: "C" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2832 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "D" Number of atoms: 19073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19073 Classifications: {'peptide': 2363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 64, 'TRANS': 2298} Chain breaks: 10 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2773 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Chain: "F" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2832 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ADP': 1, 'ATP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ADP': 1, 'ATP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 21.52, per 1000 atoms: 0.43 Number of scatterers: 49596 At special positions: 0 Unit cell: (224.01, 168.99, 196.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 236 16.00 P 22 15.00 O 9270 8.00 N 8330 7.00 C 31738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.76 Conformation dependent library (CDL) restraints added in 4.7 seconds 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11636 Finding SS restraints... Secondary structure from input PDB file: 238 helices and 60 sheets defined 51.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'A' and resid 1449 through 1459 Processing helix chain 'A' and resid 1464 through 1468 removed outlier: 3.547A pdb=" N ASN A1467 " --> pdb=" O ASP A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1479 Processing helix chain 'A' and resid 1516 through 1522 Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 3.555A pdb=" N GLN A1533 " --> pdb=" O ARG A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1556 through 1561 removed outlier: 3.603A pdb=" N LYS A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1556 through 1561' Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1633 Processing helix chain 'A' and resid 1635 through 1639 Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 4.031A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.785A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.902A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1850 through 1853 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'A' and resid 1861 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.578A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.615A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2007 through 2022 Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2064 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2159 through 2164 removed outlier: 3.704A pdb=" N GLU A2164 " --> pdb=" O PRO A2160 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.603A pdb=" N LEU A2237 " --> pdb=" O SER A2233 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2257 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.488A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 removed outlier: 3.568A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2302 Processing helix chain 'A' and resid 2306 through 2328 Processing helix chain 'A' and resid 2331 through 2347 removed outlier: 3.626A pdb=" N GLY A2347 " --> pdb=" O ASN A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2374 No H-bonds generated for 'chain 'A' and resid 2372 through 2374' Processing helix chain 'A' and resid 2381 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 4.064A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2458 removed outlier: 3.594A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A2458 " --> pdb=" O ILE A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2513 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2579 Processing helix chain 'A' and resid 2580 through 2581 No H-bonds generated for 'chain 'A' and resid 2580 through 2581' Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.145A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 4.116A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2658 through 2660 No H-bonds generated for 'chain 'A' and resid 2658 through 2660' Processing helix chain 'A' and resid 2662 through 2681 removed outlier: 3.510A pdb=" N LYS A2666 " --> pdb=" O GLY A2662 " (cutoff:3.500A) Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 4.099A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A2833 " --> pdb=" O GLU A2829 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2845 removed outlier: 4.383A pdb=" N GLN A2845 " --> pdb=" O ASP A2842 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2910 Processing helix chain 'A' and resid 2921 through 2933 Processing helix chain 'A' and resid 2934 through 2936 No H-bonds generated for 'chain 'A' and resid 2934 through 2936' Processing helix chain 'A' and resid 2949 through 2953 Processing helix chain 'A' and resid 2960 through 2981 removed outlier: 3.591A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3058 removed outlier: 4.237A pdb=" N LYS A3036 " --> pdb=" O ASN A3032 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A3037 " --> pdb=" O GLU A3033 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3319 removed outlier: 4.845A pdb=" N PHE A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU A3302 " --> pdb=" O SER A3298 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 Processing helix chain 'A' and resid 3335 through 3337 No H-bonds generated for 'chain 'A' and resid 3335 through 3337' Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3382 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 3.904A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3467 removed outlier: 3.597A pdb=" N ILE A3466 " --> pdb=" O ILE A3462 " (cutoff:3.500A) Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 3.585A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3606 removed outlier: 3.879A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3617 removed outlier: 4.043A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3637 Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.613A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3688 through 3690 No H-bonds generated for 'chain 'A' and resid 3688 through 3690' Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 4.217A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3768 removed outlier: 4.214A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3835 Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3852 Processing helix chain 'A' and resid 3853 through 3866 removed outlier: 3.651A pdb=" N LYS A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A3860 " --> pdb=" O HIS A3856 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A3866 " --> pdb=" O THR A3862 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3890 Processing helix chain 'A' and resid 3902 through 3914 removed outlier: 3.682A pdb=" N GLN A3914 " --> pdb=" O LEU A3910 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3943 Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.588A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 3994 through 3998 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 4.045A pdb=" N ASP A4072 " --> pdb=" O GLU A4068 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A4073 " --> pdb=" O SER A4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 1450 through 1459 Processing helix chain 'D' and resid 1464 through 1468 removed outlier: 3.544A pdb=" N ASN D1467 " --> pdb=" O ASP D1464 " (cutoff:3.500A) Processing helix chain 'D' and resid 1469 through 1479 Processing helix chain 'D' and resid 1516 through 1522 Processing helix chain 'D' and resid 1523 through 1533 removed outlier: 3.556A pdb=" N GLN D1533 " --> pdb=" O ARG D1529 " (cutoff:3.500A) Processing helix chain 'D' and resid 1534 through 1540 Processing helix chain 'D' and resid 1541 through 1551 Processing helix chain 'D' and resid 1556 through 1561 removed outlier: 3.599A pdb=" N LYS D1560 " --> pdb=" O ASP D1556 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D1561 " --> pdb=" O GLN D1557 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1556 through 1561' Processing helix chain 'D' and resid 1561 through 1566 Processing helix chain 'D' and resid 1603 through 1633 Processing helix chain 'D' and resid 1635 through 1639 Processing helix chain 'D' and resid 1644 through 1665 Processing helix chain 'D' and resid 1669 through 1688 removed outlier: 4.030A pdb=" N ASN D1688 " --> pdb=" O LEU D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1717 Processing helix chain 'D' and resid 1720 through 1731 removed