Starting phenix.real_space_refine on Mon Mar 25 15:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/03_2024/8dzz_27810_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/03_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_27810/03_2024/8dzz_27810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/03_2024/8dzz_27810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/03_2024/8dzz_27810_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzz_27810/03_2024/8dzz_27810_neut_updated.pdb" } 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 Residue "A ASP 2478": "OD1" <-> "OD2" Residue "A ASP 2868": "OD1" <-> "OD2" Residue "A TYR 3268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3281": "OE1" <-> "OE2" Residue "A PHE 3635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3891": "NH1" <-> "NH2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ASP 465": "OD1" <-> "OD2" Residue "D TYR 2102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2112": "OE1" <-> "OE2" Residue "D ASP 2478": "OD1" <-> "OD2" Residue "D PHE 2827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2868": "OD1" <-> "OD2" Residue "D GLU 3469": "OE1" <-> "OE2" Residue "D GLU 3867": "OE1" <-> "OE2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ASP 465": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 26.84, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.96 Conformation dependent library (CDL) restraints added in 9.0 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... running ksdssp... Secondary structure from input PDB file: 206 helices and 56 sheets defined 45.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.01 Creating SS restraints... Processing helix chain 'A' and resid 1450 through 1458 Processing helix chain 'A' and resid 1465 through 1467 No H-bonds generated for 'chain 'A' and resid 1465 through 1467' Processing helix chain 'A' and resid 1470 through 1478 Processing helix chain 'A' and resid 1516 through 1533 removed outlier: 3.568A pdb=" N LEU A1523 " --> pdb=" O ILE A1519 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER A1524 " --> pdb=" O LYS A1520 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR A1525 " --> pdb=" O SER A1521 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A1533 " --> pdb=" O ARG A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1539 Processing helix chain 'A' and resid 1542 through 1550 Processing helix chain 'A' and resid 1557 through 1565 removed outlier: 3.511A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A1562 " --> pdb=" O VAL A1558 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1632 Processing helix chain 'A' and resid 1636 through 1638 No H-bonds generated for 'chain 'A' and resid 1636 through 1638' Processing helix chain 'A' and resid 1645 through 1664 Processing helix chain 'A' and resid 1670 through 1688 removed outlier: 4.031A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1717 Processing helix chain 'A' and resid 1721 through 1730 removed outlier: 3.785A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1788 removed outlier: 3.902A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1828 through 1841 Processing helix chain 'A' and resid 1850 through 1852 No H-bonds generated for 'chain 'A' and resid 1850 through 1852' Processing helix chain 'A' and resid 1855 through 1874 removed outlier: 3.839A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1915 removed outlier: 4.618A pdb=" N SER A1915 " --> pdb=" O ASN A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1937 Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1970 through 1982 removed outlier: 3.578A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix Processing helix chain 'A' and resid 1984 through 1987 No H-bonds generated for 'chain 'A' and resid 1984 through 1987' Processing helix chain 'A' and resid 1991 through 2005 Proline residue: A2004 - end of helix Processing helix chain 'A' and resid 2008 through 2021 Processing helix chain 'A' and resid 2032 through 2045 Processing helix chain 'A' and resid 2051 through 2066 removed outlier: 3.710A pdb=" N LYS A2065 " --> pdb=" O TYR A2061 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2095 Processing helix chain 'A' and resid 2111 through 2114 No H-bonds generated for 'chain 'A' and resid 2111 through 2114' Processing helix chain 'A' and resid 2129 through 2139 Processing helix chain 'A' and resid 2160 through 2170 removed outlier: 3.704A pdb=" N GLU A2164 " --> pdb=" O PRO A2160 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET A2166 " --> pdb=" O TYR A2162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A2167 " --> pdb=" O VAL A2163 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A2168 " --> pdb=" O GLU A2164 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2207 No H-bonds generated for 'chain 'A' and resid 2204 through 2207' Processing helix chain 'A' and resid 2222 through 2236 Processing helix chain 'A' and resid 2245 through 2256 Processing helix chain 'A' and resid 2259 through 2271 removed outlier: 4.488A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2280 through 2282 No H-bonds generated for 'chain 'A' and resid 2280 through 2282' Processing helix chain 'A' and resid 2284 through 2301 removed outlier: 3.734A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A2299 " --> pdb=" O ILE A2295 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2327 Processing helix chain 'A' and resid 2332 through 2346 Processing helix chain 'A' and resid 2371 through 2373 No H-bonds generated for 'chain 'A' and resid 2371 through 2373' Processing helix chain 'A' and resid 2382 through 2386 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2424 through 2433 Processing helix chain 'A' and resid 2451 through 2458 removed outlier: 3.690A pdb=" N LEU A2458 " --> pdb=" O ILE A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2511 Processing helix chain 'A' and resid 2548 through 2553 removed outlier: 5.073A pdb=" N HIS A2553 " --> pdb=" O ARG A2549 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2580 removed outlier: 3.796A pdb=" N LYS A2580 " --> pdb=" O LYS A2576 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2606 removed outlier: 5.145A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU A2590 " --> pdb=" O SER A2587 " (cutoff:3.500A) Proline residue: A2591 - end of helix Processing helix chain 'A' and resid 2619 through 2634 Processing helix chain 'A' and resid 2641 through 2659 removed outlier: 4.501A pdb=" N ASP A2658 " --> pdb=" O ARG A2654 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG A2659 " --> pdb=" O ILE A2655 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2709 through 2726 Processing helix chain 'A' and resid 2736 through 2750 Processing helix chain 'A' and resid 2766 through 2776 Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2819 through 2821 No H-bonds generated for 'chain 'A' and resid 2819 through 2821' Processing helix chain 'A' and resid 2825 through 2836 removed outlier: 3.651A pdb=" N THR A2833 " --> pdb=" O GLU A2829 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2843 No H-bonds generated for 'chain 'A' and resid 2841 through 2843' Processing helix chain 'A' and resid 2846 through 2863 removed outlier: 3.553A pdb=" N LYS A2851 " --> pdb=" O GLU A2848 " (cutoff:3.500A) Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2897 through 2904 Processing helix chain 'A' and resid 2906 through 2909 No H-bonds generated for 'chain 'A' and resid 2906 through 2909' Processing helix chain 'A' and resid 2922 through 2935 removed outlier: 3.595A pdb=" N ASP A2934 " --> pdb=" O ASN A2930 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2952 No H-bonds generated for 'chain 'A' and resid 2950 through 2952' Processing helix chain 'A' and resid 2961 through 2980 Processing helix chain 'A' and resid 2990 through 3057 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 3318 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 3320 through 3336 removed outlier: 4.772A pdb=" N GLY A3335 " --> pdb=" O GLU A3331 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS A3336 " --> pdb=" O THR A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3339 through 3355 Processing helix chain 'A' and resid 3366 through 3370 Processing helix chain 'A' and resid 3373 through 3381 Processing helix chain 'A' and resid 3388 through 3398 Processing helix chain 'A' and resid 3413 through 3422 Processing helix chain 'A' and resid 3436 through 3446 Processing helix chain 'A' and resid 3455 through 3457 No H-bonds generated for 'chain 'A' and resid 3455 through 3457' Processing helix chain 'A' and resid 3460 through 3466 removed outlier: 5.270A pdb=" N ARG A3464 " --> pdb=" O ILE A3461 " (cutoff:3.500A) Processing helix chain 'A' and resid 3507 through 3512 removed outlier: 3.685A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3522 through 