outlier: 3.784A pdb=" N LYS D1730 " --> pdb=" O LEU D1726 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D1731 " --> pdb=" O LEU D1727 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1788 removed outlier: 3.907A pdb=" N GLN D1788 " --> pdb=" O ASP D1784 " (cutoff:3.500A) Processing helix chain 'D' and resid 1801 through 1813 Processing helix chain 'D' and resid 1827 through 1842 Processing helix chain 'D' and resid 1850 through 1853 Processing helix chain 'D' and resid 1854 through 1861 Processing helix chain 'D' and resid 1861 through 1875 Processing helix chain 'D' and resid 1909 through 1914 Processing helix chain 'D' and resid 1925 through 1938 Processing helix chain 'D' and resid 1941 through 1960 Processing helix chain 'D' and resid 1969 through 1981 removed outlier: 3.582A pdb=" N SER D1981 " --> pdb=" O LEU D1977 " (cutoff:3.500A) Processing helix chain 'D' and resid 1983 through 1988 Processing helix chain 'D' and resid 1990 through 2003 removed outlier: 3.617A pdb=" N VAL D1994 " --> pdb=" O GLY D1990 " (cutoff:3.500A) Processing helix chain 'D' and resid 2004 through 2006 No H-bonds generated for 'chain 'D' and resid 2004 through 2006' Processing helix chain 'D' and resid 2007 through 2022 Processing helix chain 'D' and resid 2031 through 2046 Processing helix chain 'D' and resid 2050 through 2064 Processing helix chain 'D' and resid 2079 through 2096 Processing helix chain 'D' and resid 2110 through 2115 Processing helix chain 'D' and resid 2128 through 2140 Processing helix chain 'D' and resid 2159 through 2164 removed outlier: 3.696A pdb=" N GLU D2164 " --> pdb=" O PRO D2160 " (cutoff:3.500A) Processing helix chain 'D' and resid 2166 through 2171 Processing helix chain 'D' and resid 2203 through 2208 Processing helix chain 'D' and resid 2221 through 2237 removed outlier: 3.604A pdb=" N LEU D2237 " --> pdb=" O SER D2233 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2257 Processing helix chain 'D' and resid 2258 through 2270 removed outlier: 4.492A pdb=" N ASN D2264 " --> pdb=" O ALA D2260 " (cutoff:3.500A) Processing helix chain 'D' and resid 2279 through 2282 Processing helix chain 'D' and resid 2283 through 2298 removed outlier: 3.569A pdb=" N ALA D2287 " --> pdb=" O LYS D2283 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D2298 " --> pdb=" O LEU D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2299 through 2302 Processing helix chain 'D' and resid 2306 through 2328 Processing helix chain 'D' and resid 2331 through 2347 removed outlier: 3.630A pdb=" N GLY D2347 " --> pdb=" O ASN D2343 " (cutoff:3.500A) Processing helix chain 'D' and resid 2372 through 2374 No H-bonds generated for 'chain 'D' and resid 2372 through 2374' Processing helix chain 'D' and resid 2381 through 2387 Processing helix chain 'D' and resid 2394 through 2410 Processing helix chain 'D' and resid 2423 through 2434 removed outlier: 4.063A pdb=" N ASN D2434 " --> pdb=" O ASN D2430 " (cutoff:3.500A) Processing helix chain 'D' and resid 2450 through 2458 removed outlier: 3.614A pdb=" N ILE D2454 " --> pdb=" O THR D2450 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D2458 " --> pdb=" O ILE D2454 " (cutoff:3.500A) Processing helix chain 'D' and resid 2500 through 2513 Processing helix chain 'D' and resid 2547 through 2552 Processing helix chain 'D' and resid 2563 through 2579 Processing helix chain 'D' and resid 2580 through 2581 No H-bonds generated for 'chain 'D' and resid 2580 through 2581' Processing helix chain 'D' and resid 2582 through 2587 removed outlier: 5.136A pdb=" N SER D2587 " --> pdb=" O GLU D2584 " (cutoff:3.500A) Processing helix chain 'D' and resid 2588 through 2607 Processing helix chain 'D' and resid 2618 through 2635 removed outlier: 3.717A pdb=" N LEU D2622 " --> pdb=" O SER D2618 " (cutoff:3.500A) Processing helix chain 'D' and resid 2640 through 2657 Processing helix chain 'D' and resid 2658 through 2660 No H-bonds generated for 'chain 'D' and resid 2658 through 2660' Processing helix chain 'D' and resid 2662 through 2681 removed outlier: 3.516A pdb=" N LYS D2666 " --> pdb=" O GLY D2662 " (cutoff:3.500A) Processing helix chain 'D' and resid 2708 through 2727 Processing helix chain 'D' and resid 2735 through 2750 Processing helix chain 'D' and resid 2765 through 2777 Processing helix chain 'D' and resid 2791 through 2809 Processing helix chain 'D' and resid 2820 through 2822 No H-bonds generated for 'chain 'D' and resid 2820 through 2822' Processing helix chain 'D' and resid 2824 through 2837 removed outlier: 4.021A pdb=" N LEU D2828 " --> pdb=" O GLU D2824 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D2833 " --> pdb=" O GLU D2829 " (cutoff:3.500A) Processing helix chain 'D' and resid 2840 through 2845 removed outlier: 4.378A pdb=" N GLN D2845 " --> pdb=" O ASP D2842 " (cutoff:3.500A) Processing helix chain 'D' and resid 2846 through 2863 Processing helix chain 'D' and resid 2869 through 2884 Processing helix chain 'D' and resid 2896 through 2905 Processing helix chain 'D' and resid 2905 through 2910 Processing helix chain 'D' and resid 2921 through 2933 Processing helix chain 'D' and resid 2934 through 2936 No H-bonds generated for 'chain 'D' and resid 2934 through 2936' Processing helix chain 'D' and resid 2949 through 2953 Processing helix chain 'D' and resid 2960 through 2981 removed outlier: 3.625A pdb=" N ALA D2964 " --> pdb=" O THR D2960 " (cutoff:3.500A) Processing helix chain 'D' and resid 2989 through 3058 removed outlier: 4.231A pdb=" N LYS D3036 " --> pdb=" O ASN D3032 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR D3037 " --> pdb=" O GLU D3033 " (cutoff:3.500A) Processing helix chain 'D' and resid 3265 through 3319 removed outlier: 4.845A pdb=" N PHE D3301 " --> pdb=" O LYS D3297 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU D3302 " --> pdb=" O SER D3298 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D3314 " --> pdb=" O THR D3310 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS D3315 " --> pdb=" O LYS D3311 " (cutoff:3.500A) Processing helix chain 'D' and resid 3319 through 3334 Processing helix chain 'D' and resid 3335 through 3337 No H-bonds generated for 'chain 'D' and resid 3335 through 3337' Processing helix chain 'D' and resid 3338 through 3356 Processing helix chain 'D' and resid 3365 through 3371 Processing helix chain 'D' and resid 3372 through 3382 Processing helix chain 'D' and resid 3387 through 3399 Processing helix chain 'D' and resid 3412 through 3423 removed outlier: 3.909A pdb=" N THR D3416 " --> pdb=" O SER D3412 " (cutoff:3.500A) Processing helix chain 'D' and resid 3435 through 3447 Processing helix chain 'D' and resid 3454 through 3458 Processing helix chain 'D' and resid 3459 through 3461 No H-bonds generated for 'chain 'D' and resid 3459 through 3461' Processing helix chain 'D' and resid 3462 through 3468 removed outlier: 3.584A pdb=" N ILE D3466 " --> pdb=" O ILE D3462 " (cutoff:3.500A) Processing helix chain 'D' and resid 3506 through 3511 Processing helix chain 'D' and resid 3521 through 3538 Processing helix chain 'D' and resid 3538 through 3572 removed outlier: 3.600A pdb=" N GLN D3542 " --> pdb=" O ASN D3538 " (cutoff:3.500A) Processing helix chain 'D' and resid 3580 through 3606 removed outlier: 3.887A pdb=" N GLU D3606 " --> pdb=" O SER D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3617 removed outlier: 4.060A pdb=" N PHE D3611 " --> pdb=" O PHE D3607 " (cutoff:3.500A) Processing helix chain 'D' and resid 3618 through 3637 Processing helix chain 'D' and resid 3645 through 3659 removed outlier: 3.612A pdb=" N PHE D3649 " --> pdb=" O SER D3645 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D3657 " --> pdb=" O PHE D3653 " (cutoff:3.500A) Processing helix chain 'D' and resid 3670 through 3687 Processing helix chain 'D' and resid 3688 through 3690 No H-bonds generated for 'chain 'D' and resid 3688 through 3690' Processing helix chain 'D' and resid 3691 through 3711 removed outlier: 4.200A pdb=" N ASP D3709 " --> pdb=" O LEU D3705 " (cutoff:3.500A) Processing helix chain 'D' and resid 3712 through 3727 Processing helix chain 'D' and resid 3742 through 3753 Processing helix chain 'D' and resid 3755 through 3768 removed outlier: 4.221A pdb=" N PHE D3763 " --> pdb=" O ALA D3759 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS D3764 " --> pdb=" O LEU D3760 " (cutoff:3.500A) Processing helix chain 'D' and resid 3773 through 3780 Processing