3537 Processing helix chain 'A' and resid 3539 through 3571 Processing helix chain 'A' and resid 3581 through 3638 removed outlier: 3.879A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE A3607 " --> pdb=" O GLU A3603 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE A3608 " --> pdb=" O SER A3604 " (cutoff:3.500A) Proline residue: A3609 - end of helix removed outlier: 4.123A pdb=" N TYR A3618 " --> pdb=" O LEU A3614 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A3619 " --> pdb=" O VAL A3615 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3658 removed outlier: 3.828A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3689 removed outlier: 4.576A pdb=" N THR A3688 " --> pdb=" O CYS A3684 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA A3689 " --> pdb=" O GLN A3685 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3710 removed outlier: 4.217A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3726 Processing helix chain 'A' and resid 3742 through 3752 Processing helix chain 'A' and resid 3756 through 3767 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 3774 through 3779 Processing helix chain 'A' and resid 3797 through 3806 Processing helix chain 'A' and resid 3819 through 3834 Processing helix chain 'A' and resid 3844 through 3851 removed outlier: 3.807A pdb=" N LEU A3848 " --> pdb=" O GLN A3845 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER A3849 " --> pdb=" O MET A3846 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3865 removed outlier: 3.708A pdb=" N GLU A3860 " --> pdb=" O HIS A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3886 through 3889 No H-bonds generated for 'chain 'A' and resid 3886 through 3889' Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.885A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3958 through 3974 removed outlier: 3.786A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3991 Processing helix chain 'A' and resid 3995 through 3997 No H-bonds generated for 'chain 'A' and resid 3995 through 3997' Processing helix chain 'A' and resid 4001 through 4016 removed outlier: 3.804A pdb=" N CYS A4016 " --> pdb=" O ALA A4012 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4050 Processing helix chain 'A' and resid 4058 through 4061 No H-bonds generated for 'chain 'A' and resid 4058 through 4061' Processing helix chain 'A' and resid 4067 through 4090 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 363 through 368 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'D' and resid 1450 through 1458 Processing helix chain 'D' and resid 1465 through 1467 No H-bonds generated for 'chain 'D' and resid 1465 through 1467' Processing helix chain 'D' and resid 1470 through 1478 Processing helix chain 'D' and resid 1516 through 1533 removed outlier: 3.565A pdb=" N LEU D1523 " --> pdb=" O ILE D1519 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N SER D1524 " --> pdb=" O LYS D1520 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR D1525 " --> pdb=" O SER D1521 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE D1526 " --> pdb=" O SER D1522 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN D1533 " --> pdb=" O ARG D1529 " (cutoff:3.500A) Processing helix chain 'D' and resid 1535 through 1539 Processing helix chain 'D' and resid 1542 through 1550 Processing helix chain 'D' and resid 1557 through 1565 removed outlier: 3.507A pdb=" N PHE D1561 " --> pdb=" O GLN D1557 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET D1562 " --> pdb=" O VAL D1558 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS D1563 " --> pdb=" O SER D1559 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS D1564 " --> pdb=" O LYS D1560 " (cutoff:3.500A) Processing helix chain 'D' and resid 1604 through 1632 Processing helix chain 'D' and resid 1636 through 1638 No H-bonds generated for 'chain 'D' and resid 1636 through 1638' Processing helix chain 'D' and resid 1645 through 1664 Processing helix chain 'D' and resid 1670 through 1688 removed outlier: 4.030A pdb=" N ASN D1688 " --> pdb=" O LEU D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1692 through 1717 Processing helix chain 'D' and resid 1721 through 1730 removed outlier: 3.784A pdb=" N LYS D1730 " --> pdb=" O LEU D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1773 through 1788 removed outlier: 3.907A pdb=" N GLN D1788 " --> pdb=" O ASP D1784 " (cutoff:3.500A) Processing helix chain 'D' and resid 1802 through 1812 Processing helix chain 'D' and resid 1828 through 1841 Processing helix chain 'D' and resid 1850 through 1852 No H-bonds generated for 'chain 'D' and resid 1850 through 1852' Processing helix chain 'D' and resid 1855 through 1874 removed outlier: 3.837A pdb=" N SER D1862 " --> pdb=" O LEU D1858 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA D1863 " --> pdb=" O SER D1859 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN D1864 " --> pdb=" O ALA D1860 " (cutoff:3.500A) Processing helix chain 'D' and resid 1910 through 1915 removed outlier: 4.614A pdb=" N SER D1915 " --> pdb=" O ASN D1911 " (cutoff:3.500A) Processing helix chain 'D' and resid 1926 through 1937 Processing helix chain 'D' and resid 1942 through 1959 Processing helix chain 'D' and resid 1970 through 1982 removed outlier: 3.582A pdb=" N SER D1981 " --> pdb=" O LEU D1977 " (cutoff:3.500A) Proline residue: D1982 - end of helix Processing helix chain 'D' and resid 1984 through 1987 No H-bonds generated for 'chain 'D' and resid 1984 through 1987' Processing helix chain 'D' and resid 1991 through 2005 Proline residue: D2004 - end of helix Processing helix chain 'D' and resid 2008 through 2021 Processing helix chain 'D' and resid 2032 through 2045 Processing helix chain 'D' and resid 2051 through 2066 removed outlier: 3.703A pdb=" N LYS D2065 " --> pdb=" O TYR D2061 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR D2066 " --> pdb=" O TYR D2062 " (cutoff:3.500A) Processing helix chain 'D' and resid 2080 through 2095 Processing helix chain 'D' and resid 2111 through 2114 No H-bonds generated for 'chain 'D' and resid 2111 through 2114' Processing helix chain 'D' and resid 2129 through 2139 Processing helix chain 'D' and resid 2160 through 2170 removed outlier: 3.696A pdb=" N GLU D2164 " --> pdb=" O PRO D2160 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA D2165 " --> pdb=" O GLU D2161 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET D2166 " --> pdb=" O TYR D2162 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D2167 " --> pdb=" O VAL D2163 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER D2168 " --> pdb=" O GLU D2164 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL D2169 " --> pdb=" O ALA D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2204 through 2207 No H-bonds generated for 'chain 'D' and resid 2204 through 2207' Processing helix chain 'D' and resid 2222 through 2236 Processing helix chain 'D' and resid 2245 through 2256 Processing helix chain 'D' and resid 2259 through 2271 removed outlier: 4.492A pdb=" N ASN D2264 " --> pdb=" O ALA D2260 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP D2271 " --> pdb=" O THR D2267 " (cutoff:3.500A) Processing helix chain 'D' and resid 2280 through 2282 No H-bonds generated for 'chain 'D' and resid 2280 through 2282' Processing helix chain 'D' and resid 2284 through 2301 removed outlier: 3.736A pdb=" N TYR D2298 " --> pdb=" O LEU D2294 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D2299 " --> pdb=" O ILE D2295 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN D2300 " --> pdb=" O SER D2296 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TRP D2301 " --> pdb=" O SER D2297 " (cutoff:3.500A) Processing helix chain 'D' and resid 2307 through 2327 Processing helix chain 'D' and resid 2332 through 2346 Processing helix chain 'D' and resid 2371 through 2373 No H-bonds generated for 'chain 'D' and resid 2371 through 2373' Processing helix chain 'D' and resid 2382 through 2386 Processing helix chain 'D' and resid 2395 through 2409 Processing helix chain 'D' and resid 2424 through 2433 Processing helix chain 'D' and resid 2451 through 2458 removed outlier: 3.694A pdb=" N LEU D2458 " --> pdb=" O ILE D2454 " (cutoff:3.500A) Processing helix chain 'D' and resid 2501 through 2511 Processing helix chain 'D' and resid 2548 through 2553 removed outlier: 5.067A pdb=" N HIS D2553 " --> pdb=" O ARG D2549 " (cutoff:3.500A) Processing helix chain 'D' and resid 2564 through 2580 removed outlier: 3.802A pdb=" N LYS D2580 " --> pdb=" O LYS D2576 " (cutoff:3.500A) Processing helix chain 'D' and resid 2583 through 2606 removed outlier: 5.136A pdb=" N SER D2587 " --> pdb=" O GLU D2584 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU D2590 " --> pdb=" O SER D2587 " (cutoff:3.500A) Proline residue: D2591 - end of helix Processing helix chain 'D' and resid 2619 through 2634 Processing helix chain 'D' and