helix chain 'D' and resid 3796 through 3807 Processing helix chain 'D' and resid 3818 through 3835 Processing helix chain 'D' and resid 3843 through 3846 Processing helix chain 'D' and resid 3847 through 3852 Processing helix chain 'D' and resid 3853 through 3865 removed outlier: 3.655A pdb=" N LYS D3857 " --> pdb=" O THR D3853 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D3862 " --> pdb=" O HIS D3858 " (cutoff:3.500A) Processing helix chain 'D' and resid 3885 through 3890 Processing helix chain 'D' and resid 3902 through 3914 removed outlier: 3.683A pdb=" N GLN D3914 " --> pdb=" O LEU D3910 " (cutoff:3.500A) Processing helix chain 'D' and resid 3923 through 3943 Processing helix chain 'D' and resid 3957 through 3974 removed outlier: 3.592A pdb=" N PHE D3961 " --> pdb=" O ASN D3957 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR D3974 " --> pdb=" O ASN D3970 " (cutoff:3.500A) Processing helix chain 'D' and resid 3981 through 3992 Processing helix chain 'D' and resid 3994 through 3998 Processing helix chain 'D' and resid 4000 through 4015 Processing helix chain 'D' and resid 4037 through 4051 Processing helix chain 'D' and resid 4057 through 4062 Processing helix chain 'D' and resid 4066 through 4091 removed outlier: 4.045A pdb=" N ASP D4072 " --> pdb=" O GLU D4068 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR D4073 " --> pdb=" O SER D4069 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 6.714A pdb=" N ARG A1583 " --> pdb=" O GLU A1570 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE A1572 " --> pdb=" O GLY A1581 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A1581 " --> pdb=" O ILE A1572 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A1574 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A1579 " --> pdb=" O PHE A1574 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 8.391A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2117 through 2119 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.390A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.148A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N MET A2757 " --> pdb=" O TRP A2916 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A2918 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A2759 " --> pdb=" O GLY A2918 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.247A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3478 through 3481 Processing sheet with id=AB6, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 3.724A pdb=" N LYS A3872 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4021 Processing sheet with id=AB8, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.222A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 158 through 163 removed outlier: 4.451A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 201 through 208 removed outlier: 4.650A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 231 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER B 248 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 256 through 264 removed outlier: 6.936A pdb=" N VAL B 279 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 292 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 281 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.810A pdb=" N ILE B 311 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 340 through 345 removed outlier: 6.752A pdb=" N ILE B 382 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR B 412 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 384 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 420 through 426 removed outlier: 3.561A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 433 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 434 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP B 443 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS B 449 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.049A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 158 through 163 removed outlier: 4.411A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.501A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 256 through 263 removed outlier: 6.815A pdb=" N VAL C 279 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 292 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 281 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.354A pdb=" N LEU C 319 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 332 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 340 through 345 removed outlier: 4.091A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 382 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR C 412 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 384 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.566A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 439 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 452 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS C 441 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 448 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1569 through 1574 removed outlier: 6.710A pdb=" N ARG D1583 " --> pdb=" O GLU D1570 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE D1572 " --> pdb=" O GLY D1581 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY D1581 " --> pdb=" O ILE D1572 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE D1574 " --> pdb=" O ILE D1579 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE D1579 " --> pdb=" O PHE D1574 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N SER D1578 " --> pdb=" O GLU D1594 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N GLU D1594 " --> pdb=" O SER D1578 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR D1580 " --> pdb=" O LEU D1592 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1733 through 1736 Processing sheet with id=AD6, first strand: chain 'D' and resid 1817 through 1821 Processing sheet with id=AD7, first strand: chain 'D' and resid 1878 through 1881 Processing sheet with id=AD8, first strand: chain 'D' and resid 2098 through 2104 removed outlier: 8.364A pdb=" N ARG D2191 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D2150 " --> pdb=" O ARG D2191 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D2193 " --> pdb=" O ILE D2150 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL D2152 " --> pdb=" O LEU D2193 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU D2195 " --> pdb=" O VAL D2152 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE D2154 " --> pdb=" O GLU D2195 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D2069 " --> pdb=" O GLY D2211 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D2213 " --> pdb=" O ALA D2069 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE D2071 " --> pdb=" O LEU D2213 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE D2215 " --> pdb=" O ILE D2071 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL D2073 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 2117 through 2119 Processing sheet with id=AE1, first strand: chain 'D' and resid 2175 through 2177 Processing sheet with id=AE2, first strand: chain 'D' and resid 2357 through 2360 Processing sheet with id=AE3, first strand: chain 'D' and resid 2438 through 2444 removed outlier: 6.362A pdb=" N ASP D2439 " --> pdb=" O VAL D2483 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE D2485 " --> pdb=" O ASP D2439 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D2441 " --> pdb=" O PHE D2485 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP D2487 " --> pdb=" O VAL D2441 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE D2443 " --> pdb=" O ASP D2487 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D2482 " --> pdb=" O HIS D2530 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL D2532 " --> pdb=" O LEU D2482 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU D2484 " --> pdb=" O VAL D2532 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA D2534 " --> pdb=" O LEU D2484 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS D2486 " --> pdb=" O ALA D2534 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D2414 " --> pdb=" O ILE D2531 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 2462 through 2465 Processing sheet with id=AE5, first strand: chain 'D' and resid 2696 through 2697 Processing sheet with id=AE6, first strand: chain 'D' and resid 2780 through 2782 removed outlier: 6.096A pdb=" N LYS D2780 " --> pdb=" O CYS D2814 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE D2816 " --> pdb=" O LYS D2780 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL D2782 " --> pdb=" O ILE D2816 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP D2818 " --> pdb=" O VAL D2782 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR D2813 " --> pdb=" O HIS D2886 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL D2888 " --> pdb=" O THR D2813 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D2815 " --> pdb=" O VAL D2888 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR D2890 " --> pdb=" O LEU D2815 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE D2817 " --> pdb=" O THR D2890 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET D2756 " --> pdb=" O PHE D2889 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D2891 " --> pdb=" O MET D2756 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D2758 " --> pdb=" O ILE D2891 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N MET D2757 " --> pdb=" O TRP D2916 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY D2918 " --> pdb=" O MET D2757 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE D2759 " --> pdb=" O GLY D2918 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 3426 through 3430 removed outlier: 6.233A pdb=" N VAL D3427 " --> pdb=" O ILE D3451 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN D3453 " --> pdb=" O VAL D3427 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU D3429 " --> pdb=" O GLN D3453 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL D3404 " --> pdb=" O ARG D3514 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D3516 " --> pdb=" O VAL D3404 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE D3406 " --> pdb=" O VAL D3516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 3478 through 3481 Processing sheet with id=AE9, first strand: chain 'D' and resid 3811 through 3815 removed outlier: 3.613A pdb=" N LYS D3872 " --> pdb=" O GLY D3837 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4020 through 4021 Processing sheet with id=AF2, first strand: chain 'E' and resid 150 through 153 removed outlier: 4.222A pdb=" N LYS E 488 " --> pdb=" O GLY E 484 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 158 through 163 removed outlier: 4.469A pdb=" N LYS E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 201 through 208 removed outlier: 3.508A pdb=" N SER E 203 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 220 " --> pdb=" O TRP E 236 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 231 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER E 248 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL E 233 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 256 through 264 removed outlier: 6.920A pdb=" N VAL E 279 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR E 292 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE E 281 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 300 through 306 removed outlier: 3.766A pdb=" N ILE E 311 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU E 319 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL E 332 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU E 321 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 340 through 345 removed outlier: 6.747A pdb=" N ILE E 382 " --> pdb=" O THR E 412 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR E 412 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE E 384 " --> pdb=" O VAL E 410 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 420 through 426 removed outlier: 3.575A pdb=" N ASP E 422 " --> pdb=" O CYS E 433 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS E 433 " --> pdb=" O ASP E 422 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 434 " --> pdb=" O SER E 438 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP E 443 " --> pdb=" O CYS E 449 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS E 449 " --> pdb=" O ASP E 443 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 150 through 153 removed outlier: 4.048A pdb=" N LYS F 488 " --> pdb=" O GLY F 484 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 158 through 163 removed outlier: 4.411A pdb=" N LYS F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 201 through 208 removed outlier: 3.501A pdb=" N SER F 203 " --> pdb=" O ALA F 225 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU F 220 " --> pdb=" O TRP F 236 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE F 231 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER F 248 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 233 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 256 through 263 removed outlier: 6.815A pdb=" N VAL F 279 " --> pdb=" O THR F 292 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR F 292 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 281 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 300 through 306 removed outlier: 6.353A pdb=" N LEU F 319 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL F 332 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 321 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 340 through 345 removed outlier: 4.091A pdb=" N THR F 381 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE F 382 " --> pdb=" O THR F 412 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR F 412 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE F 384 " --> pdb=" O VAL F 410 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 420 through 426 removed outlier: 3.566A pdb=" N ASP F 422 " --> pdb=" O CYS F 433 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 439 " --> pdb=" O VAL F 452 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 452 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS F 441 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 448 " --> pdb=" O ASP F 443 " (cutoff:3.500A) 2692 hydrogen bonds defined for protein. 7785 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: 27.43 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8130 1.31 - 1.44: 13581 1.44 - 1.57: 28553 1.57 - 1.70: 36 1.70 - 1.82: 362 Bond restraints: 50662 Sorted by residual: bond pdb=" N VAL D3733 " pdb=" CA VAL D3733 " ideal model delta sigma weight residual 1.454 1.491 -0.036 7.70e-03 1.69e+04 2.20e+01 bond pdb=" C GLU D3276 " pdb=" O GLU D3276 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.15e+01 bond pdb=" C LEU D2625 " pdb=" O LEU D2625 " ideal model delta sigma weight residual 1.236 1.184 0.053 1.15e-02 7.56e+03 2.10e+01 bond pdb=" C ARG D2627 " pdb=" O ARG D2627 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.74e+01 bond pdb=" C GLU A3867 " pdb=" N HIS A3868 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.38e-02 5.25e+03 1.72e+01 ... (remaining 50657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 68348 4.44 - 8.88: 223 8.88 - 13.32: 3 13.32 - 17.76: 3 17.76 - 22.20: 1 Bond angle restraints: 68578 Sorted by residual: angle pdb=" PB ATP D4204 " pdb=" O3B ATP D4204 " pdb=" PG ATP D4204 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" N LYS D3863 " pdb=" CA LYS D3863 " pdb=" C LYS D3863 " ideal model delta sigma weight residual 111.07 97.93 13.14 1.07e+00 8.73e-01 1.51e+02 angle pdb=" N LYS A3863 " pdb=" CA LYS A3863 " pdb=" C LYS A3863 " ideal model delta sigma weight residual 111.28 97.95 13.33 1.09e+00 8.42e-01 1.50e+02 angle pdb=" PA ATP D4204 " pdb=" O3A ATP D4204 " pdb=" PB ATP D4204 " ideal model delta sigma weight residual 136.83 128.44 8.39 1.00e+00 1.00e+00 7.03e+01 angle pdb=" N SER C 214 " pdb=" CA SER C 214 " pdb=" C SER C 214 " ideal model delta sigma weight residual 111.28 102.62 8.66 1.09e+00 8.42e-01 6.31e+01 ... (remaining 68573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 29955 35.63 - 71.26: 449 71.26 - 106.90: 28 106.90 - 142.53: 2 142.53 - 178.16: 4 Dihedral angle restraints: 30438 sinusoidal: 12546 harmonic: 17892 Sorted by residual: dihedral pdb=" C THR D3862 " pdb=" N THR D3862 " pdb=" CA THR D3862 " pdb=" CB THR D3862 " ideal model delta harmonic sigma weight residual -122.00 -140.78 18.78 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" C THR A3862 " pdb=" N THR A3862 " pdb=" CA THR A3862 " pdb=" CB THR A3862 " ideal model delta harmonic sigma weight residual -122.00 -140.73 18.73 0 2.50e+00 1.60e-01 5.61e+01 dihedral pdb=" O1B ADP A4203 " pdb=" O3A ADP A4203 " pdb=" PB ADP A4203 " pdb=" PA ADP A4203 " ideal model delta sinusoidal sigma weight