resid 2641 through 2659 removed outlier: 4.505A pdb=" N ASP D2658 " --> pdb=" O ARG D2654 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG D2659 " --> pdb=" O ILE D2655 " (cutoff:3.500A) Processing helix chain 'D' and resid 2663 through 2680 Processing helix chain 'D' and resid 2709 through 2726 Processing helix chain 'D' and resid 2736 through 2750 Processing helix chain 'D' and resid 2766 through 2776 Processing helix chain 'D' and resid 2792 through 2808 Processing helix chain 'D' and resid 2819 through 2821 No H-bonds generated for 'chain 'D' and resid 2819 through 2821' Processing helix chain 'D' and resid 2825 through 2836 removed outlier: 3.624A pdb=" N THR D2833 " --> pdb=" O GLU D2829 " (cutoff:3.500A) Processing helix chain 'D' and resid 2841 through 2843 No H-bonds generated for 'chain 'D' and resid 2841 through 2843' Processing helix chain 'D' and resid 2846 through 2863 removed outlier: 3.550A pdb=" N LYS D2851 " --> pdb=" O GLU D2848 " (cutoff:3.500A) Processing helix chain 'D' and resid 2870 through 2884 Processing helix chain 'D' and resid 2897 through 2904 Processing helix chain 'D' and resid 2906 through 2909 No H-bonds generated for 'chain 'D' and resid 2906 through 2909' Processing helix chain 'D' and resid 2922 through 2935 removed outlier: 3.554A pdb=" N ASP D2934 " --> pdb=" O ASN D2930 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D2935 " --> pdb=" O ASN D2931 " (cutoff:3.500A) Processing helix chain 'D' and resid 2950 through 2952 No H-bonds generated for 'chain 'D' and resid 2950 through 2952' Processing helix chain 'D' and resid 2961 through 2980 Processing helix chain 'D' and resid 2990 through 3057 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 3318 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 3320 through 3336 removed outlier: 4.786A pdb=" N GLY D3335 " --> pdb=" O GLU D3331 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS D3336 " --> pdb=" O THR D3332 " (cutoff:3.500A) Processing helix chain 'D' and resid 3339 through 3355 Processing helix chain 'D' and resid 3366 through 3370 Processing helix chain 'D' and resid 3373 through 3381 Processing helix chain 'D' and resid 3388 through 3398 Processing helix chain 'D' and resid 3413 through 3422 Processing helix chain 'D' and resid 3436 through 3446 Processing helix chain 'D' and resid 3455 through 3457 No H-bonds generated for 'chain 'D' and resid 3455 through 3457' Processing helix chain 'D' and resid 3460 through 3466 removed outlier: 5.269A pdb=" N ARG D3464 " --> pdb=" O ILE D3461 " (cutoff:3.500A) Processing helix chain 'D' and resid 3507 through 3512 removed outlier: 3.673A pdb=" N ARG D3512 " --> pdb=" O PHE D3508 " (cutoff:3.500A) Processing helix chain 'D' and resid 3522 through 3537 Processing helix chain 'D' and resid 3539 through 3571 Processing helix chain 'D' and resid 3581 through 3638 removed outlier: 3.887A pdb=" N GLU D3606 " --> pdb=" O SER D3602 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE D3607 " --> pdb=" O GLU D3603 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE D3608 " --> pdb=" O SER D3604 " (cutoff:3.500A) Proline residue: D3609 - end of helix removed outlier: 4.098A pdb=" N TYR D3618 " --> pdb=" O LEU D3614 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D3619 " --> pdb=" O VAL D3615 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE D3620 " --> pdb=" O GLU D3616 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE D3621 " --> pdb=" O GLU D3617 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE D3638 " --> pdb=" O LYS D3634 " (cutoff:3.500A) Processing helix chain 'D' and resid 3646 through 3658 removed outlier: 3.823A pdb=" N PHE D3657 " --> pdb=" O PHE D3653 " (cutoff:3.500A) Processing helix chain 'D' and resid 3670 through 3689 removed outlier: 4.586A pdb=" N THR D3688 " --> pdb=" O CYS D3684 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA D3689 " --> pdb=" O GLN D3685 " (cutoff:3.500A) Processing helix chain 'D' and resid 3692 through 3710 removed outlier: 4.200A pdb=" N ASP D3709 " --> pdb=" O LEU D3705 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3726 Processing helix chain 'D' and resid 3742 through 3752 Processing helix chain 'D' and resid 3756 through 3767 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 3774 through 3779 Processing helix chain 'D' and resid 3797 through 3806 Processing helix chain 'D' and resid 3819 through 3834 Processing helix chain 'D' and resid 3844 through 3851 removed outlier: 3.812A pdb=" N LEU D3848 " --> pdb=" O GLN D3845 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER D3849 " --> pdb=" O MET D3846 " (cutoff:3.500A) Processing helix chain 'D' and resid 3854 through 3864 removed outlier: 3.504A pdb=" N THR D3862 " --> pdb=" O HIS D3858 " (cutoff:3.500A) Processing helix chain 'D' and resid 3886 through 3889 No H-bonds generated for 'chain 'D' and resid 3886 through 3889' Processing helix chain 'D' and resid 3903 through 3913 Processing helix chain 'D' and resid 3923 through 3944 removed outlier: 3.878A pdb=" N ARG D3944 " --> pdb=" O THR D3940 " (cutoff:3.500A) Processing helix chain 'D' and resid 3958 through 3974 removed outlier: 3.789A pdb=" N THR D3974 " --> pdb=" O ASN D3970 " (cutoff:3.500A) Processing helix chain 'D' and resid 3982 through 3991 Processing helix chain 'D' and resid 3995 through 3997 No H-bonds generated for 'chain 'D' and resid 3995 through 3997' Processing helix chain 'D' and resid 4001 through 4016 removed outlier: 3.804A pdb=" N CYS D4016 " --> pdb=" O ALA D4012 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4050 Processing helix chain 'D' and resid 4058 through 4061 No H-bonds generated for 'chain 'D' and resid 4058 through 4061' Processing helix chain 'D' and resid 4067 through 4090 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 363 through 368 Processing helix chain 'F' and resid 363 through 368 Processing sheet with id= A, first strand: chain 'A' and resid 1589 through 1591 Processing sheet with id= B, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id= C, first strand: chain 'A' and resid 1916 through 1920 removed outlier: 7.004A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id= E, first strand: chain 'A' and resid 2211 through 2215 removed outlier: 8.753A pdb=" N LEU A2070 " --> pdb=" O PHE A2190 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A2192 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU A2072 " --> pdb=" O ILE A2192 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A2194 " --> pdb=" O LEU A2072 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY A2074 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR A2196 " --> pdb=" O GLY A2074 " (cutoff:3.500A) 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: 6.659A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP A2155 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A2104 " --> pdb=" O ASP A2155 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2117 through 2119 Processing sheet with id= G, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id= H, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id= I, first strand: chain 'A' and resid 2554 through 2558 removed outlier: 6.726A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (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) Processing sheet with id= J, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id= K, first strand: chain 'A' and resid 2780 through 2783 removed outlier: 6.675A pdb=" N ILE A2913 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE A2759 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A2915 " --> pdb=" O ILE A2759 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 3513 through 3517 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= M, first strand: chain 'A' and resid 3478 through 3481 Processing sheet with id= N, first strand: chain 'A' and resid 3893 through 3896 removed outlier: 8.491A pdb=" N PHE A3786 " --> pdb=" O PHE A3871 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET A3873 " --> pdb=" O PHE A3786 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N MET A3788 " --> pdb=" O MET A3873 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET A3875 " --> pdb=" O MET A3788 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER A3790 " --> pdb=" O MET A3875 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS A3877 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) Processing sheet with id= O, 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= P, first strand: chain 'B' and resid 192 through 195 removed outlier: 4.451A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 201 through 208 removed outlier: 7.188A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 256 through 264 removed outlier: 6.920A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN B 263 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.932A