residual -60.00 118.16 -178.16 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 30435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 7563 0.124 - 0.247: 169 0.247 - 0.371: 19 0.371 - 0.494: 0 0.494 - 0.618: 3 Chirality restraints: 7754 Sorted by residual: chirality pdb=" CA THR D3862 " pdb=" N THR D3862 " pdb=" C THR D3862 " pdb=" CB THR D3862 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" CA THR A3862 " pdb=" N THR A3862 " pdb=" C THR A3862 " pdb=" CB THR A3862 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.50e+00 chirality pdb=" CA ASN C 213 " pdb=" N ASN C 213 " pdb=" C ASN C 213 " pdb=" CB ASN C 213 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 7751 not shown) Planarity restraints: 8594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D3268 " -0.045 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" CG TYR D3268 " 0.104 2.00e-02 2.50e+03 pdb=" CD1 TYR D3268 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D3268 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR D3268 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR D3268 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D3268 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR D3268 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 209 " -0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C THR C 209 " 0.081 2.00e-02 2.50e+03 pdb=" O THR C 209 " -0.031 2.00e-02 2.50e+03 pdb=" N ASN C 210 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 209 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C THR F 209 " -0.080 2.00e-02 2.50e+03 pdb=" O THR F 209 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN F 210 " 0.026 2.00e-02 2.50e+03 ... (remaining 8591 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1125 2.70 - 3.25: 49304 3.25 - 3.80: 79430 3.80 - 4.35: 104478 4.35 - 4.90: 173966 Nonbonded interactions: 408303 Sorted by model distance: nonbonded pdb=" O THR C 212 " pdb=" OG1 THR C 212 " model vdw 2.145 3.040 nonbonded pdb=" OH TYR A1966 " pdb=" OD2 ASP A2010 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR D1966 " pdb=" OD2 ASP D2010 " model vdw 2.211 3.040 nonbonded pdb=" O GLU A3051 " pdb=" OG SER A3054 " model vdw 2.213 3.040 nonbonded pdb=" N GLU C 253 " pdb=" OE1 GLU C 253 " model vdw 2.223 3.120 ... (remaining 408298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 139 through 213 or resid 216 through 350 or resid 355 thro \ ugh 400 or resid 405 through 494)) selection = chain 'E' selection = (chain 'F' and (resid 139 through 213 or resid 216 through 350 or resid 355 thro \ ugh 400 or resid 405 through 494)) } 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: 2.450 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: 0.030 Extract box with map and model: 1.550 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 96.810 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.180 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.004 0.067 50662 Z= 0.249 Angle : 0.742 22.205 68578 Z= 0.433 Chirality : 0.049 0.618 7754 Planarity : 0.005 0.099 8594 Dihedral : 12.486 178.161 18802 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.57 % Favored : 98.39 % Rotamer: Outliers : 0.25 % Allowed : 1.72 % Favored : 98.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.10), residues: 6034 helix: 1.69 (0.09), residues: 2800 sheet: 0.69 (0.16), residues: 980 loop : -0.33 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 442 HIS 0.011 0.001 HIS A2400 PHE 0.042 0.002 PHE D3608 TYR 0.104 0.002 TYR D3268 ARG 0.016 0.001 ARG D2387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 4.567 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: A 1565 MET cc_start: 0.9517 (mtp) cc_final: 0.8063 (tpp) REVERT: A 3377 MET cc_start: 0.8703 (tpt) cc_final: 0.8148 (tpp) REVERT: A 3414 MET cc_start: 0.8981 (mmm) cc_final: 0.8518 (mmp) REVERT: A 3577 MET cc_start: 0.8912 (mpp) cc_final: 0.8272 (tpp) REVERT: A 3584 MET cc_start: 0.8898 (mtm) cc_final: 0.8456 (mtp) REVERT: A 3743 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 187 TYR cc_start: 0.8308 (p90) cc_final: 0.7936 (p90) REVERT: D 1565 MET cc_start: 0.8972 (tpp) cc_final: 0.8730 (tpp) REVERT: D 1937 MET cc_start: 0.9466 (mmp) cc_final: 0.9226 (mmm) REVERT: D 3282 MET cc_start: 0.8483 (ttp) cc_final: 0.8210 (tmm) REVERT: D 3377 MET cc_start: 0.8732 (tpt) cc_final: 0.8180 (tpp) REVERT: D 3577 MET cc_start: 0.8681 (mpp) cc_final: 0.8256 (mpp) REVERT: D 3631 MET cc_start: 0.8726 (tmm) cc_final: 0.8502 (tmm) REVERT: D 3846 MET cc_start: 0.8834 (mmm) cc_final: 0.8388 (mtp) REVERT: E 187 TYR cc_start: 0.8091 (p90) cc_final: 0.7698 (p90) REVERT: E 479 MET cc_start: 0.6836 (ptm) cc_final: 0.6621 (ptp) REVERT: E 493 MET cc_start: 0.7876 (ppp) cc_final: 0.7547 (ppp) outliers start: 14 outliers final: 6 residues processed: 195 average time/residue: 0.5037 time to fit residues: 172.4497 Evaluate side-chains 157 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 4.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 7.9990 chunk 462 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 478 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 553 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN A1899 ASN A3517 HIS A3878 HIS A3948 HIS B 244 GLN D1867 GLN D1899 ASN ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3878 HIS D3948 HIS E 244 GLN F 213 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 50662 Z= 0.311 Angle : 0.616 8.460 68578 Z= 0.325 Chirality : 0.043 0.242 7754 Planarity : 0.004 0.040 8594 Dihedral : 8.985 173.430 6744 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.11), residues: 6034 helix: 2.29 (0.09), residues: 2796 sheet: 0.75 (0.16), residues: 1020 loop : -0.29 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 299 HIS 0.007 0.002 HIS A2383 PHE 0.031 0.002 PHE F 338 TYR 0.049 0.002 TYR D3268 ARG 0.009 0.001 ARG A2747 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9469 (mtp) cc_final: 0.8677 (tpp) REVERT: A 1655 MET cc_start: 0.9091 (mmm) cc_final: 0.8392 (mpp) REVERT: A 1678 MET cc_start: 0.9381 (mmp) cc_final: 0.9169 (mmm) REVERT: A 1921 MET cc_start: 0.8863 (mtp) cc_final: 0.8499 (mtm) REVERT: A 2063 MET cc_start: 0.9312 (mmt) cc_final: 0.9078 (mmp) REVERT: A 2259 MET cc_start: 0.8277 (mmm) cc_final: 0.7825 (mmt) REVERT: A 2546 MET cc_start: 0.7690 (mtp) cc_final: 0.7020 (ttm) REVERT: A 3377 MET cc_start: 0.8845 (tpt) cc_final: 0.8304 (tpp) REVERT: A 3414 MET cc_start: 0.9133 (mmm) cc_final: 0.8749 (mmm) REVERT: A 3577 MET cc_start: 0.8963 (mpp) cc_final: 0.8381 (mpp) REVERT: A 3584 MET cc_start: 0.8942 (mtm) cc_final: 0.8639 (mtp) REVERT: A 3631 MET cc_start: 0.8983 (tmm) cc_final: 0.8527 (tmm) REVERT: A 3696 MET cc_start: 0.8580 (ptp) cc_final: 0.8285 (ptp) REVERT: B 370 MET cc_start: 0.8530 (ptt) cc_final: 0.8133 (mmp) REVERT: D 1565 MET cc_start: 0.9051 (tpp) cc_final: 0.8730 (tpp) REVERT: D 1678 MET cc_start: 0.9376 (mmp) cc_final: 0.9089 (mmm) REVERT: D 1921 MET cc_start: 0.8835 (mtp) cc_final: 0.8513 (mtm) REVERT: D 1937 MET cc_start: 0.9292 (mmp) cc_final: 0.8788 (mmm) REVERT: D 2118 MET cc_start: 0.6909 (tpt) cc_final: 0.6701 (tpt) REVERT: D 2259 MET cc_start: 0.8432 (mmm) cc_final: 0.7897 (mmt) REVERT: D 3282 MET cc_start: 0.8494 (ttp) cc_final: 0.8286 (tmm) REVERT: D 3377 MET cc_start: 0.8714 (tpt) cc_final: 0.8372 (tpp) REVERT: D 3577 MET cc_start: 0.8732 (mpp) cc_final: 0.8342 (mpp) REVERT: D 3722 MET cc_start: 0.9184 (mmp) cc_final: 0.8920 (mmp) REVERT: E 493 MET cc_start: 0.8224 (ppp) cc_final: 0.7749 (ppp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.5863 time to fit residues: 161.3441 Evaluate side-chains 136 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 461 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 554 optimal weight: 10.0000 chunk 599 optimal weight: 7.9990 chunk 494 optimal weight: 3.9990 chunk 550 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 445 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 50662 Z= 0.216 Angle : 0.508 6.336 68578 Z= 0.271 Chirality : 0.041 0.148 7754 Planarity : 0.003 0.043 8594 Dihedral : 8.625 179.545 6744 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.11), residues: 6034 helix: 2.50 (0.10), residues: 2812 sheet: 0.81 (0.16), residues: 1024 loop : -0.31 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D2084 HIS 0.007 0.001 HIS B 254 PHE 0.016 0.001 PHE D3530 TYR 0.031 0.001 TYR D3268 ARG 0.005 0.000 ARG D3439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9467 (mtp) cc_final: 0.8064 (tpp) REVERT: A 1655 MET cc_start: 0.9096 (mmm) cc_final: 0.8411 (mpp) REVERT: A 1678 MET cc_start: 0.9389 (mmp) cc_final: 0.9146 (mmm) REVERT: A 1921 MET cc_start: 0.9004 (mtp) cc_final: 0.8666 (mtp) REVERT: A 2118 MET cc_start: 0.6666 (tpt) cc_final: 0.6406 (tpt) REVERT: A 2510 MET cc_start: 0.8444 (ttm) cc_final: 0.8187 (ttm) REVERT: A 3377 MET cc_start: 0.8875 (tpt) cc_final: 0.8333 (tpp) REVERT: A 3414 MET cc_start: 0.9016 (mmm) cc_final: 0.8787 (mmm) REVERT: A 3541 MET cc_start: 0.8555 (mmt) cc_final: 0.8321 (tpp) REVERT: A 3577 MET cc_start: 0.8955 (mpp) cc_final: 0.8550 (mpp) REVERT: A 3631 MET cc_start: 0.9048 (tmm) cc_final: 0.8600 (tmm) REVERT: A 3696 MET cc_start: 0.8657 (ptp) cc_final: 0.8407 (ptp) REVERT: B 370 MET cc_start: 0.8443 (ptt) cc_final: 0.8132 (mmt) REVERT: B 480 MET cc_start: 0.8379 (ppp) cc_final: 0.8109 (ppp) REVERT: D 1472 GLU cc_start: 0.7299 (mp0) cc_final: 0.7066 (mt-10) REVERT: D 1655 MET cc_start: 0.9094 (mmm) cc_final: 0.8422 (mpp) REVERT: D 1678 MET cc_start: 0.9399 (mmp) cc_final: 0.9123 (mmm) REVERT: D 1921 MET cc_start: 0.8981 (mtp) cc_final: 0.8755 (mtp) REVERT: D 1937 MET cc_start: 0.9269 (mmp) cc_final: 0.8778 (mmm) REVERT: D 2118 MET cc_start: 0.6800 (tpt) cc_final: 0.6393 (tpt) REVERT: D 2546 MET cc_start: 0.7734 (mtp) cc_final: 0.7151 (ttm) REVERT: D 2756 MET cc_start: 0.8699 (pmm) cc_final: 0.8473 (pmm) REVERT: D 3282 MET cc_start: 0.8476 (ttp) cc_final: 0.8270 (tmm) REVERT: D 3377 MET cc_start: 0.8720 (tpt) cc_final: 0.8470 (tpp) REVERT: D 3414 MET cc_start: 0.8931 (mmm) cc_final: 0.8644 (mpp) REVERT: D 3541 MET cc_start: 0.8363 (mmt) cc_final: 0.8052 (tpp) REVERT: D 3577 MET cc_start: 0.8762 (mpp) cc_final: 0.8461 (mpp) REVERT: D 3631 MET cc_start: 0.8746 (tmm) cc_final: 0.8491 (tmm) REVERT: D 3722 MET cc_start: 0.9181 (mmp) cc_final: 0.8938 (mmp) REVERT: E 479 MET cc_start: 0.7448 (ptp) cc_final: 0.7200 (ptp) REVERT: E 493 MET cc_start: 0.8259 (ppp) cc_final: 0.7797 (ppp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.5667 time to fit residues: 148.5732 Evaluate side-chains 133 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 10.0000 chunk 417 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 372 optimal weight: 1.9990 chunk 556 optimal weight: 5.9990 chunk 589 optimal weight: 0.8980 chunk 290 optimal weight: 5.9990 chunk 527 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1757 GLN A1911 ASN A2099 ASN A2201 HIS A2383 HIS A2488 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN D1757 GLN D1911 ASN D2099 ASN D2383 HIS D2488 GLN D2927 GLN F 328 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 50662 Z= 0.289 Angle : 0.559 7.446 68578 Z= 0.294 Chirality : 0.041 0.170 7754 Planarity : 0.004 0.046 8594 Dihedral : 8.375 176.428 6744 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.11), residues: 6034 helix: 2.45 (0.10), residues: 2812 sheet: 0.75 (0.16), residues: 998 loop : -0.42 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A3850 HIS 0.007 0.001 HIS D2741 PHE 0.018 0.002 PHE D2992 TYR 0.025 0.002 TYR D3268 ARG 0.004 0.000 ARG C 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 4.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9363 (mtp) cc_final: 0.8090 (tpp) REVERT: A 1678 MET cc_start: 0.9410 (mmp) cc_final: 0.9154 (mmm) REVERT: A 1921 MET cc_start: 0.8950 (mtp) cc_final: 0.8613 (mtp) REVERT: A 2546 MET cc_start: 0.8065 (mtp) cc_final: 0.7577 (ttm) REVERT: A 3377 MET cc_start: 0.8946 (tpt) cc_final: 0.8323 (tpp) REVERT: A 3414 MET cc_start: 0.9027 (mmm) cc_final: 0.8819 (mmm) REVERT: A 3541 MET cc_start: 0.8558 (mmt) cc_final: 0.8338 (tpp) REVERT: A 3577 MET cc_start: 0.8826 (mpp) cc_final: 0.8502 (mpp) REVERT: A 3584 MET cc_start: 0.8833 (mtp) cc_final: 0.8579 (mtm) REVERT: A 3631 MET cc_start: 0.9049 (tmm) cc_final: 0.8498 (tmm) REVERT: A 3696 MET cc_start: 0.8733 (ptp) cc_final: 0.8497 (ptp) REVERT: B 370 MET cc_start: 0.8449 (ptt) cc_final: 0.8178 (mmt) REVERT: B 480 MET cc_start: 0.8470 (ppp) cc_final: 0.8199 (tmm) REVERT: D 1565 MET cc_start: 0.9188 (tpp) cc_final: 0.8798 (tpp) REVERT: D 1678 MET cc_start: 0.9426 (mmp) cc_final: 0.9139 (mmm) REVERT: D 1921 MET cc_start: 0.8833 (mtp) cc_final: 0.8505 (mtp) REVERT: D 1937 MET cc_start: 0.9185 (mmp) cc_final: 0.8811 (mmm) REVERT: D 2546 MET cc_start: 0.8187 (mtp) cc_final: 0.7203 (ttm) REVERT: D 3282 MET cc_start: 0.8498 (ttp) cc_final: 0.8268 (tmm) REVERT: D 3377 MET cc_start: 0.8771 (tpt) cc_final: 0.8524 (tpp) REVERT: D 3414 MET cc_start: 0.8944 (mmm) cc_final: 0.8595 (mpp) REVERT: D 3541 MET cc_start: 0.8485 (mmt) cc_final: 0.8191 (tpt) REVERT: D 3577 MET cc_start: 0.8835 (mpp) cc_final: 0.8341 (mpp) REVERT: D 3722 MET cc_start: 0.9178 (mmp) cc_final: 0.8932 (mmp) REVERT: E 493 MET cc_start: 0.8269 (ppp) cc_final: 0.7849 (ppp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.4809 time to fit residues: 123.2848 Evaluate side-chains 134 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 0.8980 chunk 334 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 439 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 503 optimal weight: 9.9990 chunk 407 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 301 optimal weight: 4.9990 chunk 529 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1466 GLN A2488 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2488 GLN D3714 GLN ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50662 Z= 0.234 Angle : 0.506 7.550 68578 Z= 0.268 Chirality : 0.041 0.207 7754 Planarity : 0.003 0.047 8594 Dihedral : 8.080 170.187 6744 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.11), residues: 6034 helix: 2.57 (0.10), residues: 2800 sheet: 0.77 (0.16), residues: 986 loop : -0.40 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.008 0.001 HIS D2741 PHE 0.016 0.001 PHE D3530 TYR 0.022 0.001 TYR D3268 ARG 0.004 0.000 ARG A2552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 4.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9341 (mtp) cc_final: 0.8104 (tpp) REVERT: A 1678 MET cc_start: 0.9429 (mmp) cc_final: 0.9168 (mmm) REVERT: A 1921 MET cc_start: 0.8987 (mtp) cc_final: 0.8645 (mtp) REVERT: A 2063 MET cc_start: 0.9300 (mmt) cc_final: 0.9036 (mmm) REVERT: A 2118 MET cc_start: 0.6773 (tpt) cc_final: 0.6532 (tpt) REVERT: A 2546 MET cc_start: 0.8130 (mtp) cc_final: 0.7494 (ttm) REVERT: A 3377 MET cc_start: 0.8949 (tpt) cc_final: 0.8313 (tpp) REVERT: A 3577 MET cc_start: 0.8838 (mpp) cc_final: 0.8553 (mpp) REVERT: A 3631 MET cc_start: 0.8993 (tmm) cc_final: 0.8554 (tmm) REVERT: B 370 MET cc_start: 0.8459 (ptt) cc_final: 0.8167 (mmt) REVERT: B 480 MET cc_start: 0.8504 (ppp) cc_final: 0.8184 (tmm) REVERT: D 1472 GLU cc_start: 0.7656 (mp0) cc_final: 0.6926 (mt-10) REVERT: D 1565 MET cc_start: 0.9130 (tpp) cc_final: 0.8614 (tpp) REVERT: D 1678 MET cc_start: 0.9462 (mmp) cc_final: 0.9157 (mmm) REVERT: D 1921 MET cc_start: 0.8902 (mtp) cc_final: 0.8597 (mtp) REVERT: D 1937 MET cc_start: 0.9206 (mmp) cc_final: 0.8820 (mmm) REVERT: D 2063 MET cc_start: 0.9321 (mmt) cc_final: 0.8877 (mmp) REVERT: D 2118 MET cc_start: 0.6576 (tpt) cc_final: 0.6315 (tpt) REVERT: D 2546 MET cc_start: 0.8130 (mtp) cc_final: 0.7432 (ttm) REVERT: D 3282 MET cc_start: 0.8484 (ttp) cc_final: 0.8250 (tmm) REVERT: D 3377 MET cc_start: 0.8697 (tpt) cc_final: 0.8457 (tpp) REVERT: D 3414 MET cc_start: 0.8924 (mmm) cc_final: 0.8571 (mpp) REVERT: D 3541 MET cc_start: 0.8431 (mmt) cc_final: 0.8150 (tpt) REVERT: D 3577 MET cc_start: 0.8796 (mpp) cc_final: 0.8266 (tpp) REVERT: D 3584 MET cc_start: 0.9236 (ptp) cc_final: 0.8303 (ptp) REVERT: D 3696 MET cc_start: 0.8019 (pmm) cc_final: 0.7793 (pmm) REVERT: D 3722 MET cc_start: 0.9184 (mmp) cc_final: 0.8961 (mmp) REVERT: E 479 MET cc_start: 0.7509 (ptp) cc_final: 0.7066 (ptp) REVERT: E 493 MET cc_start: 0.8410 (ppp) cc_final: 0.8084 (ppp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.4870 time to fit residues: 124.8474 Evaluate side-chains 135 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 6.9990 chunk 530 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 590 optimal weight: 5.9990 chunk 489 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1788 GLN A2488 GLN A3318 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1466 GLN D2201 HIS D2488 GLN ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3856 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 50662 Z= 0.291 Angle : 0.554 8.080 