pdb=" N GLY B 313 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 303 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 311 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 305 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS B 323 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLY B 329 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 340 through 346 removed outlier: 6.879A pdb=" N ALA B 376 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 343 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 374 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE B 345 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR B 372 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU B 386 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS B 409 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 420 through 426 removed outlier: 6.444A pdb=" N CYS B 433 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 423 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B 431 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE B 425 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR B 429 " --> pdb=" O ILE B 425 " (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= V, 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= W, first strand: chain 'C' and resid 192 through 195 removed outlier: 4.411A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.962A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (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: 5.568A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 256 through 263 removed outlier: 6.793A pdb=" N CYS C 273 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 271 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE C 261 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS C 269 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.742A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.844A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 420 through 426 removed outlier: 6.603A pdb=" N CYS C 433 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 423 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE C 431 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 425 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1589 through 1591 Processing sheet with id= AD, first strand: chain 'D' and resid 1733 through 1736 Processing sheet with id= AE, first strand: chain 'D' and resid 1916 through 1920 removed outlier: 7.006A pdb=" N GLY D1791 " --> pdb=" O ARG D1917 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE D1919 " --> pdb=" O GLY D1791 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS D1793 " --> pdb=" O PHE D1919 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 1878 through 1881 Processing sheet with id= AG, first strand: chain 'D' and resid 2211 through 2215 removed outlier: 8.711A pdb=" N LEU D2070 " --> pdb=" O PHE D2190 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE D2192 " --> pdb=" O LEU D2070 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU D2072 " --> pdb=" O ILE D2192 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D2194 " --> pdb=" O LEU D2072 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY D2074 " --> pdb=" O PHE D2194 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR D2196 " --> pdb=" O GLY D2074 " (cutoff:3.500A) 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: 6.672A pdb=" N ALA D2098 " --> pdb=" O ARG D2149 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TRP D2151 " --> pdb=" O ALA D2098 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D2100 " --> pdb=" O TRP D2151 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL D2153 " --> pdb=" O VAL D2100 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR D2102 " --> pdb=" O VAL D2153 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP D2155 " --> pdb=" O TYR D2102 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE D2104 " --> pdb=" O ASP D2155 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 2117 through 2119 Processing sheet with id= AI, first strand: chain 'D' and resid 2175 through 2177 Processing sheet with id= AJ, first strand: chain 'D' and resid 2357 through 2360 Processing sheet with id= AK, first strand: chain 'D' and resid 2554 through 2558 removed outlier: 6.723A pdb=" N GLY D2413 " --> pdb=" O ALA D2555 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU D2557 " --> pdb=" O GLY D2413 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE D2415 " --> pdb=" O LEU D2557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D2414 " --> pdb=" O ILE D2531 " (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) Processing sheet with id= AL, first strand: chain 'D' and resid 2462 through 2465 Processing sheet with id= AM, first strand: chain 'D' and resid 2780 through 2783 removed outlier: 3.694A pdb=" N MET D2756 " --> pdb=" O VAL D2887 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE D2913 " --> pdb=" O MET D2757 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE D2759 " --> pdb=" O ILE D2913 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN D2915 " --> pdb=" O ILE D2759 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 3513 through 3517 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= AO, first strand: chain 'D' and resid 3478 through 3481 Processing sheet with id= AP, first strand: chain 'D' and resid 3893 through 3896 removed outlier: 8.411A pdb=" N PHE D3786 " --> pdb=" O PHE D3871 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET D3873 " --> pdb=" O PHE D3786 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET D3788 " --> pdb=" O MET D3873 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET D3875 " --> pdb=" O MET D3788 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER D3790 " --> pdb=" O MET D3875 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS D3877 " --> pdb=" O SER D3790 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY D3837 " --> pdb=" O LYS D3872 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE D3874 " --> pdb=" O GLY D3837 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE D3839 " --> pdb=" O PHE D3874 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR D3876 " --> pdb=" O ILE D3839 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU D3841 " --> pdb=" O THR D3876 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N HIS D3878 " --> pdb=" O LEU D3841 " (cutoff:3.500A) Processing sheet with id= AQ, 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= AR, first strand: chain 'E' and resid 192 through 195 removed outlier: 4.469A pdb=" N LYS E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 201 through 208 removed outlier: 7.219A pdb=" N ALA E 225 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET E 204 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL E 223 " --> pdb=" O MET E 204 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL E 206 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL E 221 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 220 " --> pdb=" O TRP E 236 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS E 235 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLN E 245 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL E 237 " --> pdb=" O PHE E 243 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE E 243 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'E' and resid 256 through 264 removed outlier: 6.881A pdb=" N CYS E 273 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 259 " --> pdb=" O ALA E 271 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 271 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE E 261 " --> pdb=" O HIS E 269 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS E 269 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN E 263 " --> pdb=" O ASP E 267 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP E 267 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'E' and resid 300 through 306 removed outlier: 6.922A pdb=" N GLY E 313 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE E 303 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE E 311 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL E 305 " --> pdb=" O TYR E 309 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS E 323 " --> pdb=" O GLY E 329 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY E 329 " --> pdb=" O HIS E 323 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 340 through 346 removed outlier: 6.846A pdb=" N ALA E 376 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL E 343 " --> pdb=" O VAL E 374 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL E 374 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE E 345 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR E 372 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU E 