68578 Z= 0.291 Chirality : 0.041 0.160 7754 Planarity : 0.004 0.048 8594 Dihedral : 7.788 170.250 6744 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.11), residues: 6034 helix: 2.42 (0.10), residues: 2814 sheet: 0.69 (0.16), residues: 960 loop : -0.51 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2084 HIS 0.010 0.001 HIS A2741 PHE 0.021 0.002 PHE A2720 TYR 0.022 0.002 TYR D3268 ARG 0.003 0.000 ARG A3053 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9349 (mtp) cc_final: 0.8141 (tpp) REVERT: A 1655 MET cc_start: 0.8986 (tpt) cc_final: 0.8487 (mpp) REVERT: A 1678 MET cc_start: 0.9452 (mmp) cc_final: 0.9161 (mmm) REVERT: A 1921 MET cc_start: 0.8689 (mtp) cc_final: 0.8387 (mtp) REVERT: A 2118 MET cc_start: 0.6973 (tpt) cc_final: 0.6680 (tpt) REVERT: A 2546 MET cc_start: 0.8309 (mtp) cc_final: 0.7589 (ttm) REVERT: A 3377 MET cc_start: 0.8988 (tpt) cc_final: 0.8362 (tpp) REVERT: A 3696 MET cc_start: 0.8617 (ptp) cc_final: 0.8400 (ptp) REVERT: B 370 MET cc_start: 0.8461 (ptt) cc_final: 0.8196 (mmt) REVERT: B 480 MET cc_start: 0.8563 (ppp) cc_final: 0.8360 (tmm) REVERT: D 1472 GLU cc_start: 0.7674 (mp0) cc_final: 0.6801 (mt-10) REVERT: D 1565 MET cc_start: 0.9118 (tpp) cc_final: 0.8511 (tpp) REVERT: D 1655 MET cc_start: 0.8839 (tpt) cc_final: 0.8511 (tpp) REVERT: D 1678 MET cc_start: 0.9473 (mmp) cc_final: 0.9159 (mmm) REVERT: D 1921 MET cc_start: 0.8679 (mtp) cc_final: 0.8439 (mtp) REVERT: D 1937 MET cc_start: 0.9225 (mmp) cc_final: 0.8850 (mmm) REVERT: D 2546 MET cc_start: 0.8198 (mtp) cc_final: 0.7520 (ttm) REVERT: D 2756 MET cc_start: 0.8842 (pmm) cc_final: 0.8164 (pmm) REVERT: D 3282 MET cc_start: 0.8443 (ttp) cc_final: 0.8163 (tmm) REVERT: D 3377 MET cc_start: 0.8745 (tpt) cc_final: 0.8475 (tpp) REVERT: D 3414 MET cc_start: 0.8934 (mmm) cc_final: 0.8570 (mpp) REVERT: D 3541 MET cc_start: 0.8512 (mmt) cc_final: 0.8240 (tpt) REVERT: D 3577 MET cc_start: 0.8902 (mpp) cc_final: 0.8234 (tmm) REVERT: D 3584 MET cc_start: 0.9139 (ptp) cc_final: 0.8916 (ptp) REVERT: D 3722 MET cc_start: 0.9193 (mmp) cc_final: 0.8982 (mmp) REVERT: E 480 MET cc_start: 0.8658 (ppp) cc_final: 0.8395 (ppp) REVERT: E 493 MET cc_start: 0.8416 (ppp) cc_final: 0.8047 (ppp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4786 time to fit residues: 116.6060 Evaluate side-chains 129 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 chunk 431 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 496 optimal weight: 3.9990 chunk 329 optimal weight: 9.9990 chunk 587 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2488 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3842 GLN D2488 GLN D3842 GLN D3856 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 50662 Z= 0.180 Angle : 0.479 8.594 68578 Z= 0.253 Chirality : 0.040 0.154 7754 Planarity : 0.003 0.049 8594 Dihedral : 7.456 161.424 6744 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.11), residues: 6034 helix: 2.69 (0.10), residues: 2790 sheet: 0.77 (0.16), residues: 974 loop : -0.41 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.008 0.001 HIS A2741 PHE 0.015 0.001 PHE D3530 TYR 0.017 0.001 TYR D3268 ARG 0.003 0.000 ARG A3053 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9320 (mtp) cc_final: 0.8132 (tpp) REVERT: A 1655 MET cc_start: 0.8964 (tpt) cc_final: 0.8471 (mpp) REVERT: A 1678 MET cc_start: 0.9487 (mmp) cc_final: 0.9173 (mmm) REVERT: A 1921 MET cc_start: 0.8801 (mtp) cc_final: 0.8494 (mtp) REVERT: A 1937 MET cc_start: 0.9049 (mmm) cc_final: 0.8835 (mpp) REVERT: A 2063 MET cc_start: 0.9321 (mmt) cc_final: 0.9074 (mmp) REVERT: A 2118 MET cc_start: 0.7086 (tpt) cc_final: 0.6804 (tpt) REVERT: A 2259 MET cc_start: 0.8383 (mmm) cc_final: 0.7823 (mmm) REVERT: A 2510 MET cc_start: 0.8725 (ttm) cc_final: 0.8346 (ttm) REVERT: A 2546 MET cc_start: 0.8241 (mtp) cc_final: 0.7710 (ttm) REVERT: A 3377 MET cc_start: 0.8982 (tpt) cc_final: 0.8375 (tpp) REVERT: A 3414 MET cc_start: 0.8655 (mpp) cc_final: 0.8115 (mpp) REVERT: A 3577 MET cc_start: 0.8768 (mpp) cc_final: 0.8232 (mpp) REVERT: A 3696 MET cc_start: 0.8567 (ptp) cc_final: 0.8245 (ptp) REVERT: B 370 MET cc_start: 0.8442 (ptt) cc_final: 0.8084 (mmm) REVERT: B 480 MET cc_start: 0.8571 (ppp) cc_final: 0.8353 (tmm) REVERT: C 370 MET cc_start: 0.8256 (ptp) cc_final: 0.7954 (ptp) REVERT: D 1472 GLU cc_start: 0.7647 (mp0) cc_final: 0.6851 (mt-10) REVERT: D 1565 MET cc_start: 0.9160 (tpp) cc_final: 0.8576 (tpp) REVERT: D 1655 MET cc_start: 0.8801 (tpt) cc_final: 0.8473 (tpp) REVERT: D 1678 MET cc_start: 0.9484 (mmp) cc_final: 0.9160 (mmm) REVERT: D 1921 MET cc_start: 0.8788 (mtp) cc_final: 0.8508 (mtp) REVERT: D 1937 MET cc_start: 0.9218 (mmp) cc_final: 0.8816 (mmm) REVERT: D 2063 MET cc_start: 0.9305 (mmt) cc_final: 0.9050 (mmp) REVERT: D 2118 MET cc_start: 0.6836 (tpt) cc_final: 0.6610 (tpt) REVERT: D 2546 MET cc_start: 0.8189 (mtp) cc_final: 0.7749 (ttm) REVERT: D 2756 MET cc_start: 0.8850 (pmm) cc_final: 0.8327 (pmm) REVERT: D 3282 MET cc_start: 0.8492 (ttp) cc_final: 0.8243 (tmm) REVERT: D 3377 MET cc_start: 0.8726 (tpt) cc_final: 0.8468 (tpp) REVERT: D 3414 MET cc_start: 0.8929 (mmm) cc_final: 0.8549 (mpp) REVERT: D 3541 MET cc_start: 0.8516 (mmt) cc_final: 0.8263 (tpt) REVERT: D 3577 MET cc_start: 0.8912 (mpp) cc_final: 0.8240 (tmm) REVERT: D 3584 MET cc_start: 0.9146 (ptp) cc_final: 0.8912 (ptp) REVERT: D 3696 MET cc_start: 0.8015 (pmm) cc_final: 0.7739 (pmm) REVERT: D 3722 MET cc_start: 0.9193 (mmp) cc_final: 0.8993 (mmp) REVERT: E 480 MET cc_start: 0.8597 (ppp) cc_final: 0.8379 (ppp) REVERT: E 493 MET cc_start: 0.8447 (ppp) cc_final: 0.7966 (ppp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.4900 time to fit residues: 120.3133 Evaluate side-chains 129 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 400 optimal weight: 8.9990 chunk 290 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 462 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1840 GLN A2282 ASN A2488 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS C 328 ASN D1788 GLN D1840 GLN D2068 GLN D2282 ASN D2488 GLN D3517 HIS D3856 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 50662 Z= 0.333 Angle : 0.597 9.157 68578 Z= 0.312 Chirality : 0.042 0.154 7754 Planarity : 0.004 0.047 8594 Dihedral : 7.350 150.288 6744 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.11), residues: 6034 helix: 2.37 (0.10), residues: 2806 sheet: 0.57 (0.16), residues: 970 loop : -0.56 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D2084 HIS 0.009 0.002 HIS D2741 PHE 0.018 0.002 PHE D2877 TYR 0.036 0.002 TYR A2574 ARG 0.004 0.001 ARG A2659 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.632 Fit side-chains revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9348 (mtp) cc_final: 0.8190 (tpp) REVERT: A 1678 MET cc_start: 0.9491 (mmp) cc_final: 0.9176 (mmm) REVERT: A 1921 MET cc_start: 0.8654 (mtp) cc_final: 0.8318 (mtp) REVERT: A 2063 MET cc_start: 0.9297 (mmt) cc_final: 0.9006 (mmp) REVERT: A 2118 MET cc_start: 0.7111 (tpt) cc_final: 0.6839 (tpt) REVERT: A 2546 MET cc_start: 0.8350 (mtp) cc_final: 0.7705 (ttm) REVERT: A 2866 LEU cc_start: 0.8617 (tp) cc_final: 0.8328 (pt) REVERT: A 3377 MET cc_start: 0.8984 (tpt) cc_final: 0.8391 (tpp) REVERT: A 3414 MET cc_start: 0.8368 (mpp) cc_final: 0.7157 (mpp) REVERT: A 3696 MET cc_start: 0.8617 (ptp) cc_final: 0.8353 (ptp) REVERT: B 370 MET cc_start: 0.8446 (ptt) cc_final: 0.8190 (mmm) REVERT: B 480 MET cc_start: 0.8592 (ppp) cc_final: 0.8377 (tmm) REVERT: C 370 MET cc_start: 0.8383 (ptp) cc_final: 0.8075 (ptp) REVERT: D 1472 GLU cc_start: 0.7764 (mp0) cc_final: 0.6738 (mt-10) REVERT: D 1565 MET cc_start: 0.9072 (tpp) cc_final: 0.8473 (tpp) REVERT: D 1655 MET cc_start: 0.8877 (tpt) cc_final: 0.8470 (mpp) REVERT: D 1678 MET cc_start: 0.9492 (mmp) cc_final: 0.9173 (mmm) REVERT: D 1921 MET cc_start: 0.8685 (mtp) cc_final: 0.8373 (mtp) REVERT: D 1937 MET cc_start: 0.9311 (mmp) cc_final: 0.8921 (mmm) REVERT: D 2063 MET cc_start: 0.9299 (mmt) cc_final: 0.9006 (mmp) REVERT: D 2546 MET cc_start: 0.8352 (mtp) cc_final: 0.7920 (ttm) REVERT: D 2756 MET cc_start: 0.8743 (pmm) cc_final: 0.8230 (pmm) REVERT: D 3282 MET cc_start: 0.8444 (ttp) cc_final: 0.8150 (tmm) REVERT: D 3377 MET cc_start: 0.8928 (tpt) cc_final: 0.8565 (tpp) REVERT: D 3414 MET cc_start: 0.8948 (mmm) cc_final: 0.8590 (mpp) REVERT: D 3577 MET cc_start: 0.8989 (mpp) cc_final: 0.8429 (tpp) REVERT: D 3584 MET cc_start: 0.9178 (ptp) cc_final: 0.8284 (ptp) REVERT: D 3696 MET