386 " --> pdb=" O CYS E 409 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N CYS E 409 " --> pdb=" O GLU E 386 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 420 through 426 removed outlier: 6.471A pdb=" N CYS E 433 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE E 423 " --> pdb=" O PHE E 431 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE E 431 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE E 425 " --> pdb=" O TYR E 429 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR E 429 " --> pdb=" O ILE E 425 " (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= AX, 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= AY, first strand: chain 'F' and resid 192 through 195 removed outlier: 4.411A pdb=" N LYS F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'F' and resid 201 through 208 removed outlier: 6.962A pdb=" N ALA F 225 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET F 204 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL F 223 " --> pdb=" O MET F 204 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL F 206 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL F 221 " --> pdb=" O VAL F 206 " (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: 5.568A pdb=" N LYS F 235 " --> pdb=" O GLN F 245 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN F 245 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL F 237 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE F 243 " --> pdb=" O VAL F 237 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'F' and resid 256 through 263 removed outlier: 6.795A pdb=" N CYS F 273 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL F 259 " --> pdb=" O ALA F 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA F 271 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE F 261 " --> pdb=" O HIS F 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N HIS F 269 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'F' and resid 300 through 306 removed outlier: 6.741A pdb=" N GLY F 313 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE F 303 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 311 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL F 305 " --> pdb=" O TYR F 309 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS F 323 " --> pdb=" O GLY F 329 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLY F 329 " --> pdb=" O HIS F 323 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 340 through 345 removed outlier: 6.844A pdb=" N ALA F 376 " --> pdb=" O GLU F 341 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 343 " --> pdb=" O VAL F 374 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 374 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE F 345 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR F 372 " --> pdb=" O PHE F 345 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR F 381 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU F 386 " --> pdb=" O CYS F 409 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS F 409 " --> pdb=" O GLU F 386 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 420 through 426 removed outlier: 6.603A pdb=" N CYS F 433 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE F 423 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE F 431 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE F 425 " --> pdb=" O TYR F 429 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR F 429 " --> pdb=" O ILE F 425 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP F 443 " --> pdb=" O CYS F 449 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N CYS F 449 " --> pdb=" O ASP F 443 " (cutoff:3.500A) 2342 hydrogen bonds defined for protein. 6654 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: 30.17 Time building geometry restraints manager: 21.57 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: 97.46 - 105.93: 908 105.93 - 114.39: 30099 114.39 - 122.86: 32944 122.86 - 131.32: 4467 131.32 - 139.79: 160 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: 1169 2.70 - 3.25: 49558 3.25 - 3.80: 79700 3.80 - 4.35: 105175 4.35 - 4.90: 174101 Nonbonded interactions: 409703 Sorted by model distance: nonbonded pdb=" O THR C 212 " pdb=" OG1 THR C 212 " model vdw 2.145 2.440 nonbonded pdb=" OH TYR A1966 " pdb=" OD2 ASP A2010 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR D1966 " pdb=" OD2 ASP D2010 " model vdw 2.211 2.440 nonbonded pdb=" O GLU A3051 " pdb=" OG SER A3054 " model vdw 2.213 2.440 nonbonded pdb=" N GLU C 253 " pdb=" OE1 GLU C 253 " model vdw 2.223 2.520 ... (remaining 409698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 3.460 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: 0.050 Extract box with map and model: 12.200 Check model and map are aligned: 0.850 Set scattering table: 0.500 Process input model: 141.940 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.270 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.030 ------------------------------------------------------------------------------- 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= 0.250 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 : 5.989 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: 0.5954 time to fit residues: 202.9944 Evaluate side-chains 157 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 6.042 ------------------------------------------------------------------------------- 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: 5.9990 chunk 256 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 478 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 chunk 553 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1757 GLN A1867 GLN ** A1911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 GLN A2099 ASN A2201 HIS A2845 GLN ** A3878 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3948 HIS C 176 HIS C 328 ASN D1757 GLN D1867 GLN ** D1911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2068 GLN D2099 ASN D2201 HIS D2845 GLN ** D2927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3878 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3948 HIS E 244 GLN F 176 HIS F 328 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 50662 Z= 0.389 Angle : 0.689 8.258 68578 Z= 0.359 Chirality : 0.044 0.163 7754 Planarity : 0.005 0.050 8594 Dihedral : 9.062 174.537 6744 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.41 % 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: 1.15 (0.10), residues: 6034 helix: 1.80 (0.09), residues: 2820 sheet: 0.61 (0.16), residues: 1008 loop : -0.48 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 299 HIS 0.012 0.002 HIS D2755 PHE 0.025 0.002 PHE A2992 TYR 0.047 0.002 TYR D3268 ARG 0.014 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 156 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 6.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9443 (mtp) cc_final: 0.8457 (tpp) REVERT: A 1678 MET cc_start: 0.9367 (mmp) cc_final: 0.9146 (mmm) REVERT: A 2063 MET cc_start: 0.9324 (mmt) cc_final: 0.9039 (mmp) REVERT: A 3377 MET cc_start: 0.8819 (tpt) cc_final: 0.8284 (tpp) REVERT: A 3414 MET cc_start: 0.9176 (mmm) cc_final: 0.8568 (mpp) REVERT: A 3577 MET cc_start: 0.8995 (mpp) cc_final: 0.8413 (mpp) REVERT: A 3631 MET cc_start: 0.8979 (tmm) cc_final: 0.8475 (tmm) REVERT: A 3696 MET cc_start: 0.8725 (ptp) cc_final: 0.8372 (ptp) REVERT: A 3873 MET cc_start: 0.8258 (tmm) cc_final: 0.7956 (tmm) REVERT: D 1472 GLU cc_start: 0.7478 (mp0) cc_final: 0.7202 (mt-10) REVERT: D 1678 MET cc_start: 0.9365 (mmp) cc_final: 0.9103 (mmm) REVERT: D 1937 MET cc_start: 0.9387 (mmp) cc_final: 0.8884 (mmm) REVERT: D 2259 MET cc_start: 0.8313 (mmm) cc_final: 0.7977 (mmm) REVERT: D 3282 MET cc_start: 0.8535 (ttp) cc_final: 0.8299 (tmm) REVERT: D 3377 MET cc_start: 0.8658 (tpt) cc_final: 0.8383 (tpp) REVERT: D 3414 MET cc_start: 0.8905 (mmm) cc_final: 0.8484 (mpp) REVERT: D 3577 MET cc_start: 0.8839 (mpp) cc_final: 0.8267 (mpp) REVERT: D 3722 MET cc_start: 0.9190 (mmp) cc_final: 0.8922 (mmp) REVERT: E 493 MET cc_start: 0.8220 (ppp) cc_final: 0.7759 (ppp) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.5985 time to fit residues: 164.8506 Evaluate side-chains 137 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 6.102 ------------------------------------------------------------------------------- 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: 6.9990 chunk 171 optimal weight: 8.9990 chunk 461 optimal weight: 6.9990 chunk 377 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 554 optimal weight: 2.9990 chunk 599 optimal weight: 10.0000 chunk 494 optimal weight: 0.2980 chunk 550 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 445 optimal weight: 0.0010 overall best weight: 2.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1911 ASN ** A2845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3517 HIS A3878 HIS D1911 ASN ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3878 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 50662 Z= 0.203 Angle : 0.495 6.601 68578 Z= 0.264 Chirality : 0.040 0.148 7754 Planarity : 0.003 0.036 8594 Dihedral : 8.502 178.451 6744 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: 1.49 (0.11), residues: 6034 helix: 2.19 (0.10), residues: 2802 sheet: 0.73 (0.16), residues: 1006 loop : -0.42 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 299 HIS 0.006 0.001 HIS A2400 PHE 0.021 0.001 PHE D3611 TYR 0.029 0.001 TYR D3268 ARG 0.004 0.000 ARG F 364 *********************** 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 149 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 6.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9457 (mtp) cc_final: 0.7952 (tpp) REVERT: A 1655 MET cc_start: 0.9199 (tpt) cc_final: 0.8976 (mpp) REVERT: A 1678 MET cc_start: 0.9398 (mmp) cc_final: 0.9168 (mmm) REVERT: A 2259 MET cc_start: 0.8329 (mmm) cc_final: 0.7921 (mmm) REVERT: A 2756 MET cc_start: 0.7855 (mmm) cc_final: 0.7570 (mmp) REVERT: A 3377 MET cc_start: 0.8877 (tpt) cc_final: 0.8276 (tpp) REVERT: A 3414 MET cc_start: 0.9165 (mmm) cc_final: 0.8551 (mpp) REVERT: A 3577 MET cc_start: 0.8887 (mpp) cc_final: 0.8479 (mpp) REVERT: A 3631 MET cc_start: 0.9023 (tmm) cc_final: 0.8564 (tmm) REVERT: A 3696 MET cc_start: 0.8635 (ptp) cc_final: 0.8313 (ptp) REVERT: A 3873 MET cc_start: 0.8002 (tmm) cc_final: 0.7708 (tmm) REVERT: D 1472 GLU cc_start: 0.7465 (mp0) cc_final: 0.7150 (mt-10) REVERT: D 1565 MET cc_start: 0.9026 (tpp) cc_final: 0.8649 (tpp) REVERT: D 1678 MET cc_start: 0.9403 (mmp) cc_final: 0.9125 (mmm) REVERT: D 1921 MET cc_start: 0.9119 (mtp) cc_final: 0.8892 (mtp) REVERT: D 1937 MET cc_start: 0.9396 (mmp) cc_final: 0.8886 (mmm) REVERT: D 2259 MET cc_start: 0.8369 (mmm) cc_final: 0.7836 (mmt) REVERT: D 2980 MET cc_start: 0.8153 (tpp) cc_final: 0.7885 (tpp) REVERT: D 3282 MET cc_start: 0.8494 (ttp) cc_final: 0.8274 (tmm) REVERT: D 3377 MET cc_start: 0.8679 (tpt) cc_final: 0.8440 (tpp) REVERT: D 3414 MET cc_start: 0.8915 (mmm) cc_final: 0.8400 (mpp) REVERT: D 3577 MET cc_start: 0.8675 (mpp) cc_final: 0.8205 (tpp) REVERT: D 3584 MET cc_start: 0.9244 (ptp) cc_final: 0.8138 (ptp) REVERT: D 3696 MET cc_start: 0.7868 (pmm) cc_final: 0.7561 (pmm) REVERT: D 3722 MET cc_start: 0.9196 (mmp) cc_final: 0.8960 (mmp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.6235 time to fit residues: 164.0180 Evaluate side-chains 137 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 6.300 ------------------------------------------------------------------------------- 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: 7.9990 chunk 417 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 chunk 556 optimal weight: 20.0000 chunk 589 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 527 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 GLN ** A2845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN D2068 GLN D2845 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 50662 Z= 0.186 Angle : 0.473 6.709 68578 Z= 0.251 Chirality : 0.040 0.139 7754 Planarity : 0.003 0.040 8594 Dihedral : 7.926 173.542 6744 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.31 (0.10), residues: 2796 sheet: 0.89 (0.16), residues: 976 loop : -0.45 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D3850 HIS 0.005 0.001 HIS D2400 PHE 0.015 0.001 PHE A3530 TYR 0.023 0.001 TYR D3268 ARG 0.005 0.000 ARG F 408 *********************** 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 148 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 6.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9325 (mtp) cc_final: 0.7959 (tpp) REVERT: A 1678 MET cc_start: 0.9412 (mmp) cc_final: 0.9173 (mmm) REVERT: A 2259 MET cc_start: 0.8333 (mmm) cc_final: 0.7929 (mmm) REVERT: A 2510 MET cc_start: 0.8423 (ttm) cc_final: 0.8139 (ttm) REVERT: A 2756 MET cc_start: 0.7692 (mmm) cc_final: 0.7410 (mmp) REVERT: A 2932 MET cc_start: 0.9182 (tpp) cc_final: 0.8470 (mpp) REVERT: A 3377 MET cc_start: 0.8908 (tpt) cc_final: 0.8310 (tpp) REVERT: A 3414 MET cc_start: 0.9055 (mmm) cc_final: 0.8446 (mpp) REVERT: A 3577 MET cc_start: 0.9079 (mpp) cc_final: 0.8580 (mpp) REVERT: A 3631 MET cc_start: 0.8856 (tmm) cc_final: 0.8484 (tmm) REVERT: A 3696 MET cc_start: 0.8694 (ptp) cc_final: 0.8424 (ptp) REVERT: A 3873 MET cc_start: 0.7962 (tmm) cc_final: 0.7699 (tmm) REVERT: B 480 MET cc_start: 0.8317 (ppp) cc_final: 0.8014 (tmm) REVERT: B 493 MET cc_start: 0.7770 (ttm) cc_final: 0.7445 (ttm) REVERT: D 1565 MET cc_start: 0.9049 (tpp) cc_final: 0.8832 (tpp) REVERT: D 1655 MET cc_start: 0.9105 (mmm) cc_final: 0.8447 (mmm) REVERT: D 1678 MET cc_start: 0.9419 (mmp) cc_final: 0.9132 (mmm) REVERT: D 1921 MET cc_start: 0.9044 (mtp) cc_final: 0.8823 (mtp) REVERT: D 1937 MET cc_start: 0.9403 (mmp) cc_final: 0.8883 (mmm) REVERT: D 2118 MET cc_start: 0.6433 (tpt) cc_final: 0.6187 (tpt) REVERT: D 2259 MET cc_start: 0.8374 (mmm) cc_final: 0.7853 (mmt) REVERT: D 2932 MET cc_start: 0.9174 (tpp) cc_final: 0.8894 (mmt) REVERT: D 2980 MET cc_start: 0.8154 (tpp) cc_final: 0.7951 (tpp) REVERT: D 3282 MET cc_start: 0.8473 (ttp) cc_final: 0.8258 (tmm) REVERT: D 3377 MET cc_start: 0.8738 (tpt) cc_final: 0.8499 (tpp) REVERT: D 3414 MET cc_start: 0.8923 (mmm) cc_final: 0.8393 (mpp) REVERT: D 3577 MET cc_start: 0.8725 (mpp) cc_final: 0.8259 (tpp) REVERT: D 3584 MET cc_start: 0.9269 (ptp) cc_final: 0.8092 (ptp) REVERT: D 3696 MET cc_start: 0.8051 (pmm) cc_final: 0.7824 (pmm) REVERT: D 3722 MET cc_start: 0.9193 (mmp) cc_final: 0.8966 (mmp) REVERT: D 3873 MET cc_start: 0.8073 (tmm) cc_final: 0.7345 (tmm) REVERT: E 480 MET cc_start: 0.8528 (ppp) cc_final: 0.8264 (ppp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.6349 time to fit residues: 168.7611 Evaluate side-chains 135 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 5.932 ------------------------------------------------------------------------------- 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: 9.9990 chunk 334 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 439 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 503 optimal weight: 0.7980 chunk 407 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 301 optimal weight: 4.9990 chunk 529 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1788 GLN A2845 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2383 HIS ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 50662 Z= 0.196 Angle : 0.474 7.091 68578 Z= 0.251 Chirality : 0.040 0.175 7754 Planarity : 0.003 0.042 8594 Dihedral : 7.449 159.065 6744 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 1.65 (0.11), residues: 6034 helix: 2.35 (0.10), residues: 2810 sheet: 0.98 (0.16), residues: 952 loop : -0.48 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 299 HIS 0.005 0.001 HIS A2400 PHE 0.015 0.001 PHE A3530 TYR 0.019 0.001 TYR D3268 ARG 0.003 0.000 ARG D2387 *********************** 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 146 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 6.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9321 (mtp) cc_final: 0.7997 (tpp) REVERT: A 1655 MET cc_start: 0.8946 (tpt) cc_final: 0.8465 (tpp) REVERT: A 1678 MET cc_start: 0.9418 (mmp) cc_final: 0.9154 (mmm) REVERT: A 2756 MET cc_start: 0.7720 (mmm) cc_final: 0.7430 (mmp) REVERT: A 2932 MET cc_start: 0.9181 (tpp) cc_final: 0.8875 (mmt) REVERT: A 3377 MET cc_start: 0.8931 (tpt) cc_final: 0.8340 (tpp) REVERT: A 3414 MET cc_start: 0.9051 (mmm) cc_final: 0.8529 (mpp) REVERT: A 3577 MET cc_start: 0.9113 (mpp) cc_final: 0.8907 (mmt) REVERT: A 3631 MET cc_start: 0.9055 (tmm) cc_final: 0.8764 (tmm) REVERT: A 3696 MET cc_start: 0.8689 (ptp) cc_final: 0.8380 (ptp) REVERT: B 480 MET cc_start: 0.8384 (ppp) cc_final: 0.8128 (tmm) REVERT: D 1472 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6575 (mp0) REVERT: D 1565 MET cc_start: 0.9134 (tpp) cc_final: 0.8854 (tpp) REVERT: D 1678 MET cc_start: 0.9459 (mmp) cc_final: 0.9162 (mmm) REVERT: D 1921 MET cc_start: 0.9053 (mtp) cc_final: 0.8811 (mtp) REVERT: D 1937 MET cc_start: 0.9406 (mmp) cc_final: 0.8902 (mmm) REVERT: D 2259 MET cc_start: 0.8380 (mmm) cc_final: 0.7873 (mmt) REVERT: D 2546 MET cc_start: 0.7917 (mtp) cc_final: 0.7429 (ttm) REVERT: D 2932 MET cc_start: 0.9135 (tpp) cc_final: 0.8815 (mmt) REVERT: D 2980 MET cc_start: 0.8232 (tpp) cc_final: 0.8009 (tpp) REVERT: D 3282 MET cc_start: 0.8460 (ttp) cc_final: 0.8244 (tmm) REVERT: D 3377 MET cc_start: 0.8731 (tpt) cc_final: 0.8467 (tpp) REVERT: D 3414 MET cc_start: 0.8997 (mmm) cc_final: 0.8577 (mpp) REVERT: D 3577 MET cc_start: 0.8816 (mpp) cc_final: 0.8310 (tpp) REVERT: D 3584 MET cc_start: 0.9300 (ptp) cc_final: 0.8097 (ptp) REVERT: D 3722 MET cc_start: 0.9203 (mmp) cc_final: 0.8988 (mmp) REVERT: D 3873 MET cc_start: 0.7911 (tmm) cc_final: 0.7560 (tmm) REVERT: E 480 MET cc_start: 