cc_start: 0.8145 (pmm) cc_final: 0.7788 (pmm) REVERT: D 3722 MET cc_start: 0.9173 (mmp) cc_final: 0.8959 (mmp) REVERT: E 479 MET cc_start: 0.7663 (ptp) cc_final: 0.7147 (ptp) REVERT: E 480 MET cc_start: 0.8550 (ppp) cc_final: 0.8331 (ppp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.4920 time to fit residues: 120.4384 Evaluate side-chains 129 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 8.9990 chunk 563 optimal weight: 5.9990 chunk 513 optimal weight: 1.9990 chunk 547 optimal weight: 6.9990 chunk 329 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 495 optimal weight: 10.0000 chunk 518 optimal weight: 0.9980 chunk 545 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1840 GLN A2488 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1840 GLN D2488 GLN D2985 ASN D3856 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50662 Z= 0.215 Angle : 0.517 9.309 68578 Z= 0.271 Chirality : 0.041 0.149 7754 Planarity : 0.003 0.049 8594 Dihedral : 7.164 135.477 6744 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.11), residues: 6034 helix: 2.49 (0.10), residues: 2808 sheet: 0.67 (0.16), residues: 960 loop : -0.53 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 368 HIS 0.008 0.001 HIS D2741 PHE 0.026 0.001 PHE A3635 TYR 0.018 0.001 TYR D3268 ARG 0.005 0.000 ARG F 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 4.655 Fit side-chains revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9314 (mtp) cc_final: 0.8257 (tpp) REVERT: A 1655 MET cc_start: 0.8970 (tpt) cc_final: 0.8495 (mpp) REVERT: A 1678 MET cc_start: 0.9495 (mmp) cc_final: 0.9174 (mmm) REVERT: A 1921 MET cc_start: 0.8775 (mtp) cc_final: 0.8451 (mtp) REVERT: A 1937 MET cc_start: 0.9090 (mmm) cc_final: 0.8841 (mpp) REVERT: A 2063 MET cc_start: 0.9268 (mmt) cc_final: 0.8961 (mmp) REVERT: A 2118 MET cc_start: 0.7093 (tpt) cc_final: 0.6829 (tpt) REVERT: A 2546 MET cc_start: 0.8262 (mtp) cc_final: 0.7634 (ttm) REVERT: A 2866 LEU cc_start: 0.8586 (tp) cc_final: 0.8332 (pt) REVERT: A 2925 MET cc_start: 0.8497 (mtp) cc_final: 0.8162 (tpp) REVERT: A 3377 MET cc_start: 0.8979 (tpt) cc_final: 0.8409 (tpp) REVERT: A 3414 MET cc_start: 0.8349 (mpp) cc_final: 0.7407 (mpp) REVERT: A 3577 MET cc_start: 0.8766 (mpp) cc_final: 0.8347 (mpp) REVERT: A 3595 MET cc_start: 0.9119 (mpp) cc_final: 0.8916 (mpp) REVERT: A 3696 MET cc_start: 0.8545 (ptp) cc_final: 0.8312 (ptp) REVERT: B 370 MET cc_start: 0.8639 (ptt) cc_final: 0.8282 (mmm) REVERT: B 480 MET cc_start: 0.8585 (ppp) cc_final: 0.8342 (tmm) REVERT: C 370 MET cc_start: 0.8402 (ptp) cc_final: 0.8105 (ptp) REVERT: D 1472 GLU cc_start: 0.7699 (mp0) cc_final: 0.6694 (mt-10) REVERT: D 1565 MET cc_start: 0.9224 (tpp) cc_final: 0.8649 (tpp) REVERT: D 1655 MET cc_start: 0.8841 (tpt) cc_final: 0.8442 (mpp) REVERT: D 1678 MET cc_start: 0.9493 (mmp) cc_final: 0.9172 (mmm) REVERT: D 1921 MET cc_start: 0.8824 (mtp) cc_final: 0.8511 (mtp) REVERT: D 1937 MET cc_start: 0.9324 (mmp) cc_final: 0.8919 (mmm) REVERT: D 2063 MET cc_start: 0.9267 (mmt) cc_final: 0.8959 (mmp) REVERT: D 2546 MET cc_start: 0.8319 (mtp) cc_final: 0.7884 (ttm) REVERT: D 2932 MET cc_start: 0.8909 (mmt) cc_final: 0.8566 (tpp) REVERT: D 3282 MET cc_start: 0.8501 (ttp) cc_final: 0.8235 (tmm) REVERT: D 3377 MET cc_start: 0.8840 (tpt) cc_final: 0.8460 (tpp) REVERT: D 3414 MET cc_start: 0.8928 (mmm) cc_final: 0.8550 (mpp) REVERT: D 3577 MET cc_start: 0.8975 (mpp) cc_final: 0.8689 (mpp) REVERT: D 3696 MET cc_start: 0.8185 (pmm) cc_final: 0.7816 (pmm) REVERT: E 479 MET cc_start: 0.7620 (ptp) cc_final: 0.7197 (ptp) REVERT: E 480 MET cc_start: 0.8580 (ppp) cc_final: 0.8333 (ppp) REVERT: E 493 MET cc_start: 0.8199 (ppp) cc_final: 0.7782 (ppp) REVERT: F 370 MET cc_start: 0.8469 (ptp) cc_final: 0.8134 (ptp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.4649 time to fit residues: 111.9208 Evaluate side-chains 129 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 8.9990 chunk 579 optimal weight: 10.0000 chunk 353 optimal weight: 20.0000 chunk 274 optimal weight: 9.9990 chunk 402 optimal weight: 5.9990 chunk 607 optimal weight: 10.0000 chunk 559 optimal weight: 4.9990 chunk 483 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1840 GLN A2488 GLN A2985 ASN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1840 GLN D2488 GLN D3856 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 50662 Z= 0.292 Angle : 0.568 9.564 68578 Z= 0.296 Chirality : 0.042 0.153 7754 Planarity : 0.004 0.048 8594 Dihedral : 7.122 122.504 6744 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.11), residues: 6034 helix: 2.39 (0.10), residues: 2812 sheet: 0.52 (0.16), residues: 966 loop : -0.60 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 288 HIS 0.008 0.001 HIS A2741 PHE 0.020 0.002 PHE A3635 TYR 0.029 0.001 TYR D2574 ARG 0.004 0.000 ARG F 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12068 Ramachandran restraints generated. 6034 Oldfield, 0 Emsley, 6034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 4.643 Fit side-chains revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9322 (mtp) cc_final: 0.8530 (tpp) REVERT: A 1655 MET cc_start: 0.8990 (tpt) cc_final: 0.8508 (mpp) REVERT: A 1678 MET cc_start: 0.9500 (mmp) cc_final: 0.9179 (mmm) REVERT: A 1921 MET cc_start: 0.8649 (mtp) cc_final: 0.8299 (mtp) REVERT: A 1937 MET cc_start: 0.9129 (mmm) cc_final: 0.8840 (mpp) REVERT: A 2063 MET cc_start: 0.9289 (mmt) cc_final: 0.8980 (mmp) REVERT: A 2546 MET cc_start: 0.8341 (mtp) cc_final: 0.7706 (ttm) REVERT: A 2866 LEU cc_start: 0.8629 (tp) cc_final: 0.8357 (pt) REVERT: A 2925 MET cc_start: 0.8515 (mtp) cc_final: 0.8174 (tpp) REVERT: A 2932 MET cc_start: 0.9091 (mmt) cc_final: 0.8860 (mmt) REVERT: A 3377 MET cc_start: 0.9004 (tpt) cc_final: 0.8429 (tpp) REVERT: A 3414 MET cc_start: 0.8393 (mpp) cc_final: 0.7427 (mpp) REVERT: A 3696 MET cc_start: 0.8629 (ptp) cc_final: 0.8427 (ptp) REVERT: B 480 MET cc_start: 0.8618 (ppp) cc_final: 0.8417 (tmm) REVERT: C 370 MET cc_start: 0.8476 (ptp) cc_final: 0.8189 (ptp) REVERT: D 1565 MET cc_start: 0.9172 (tpp) cc_final: 0.8621 (tpp) REVERT: D 1655 MET cc_start: 0.8883 (tpt) cc_final: 0.8485 (mpp) REVERT: D 1678 MET cc_start: 0.9482 (mmp) cc_final: 0.9155 (mmm) REVERT: D 1921 MET cc_start: 0.8710 (mtp) cc_final: 0.8372 (mtp) REVERT: D 1937 MET cc_start: 0.9338 (mmp) cc_final: 0.8935 (mmm) REVERT: D 2063 MET cc_start: 0.9287 (mmt) cc_final: 0.8980 (mmp) REVERT: D 2546 MET cc_start: 0.8394 (mtp) cc_final: 0.7871 (ttm) REVERT: D 2932 MET cc_start: 0.8923 (mmt) cc_final: 0.8581 (tpp) REVERT: D 3282 MET cc_start: 0.8439 (ttp) cc_final: 0.8147 (tmm) REVERT: D 3377 MET cc_start: 0.8820 (tpt) cc_final: 0.8387 (tpp) REVERT: D 3414 MET cc_start: 0.8947 (mmm) cc_final: 0.8576 (mpp) REVERT: D 3577 MET cc_start: 0.8747 (mpp) cc_final: 0.8298 (tpp) REVERT: D 3696 MET cc_start: 0.8176 (pmm) cc_final: 0.7842 (pmm) REVERT: E 479 MET cc_start: 0.7678 (ptp) cc_final: 0.7242 (ptp) REVERT: E 493 MET cc_start: 0.8173 (ppp) cc_final: 0.7797 (ppp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4787 time to fit residues: 114.4948 Evaluate side-chains 128 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 4.9990 chunk 515 optimal weight: 5.9990 chunk 148 optimal weight: 0.0870 chunk 446 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 484 optimal weight: 0.0770 chunk 202 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1840 GLN A2488 GLN ** A2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3318 GLN D1840 GLN D2488 GLN D2741 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.037142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.028910 restraints weight = 504434.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.029812 restraints weight = 295504.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.030639 restraints weight = 181726.958| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 50662 Z= 0.121 Angle : 0.478 9.500 68578 Z= 0.250 Chirality : 0.041 0.170 7754 Planarity : 0.003 0.051 8594 Dihedral : 6.650 87.246 6744 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.11), residues: 6034 helix: 2.63 (0.10), residues: 2818 sheet: 0.82 (0.17), residues: 962 loop : -0.48 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 288 HIS 0.005 0.001 HIS A2741 PHE 0.025 0.001 PHE A3635 TYR 0.017 0.001 TYR D2571 ARG 0.005 0.000 ARG F 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.25 seconds wall clock time: 97 minutes 8.59 seconds (5828.59 seconds total)