0.8609 (ppp) cc_final: 0.8394 (ppp) REVERT: E 493 MET cc_start: 0.8189 (ppp) cc_final: 0.7815 (ppp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.5883 time to fit residues: 154.7782 Evaluate side-chains 134 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 5.944 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 4.9990 chunk 346 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 590 optimal weight: 8.9990 chunk 489 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1757 GLN A2068 GLN A2383 HIS A2488 GLN A2910 ASN A3318 GLN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN D1530 GLN D1757 GLN D1788 GLN D1899 ASN D2068 GLN D2282 ASN D2488 GLN D2910 ASN ** D2985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 50662 Z= 0.337 Angle : 0.607 11.452 68578 Z= 0.316 Chirality : 0.042 0.192 7754 Planarity : 0.004 0.049 8594 Dihedral : 7.457 149.906 6744 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 1.30 (0.11), residues: 6034 helix: 2.09 (0.10), residues: 2804 sheet: 0.81 (0.17), residues: 944 loop : -0.66 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 385 HIS 0.009 0.002 HIS A2741 PHE 0.024 0.002 PHE A2992 TYR 0.022 0.002 TYR D3268 ARG 0.004 0.001 ARG A2552 *********************** 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 136 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 6.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9370 (mtp) cc_final: 0.8159 (tpp) REVERT: A 1678 MET cc_start: 0.9445 (mmp) cc_final: 0.9145 (mmm) REVERT: A 1932 MET cc_start: 0.8974 (mmp) cc_final: 0.8762 (mmp) REVERT: A 2063 MET cc_start: 0.9374 (mmt) cc_final: 0.9120 (mmp) REVERT: A 2756 MET cc_start: 0.7730 (mmm) cc_final: 0.7505 (mmp) REVERT: A 2866 LEU cc_start: 0.8562 (tp) cc_final: 0.8216 (pt) REVERT: A 3377 MET cc_start: 0.8938 (tpt) cc_final: 0.8341 (tpp) REVERT: A 3577 MET cc_start: 0.9159 (mpp) cc_final: 0.8935 (mmt) REVERT: A 3696 MET cc_start: 0.8686 (ptp) cc_final: 0.8332 (ptp) REVERT: B 480 MET cc_start: 0.8422 (ppp) cc_final: 0.8100 (tmm) REVERT: D 1565 MET cc_start: 0.9144 (tpp) cc_final: 0.8852 (tpp) REVERT: D 1678 MET cc_start: 0.9437 (mmp) cc_final: 0.9110 (mmm) REVERT: D 1921 MET cc_start: 0.8906 (mtp) cc_final: 0.8628 (mtp) REVERT: D 1937 MET cc_start: 0.9428 (mmp) cc_final: 0.8932 (mmm) REVERT: D 2063 MET cc_start: 0.9376 (mmt) cc_final: 0.8962 (mmp) REVERT: D 2546 MET cc_start: 0.8175 (mtp) cc_final: 0.7510 (ttm) REVERT: D 2980 MET cc_start: 0.8507 (tpp) cc_final: 0.8113 (tpp) REVERT: D 3282 MET cc_start: 0.8462 (ttp) cc_final: 0.8175 (tmm) REVERT: D 3377 MET cc_start: 0.8671 (tpt) cc_final: 0.8378 (tpp) REVERT: D 3414 MET cc_start: 0.8990 (mmm) cc_final: 0.8604 (mpp) REVERT: D 3577 MET cc_start: 0.8980 (mpp) cc_final: 0.8410 (tpp) REVERT: D 3584 MET cc_start: 0.9333 (ptp) cc_final: 0.8049 (ptp) REVERT: D 3696 MET cc_start: 0.8071 (pmm) cc_final: 0.7830 (pmm) REVERT: D 3722 MET cc_start: 0.9212 (mmp) cc_final: 0.8993 (mmp) REVERT: E 480 MET cc_start: 0.8634 (ppp) cc_final: 0.8352 (ppp) REVERT: E 493 MET cc_start: 0.8222 (ppp) cc_final: 0.7921 (ppp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.5617 time to fit residues: 138.9312 Evaluate side-chains 131 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 6.008 ------------------------------------------------------------------------------- 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: 20.0000 chunk 66 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 431 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 496 optimal weight: 0.8980 chunk 329 optimal weight: 4.9990 chunk 587 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1466 GLN ** A1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3517 HIS ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 50662 Z= 0.217 Angle : 0.498 8.343 68578 Z= 0.262 Chirality : 0.040 0.152 7754 Planarity : 0.003 0.047 8594 Dihedral : 7.158 135.502 6744 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1.47 (0.11), residues: 6034 helix: 2.29 (0.10), residues: 2802 sheet: 0.85 (0.16), residues: 950 loop : -0.65 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 385 HIS 0.006 0.001 HIS A2741 PHE 0.021 0.001 PHE D2720 TYR 0.021 0.001 TYR A3994 ARG 0.003 0.000 ARG D2659 *********************** 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 132 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 6.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9334 (mtp) cc_final: 0.8120 (tpp) REVERT: A 1678 MET cc_start: 0.9461 (mmp) cc_final: 0.9151 (mmm) REVERT: A 1932 MET cc_start: 0.8966 (mmp) cc_final: 0.8730 (mmp) REVERT: A 1937 MET cc_start: 0.9170 (mmm) cc_final: 0.8829 (mpp) REVERT: A 2510 MET cc_start: 0.8967 (ttm) cc_final: 0.8663 (ttm) REVERT: A 2932 MET cc_start: 0.9190 (tpp) cc_final: 0.8740 (mmt) REVERT: A 3377 MET cc_start: 0.8962 (tpt) cc_final: 0.8388 (tpp) REVERT: A 3414 MET cc_start: 0.8911 (mmm) cc_final: 0.8431 (mpp) REVERT: A 3577 MET cc_start: 0.9124 (mpp) cc_final: 0.8881 (mmt) REVERT: A 3696 MET cc_start: 0.8674 (ptp) cc_final: 0.8380 (ptp) REVERT: B 480 MET cc_start: 0.8346 (ppp) cc_final: 0.8051 (tmm) REVERT: C 370 MET cc_start: 0.8330 (ptp) cc_final: 0.7956 (ptp) REVERT: D 1565 MET cc_start: 0.9194 (tpp) cc_final: 0.8633 (tpp) REVERT: D 1655 MET cc_start: 0.8840 (tpt) cc_final: 0.8463 (tpp) REVERT: D 1678 MET cc_start: 0.9480 (mmp) cc_final: 0.9159 (mmm) REVERT: D 1921 MET cc_start: 0.8985 (mtp) cc_final: 0.8731 (mtp) REVERT: D 1937 MET cc_start: 0.9443 (mmp) cc_final: 0.8931 (mmm) REVERT: D 2259 MET cc_start: 0.8512 (mmm) cc_final: 0.7911 (mmm) REVERT: D 2546 MET cc_start: 0.8182 (mtp) cc_final: 0.7861 (ttm) REVERT: D 2932 MET cc_start: 0.9144 (tpp) cc_final: 0.8709 (mmt) REVERT: D 2938 MET cc_start: 0.8114 (mmt) cc_final: 0.7705 (mpp) REVERT: D 2980 MET cc_start: 0.8346 (tpp) cc_final: 0.7990 (tpp) REVERT: D 3282 MET cc_start: 0.8432 (ttp) cc_final: 0.8154 (tmm) REVERT: D 3377 MET cc_start: 0.8682 (tpt) cc_final: 0.8400 (tpp) REVERT: D 3414 MET cc_start: 0.8887 (mmm) cc_final: 0.8544 (mpp) REVERT: D 3577 MET cc_start: 0.8954 (mpp) cc_final: 0.8339 (tmm) REVERT: D 3584 MET cc_start: 0.9346 (ptp) cc_final: 0.8940 (ptp) REVERT: D 3696 MET cc_start: 0.8283 (pmm) cc_final: 0.8017 (pmm) REVERT: D 3873 MET cc_start: 0.8072 (tmm) cc_final: 0.7718 (tmm) REVERT: E 480 MET cc_start: 0.8595 (ppp) cc_final: 0.8368 (tmm) REVERT: E 493 MET cc_start: 0.8199 (ppp) cc_final: 0.7930 (ppp) REVERT: F 204 MET cc_start: 0.8287 (ttm) cc_final: 0.7661 (ttm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5665 time to fit residues: 136.2382 Evaluate side-chains 128 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 6.394 ------------------------------------------------------------------------------- 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: 3.9990 chunk 234 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 113 optimal weight: 0.0070 chunk 373 optimal weight: 0.0370 chunk 400 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 54 optimal weight: 0.0020 chunk 462 optimal weight: 6.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- 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** A1967 HIS A2068 GLN A2340 GLN A2783 GLN A3318 GLN A4077 GLN ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1967 HIS D2068 GLN D2340 GLN D4077 GLN E 252 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 50662 Z= 0.116 Angle : 0.451 11.257 68578 Z= 0.236 Chirality : 0.040 0.178 7754 Planarity : 0.003 0.044 8594 Dihedral : 6.610 100.335 6744 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.78 (0.11), residues: 6034 helix: 2.51 (0.10), residues: 2776 sheet: 1.04 (0.16), residues: 968 loop : -0.45 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 385 HIS 0.005 0.001 HIS A2741 PHE 0.028 0.001 PHE A3635 TYR 0.017 0.001 TYR A2571 ARG 0.003 0.000 ARG D1971 *********************** 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 139 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 6.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9276 (mtp) cc_final: 0.8161 (tpp) REVERT: A 1655 MET cc_start: 0.8904 (tpt) cc_final: 0.8449 (mpp) REVERT: A 1678 MET cc_start: 0.9486 (mmp) cc_final: 0.9192 (mmm) REVERT: A 1932 MET cc_start: 0.8992 (mmp) cc_final: 0.8764 (mmp) REVERT: A 1937 MET cc_start: 0.9151 (mmm) cc_final: 0.8837 (mpp) REVERT: A 2063 MET cc_start: 0.9326 (mmt) cc_final: 0.8764 (mmp) REVERT: A 2510 MET cc_start: 0.8892 (ttm) cc_final: 0.8553 (ttm) REVERT: A 2756 MET cc_start: 0.7607 (mmm) cc_final: 0.7403 (mmp) REVERT: A 2932 MET cc_start: 0.9161 (tpp) cc_final: 0.8742 (mmt) REVERT: A 3377 MET cc_start: 0.8927 (tpt) cc_final: 0.8326 (tpp) REVERT: A 3414 MET cc_start: 0.8872 (mmm) cc_final: 0.8380 (mpp) REVERT: A 3577 MET cc_start: 0.9115 (mpp) cc_final: 0.8862 (mmt) REVERT: A 3696 MET cc_start: 0.8641 (ptp) cc_final: 0.8386 (ptp) REVERT: A 3875 MET cc_start: 0.8515 (mtt) cc_final: 0.7950 (mtt) REVERT: B 480 MET cc_start: 0.8304 (ppp) cc_final: 0.7990 (tmm) REVERT: C 370 MET cc_start: 0.8158 (ptp) cc_final: 0.7822 (ptp) REVERT: D 1565 MET cc_start: 0.9190 (tpp) cc_final: 0.8611 (tpp) REVERT: D 1655 MET cc_start: 0.8751 (tpt) cc_final: 0.8409 (tpp) REVERT: D 1678 MET cc_start: 0.9480 (mmp) cc_final: 0.9157 (mmm) REVERT: D 1921 MET cc_start: 0.9045 (mtp) cc_final: 0.8844 (mtp) REVERT: D 1937 MET cc_start: 0.9433 (mmp) cc_final: 0.8921 (mmm) REVERT: D 2063 MET cc_start: 0.9312 (mmt) cc_final: 0.8723 (mmp) REVERT: D 2259 MET cc_start: 0.8508 (mmm) cc_final: 0.7919 (mmm) REVERT: D 2546 MET cc_start: 0.8291 (mtp) cc_final: 0.7713 (ttm) REVERT: D 2866 LEU cc_start: 0.8421 (tp) cc_final: 0.8140 (pp) REVERT: D 2932 MET cc_start: 0.9143 (tpp) cc_final: 0.8773 (mmt) REVERT: D 2938 MET cc_start: 0.8161 (mmt) cc_final: 0.7726 (mpp) REVERT: D 3282 MET cc_start: 0.8434 (ttp) cc_final: 0.8221 (tmm) REVERT: D 3377 MET cc_start: 0.8740 (tpt) cc_final: 0.8352 (tpp) REVERT: D 3398 MET cc_start: 0.9296 (tpp) cc_final: 0.9011 (tpp) REVERT: D 3414 MET cc_start: 0.8998 (mmm) cc_final: 0.8716 (mpp) REVERT: D 3577 MET cc_start: 0.8996 (mpp) cc_final: 0.8331 (tmm) REVERT: D 3584 MET cc_start: 0.9327 (ptp) cc_final: 0.9080 (ptp) REVERT: D 3696 MET cc_start: 0.8275 (pmm) cc_final: 0.7958 (pmm) REVERT: E 480 MET cc_start: 0.8609 (ppp) cc_final: 0.8398 (tmm) REVERT: E 493 MET cc_start: 0.8219 (ppp) cc_final: 0.7925 (ppp) REVERT: F 370 MET cc_start: 0.8370 (ptp) cc_final: 0.8020 (ptp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.5709 time to fit residues: 145.1028 Evaluate side-chains 131 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 6.011 ------------------------------------------------------------------------------- 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: 7.9990 chunk 563 optimal weight: 8.9990 chunk 513 optimal weight: 0.0020 chunk 547 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 430 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 495 optimal weight: 5.9990 chunk 518 optimal weight: 0.9980 chunk 545 optimal weight: 10.0000 overall best weight: 1.7992 ------------------------------------------------------------------------------- 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** ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2783 GLN D2985 ASN ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 50662 Z= 0.157 Angle : 0.459 12.650 68578 Z= 0.239 Chirality : 0.039 0.173 7754 Planarity : 0.003 0.044 8594 Dihedral : 6.420 87.524 6744 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 1.84 (0.11), residues: 6034 helix: 2.59 (0.10), residues: 2778 sheet: 0.98 (0.16), residues: 978 loop : -0.43 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 385 HIS 0.006 0.001 HIS A2741 PHE 0.024 0.001 PHE A3635 TYR 0.016 0.001 TYR D3268 ARG 0.002 0.000 ARG A3273 *********************** 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 135 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 6.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9313 (mtp) cc_final: 0.8642 (tpp) REVERT: A 1655 MET cc_start: 0.8925 (tpt) cc_final: 0.8474 (mpp) REVERT: A 1678 MET cc_start: 0.9486 (mmp) cc_final: 0.9190 (mmm) REVERT: A 1932 MET cc_start: 0.9008 (mmp) cc_final: 0.8781 (mmp) REVERT: A 1937 MET cc_start: 0.9167 (mmm) cc_final: 0.8879 (mpp) REVERT: A 2063 MET cc_start: 0.9294 (mmt) cc_final: 0.8758 (mmp) REVERT: A 2510 MET cc_start: 0.8839 (ttm) cc_final: 0.8496 (ttm) REVERT: A 2756 MET cc_start: 0.7668 (mmm) cc_final: 0.7417 (mmp) REVERT: A 2932 MET cc_start: 0.9154 (tpp) cc_final: 0.8744 (mmt) REVERT: A 3377 MET cc_start: 0.8946 (tpt) cc_final: 0.8362 (tpp) REVERT: A 3414 MET cc_start: 0.8896 (mmm) cc_final: 0.8423 (mpp) REVERT: A 3577 MET cc_start: 0.9143 (mpp) cc_final: 0.8897 (mmt) REVERT: A 3595 MET cc_start: 0.9182 (mpp) cc_final: 0.8929 (mpp) REVERT: A 3696 MET cc_start: 0.8641 (ptp) cc_final: 0.8347 (ptp) REVERT: C 370 MET cc_start: 0.8259 (ptp) cc_final: 0.7902 (ptp) REVERT: D 1565 MET cc_start: 0.9200 (tpp) cc_final: 0.8621 (tpp) REVERT: D 1655 MET cc_start: 0.8780 (tpt) cc_final: 0.8427 (tpp) REVERT: D 1678 MET cc_start: 0.9464 (mmp) cc_final: 0.9128 (mmm) REVERT: D 1921 MET cc_start: 0.8975 (mtp) cc_final: 0.8746 (mtp) REVERT: D 1937 MET cc_start: 0.9432 (mmp) cc_final: 0.8926 (mmm) REVERT: D 2063 MET cc_start: 0.9341 (mmt) cc_final: 0.8767 (mmp) REVERT: D 2118 MET cc_start: 0.8084 (mtt) cc_final: 0.7253 (mmt) REVERT: D 2259 MET cc_start: 0.8520 (mmm) cc_final: 0.8234 (mmt) REVERT: D 2546 MET cc_start: 0.8333 (mtp) cc_final: 0.7756 (ttm) REVERT: D 2756 MET cc_start: 0.8636 (pmm) cc_final: 0.8390 (pmm) REVERT: D 2866 LEU cc_start: 0.8447 (tp) cc_final: 0.8190 (pp) REVERT: D 2932 MET cc_start: 0.9124 (tpp) cc_final: 0.8707 (mmt) REVERT: D 2938 MET cc_start: 0.8169 (mmt) cc_final: 0.7949 (tpp) REVERT: D 3282 MET cc_start: 0.8443 (ttp) cc_final: 0.8227 (tmm) REVERT: D 3377 MET cc_start: 0.8763 (tpt) cc_final: 0.8461 (tpp) REVERT: D 3398 MET cc_start: 0.9314 (tpp) cc_final: 0.9035 (tpp) REVERT: D 3414 MET cc_start: 0.8958 (mmm) cc_final: 0.8530 (mpp) REVERT: D 3577 MET cc_start: 0.8945 (mpp) cc_final: 0.8433 (tpp) REVERT: D 3584 MET cc_start: 0.9330 (ptp) cc_final: 0.8271 (ptp) REVERT: E 493 MET cc_start: 0.8304 (ppp) cc_final: 0.7968 (ppp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5713 time to fit residues: 140.9150 Evaluate side-chains 131 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 5.715 ------------------------------------------------------------------------------- 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: 1.9990 chunk 579 optimal weight: 10.0000 chunk 353 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 402 optimal weight: 9.9990 chunk 607 optimal weight: 0.7980 chunk 559 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 373 optimal weight: 0.0170 chunk 296 optimal weight: 9.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- 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** A2985 ASN ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2985 ASN ** D3842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 50662 Z= 0.173 Angle : 0.471 15.236 68578 Z= 0.244 Chirality : 0.039 0.167 7754 Planarity : 0.003 0.043 8594 Dihedral : 6.321 87.211 6744 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 2.57 (0.10), residues: 2798 sheet: 0.95 (0.17), residues: 958 loop : -0.42 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 385 HIS 0.005 0.001 HIS A2741 PHE 0.027 0.001 PHE D3635 TYR 0.017 0.001 TYR D3268 ARG 0.003 0.000 ARG E 477 ********************** 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 136 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 6.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.9308 (mtp) cc_final: 0.8662 (tpp) REVERT: A 1655 MET cc_start: 0.8930 (tpt) cc_final: 0.8480 (mpp) REVERT: A 1678 MET cc_start: 0.9487 (mmp) cc_final: 0.9158 (mmm) REVERT: A 1932 MET cc_start: 0.9019 (mmp) cc_final: 0.8796 (mmp) REVERT: A 1937 MET cc_start: 0.9191 (mmm) cc_final: 0.8875 (mpp) REVERT: A 2063 MET cc_start: 0.9291 (mmt) cc_final: 0.8755 (mmp) REVERT: A 2510 MET cc_start: 0.8850 (ttm) cc_final: 0.8491 (ttm) REVERT: A 2756 MET cc_start: 0.7598 (mmm) cc_final: 0.7380 (mmp) REVERT: A 2932 MET cc_start: 0.9165 (tpp) cc_final: 0.8724 (mmt) REVERT: A 3377 MET cc_start: 0.8959 (tpt) cc_final: 0.8376 (tpp) REVERT: A 3414 MET cc_start: 0.8956 (mmm) cc_final: 0.8522 (mpp) REVERT: A 3577 MET cc_start: 0.9139 (mpp) cc_final: 0.8883 (mmt) REVERT: A 3595 MET cc_start: 0.9162 (mpp) cc_final: 0.8890 (mpp) REVERT: A 3696 MET cc_start: 0.8683 (ptp) cc_final: 0.8401 (ptp) REVERT: A 3875 MET cc_start: 0.8512 (mtt) cc_final: 0.8010 (mtt) REVERT: C 370 MET cc_start: 0.8289 (ptp) cc_final: 0.7928 (ptp) REVERT: D 1565 MET cc_start: 0.9215 (tpp) cc_final: 0.8634 (tpp) REVERT: D 1655 MET cc_start: 0.8791 (tpt) cc_final: 0.8411 (tpp) REVERT: D 1678 MET cc_start: 0.9488 (mmp) cc_final: 0.9126 (mmm) REVERT: D 1921 MET cc_start: 0.8976 (mtp) cc_final: 0.8721 (mtp) REVERT: D 1937 MET cc_start: 0.9440 (mmp) cc_final: 0.8933 (mmm) REVERT: D 2063 MET cc_start: 0.9337 (mmt) cc_final: 0.9117 (mmp) REVERT: D 2259 MET cc_start: 0.8522 (mmm) cc_final: 0.8129 (mmm) REVERT: D 2546 MET cc_start: 0.8340 (mtp) cc_final: 0.7794 (ttm) REVERT: D 2756 MET cc_start: 0.8704 (pmm) cc_final: 0.8396 (pmm) REVERT: D 2866 LEU cc_start: 0.8543 (tp) cc_final: 0.8322 (pp) REVERT: D 2932 MET cc_start: 0.9125 (tpp) cc_final: 0.8673 (mmt) REVERT: D 2938 MET cc_start: 0.8167 (mmt) cc_final: 0.7952 (tpp) REVERT: D 3282 MET cc_start: 0.8442 (ttp) cc_final: 0.8223 (tmm) REVERT: D 3377 MET cc_start: 0.8718 (tpt) cc_final: 0.8341 (tpp) REVERT: D 3398 MET cc_start: 0.9343 (tpp) cc_final: 0.9137 (tpp) REVERT: D 3577 MET cc_start: 0.8904 (mpp) cc_final: 0.8378 (tpp) REVERT: D 3584 MET cc_start: 0.9339 (ptp) cc_final: 0.8282 (ptp) REVERT: E 493 MET cc_start: 0.8328 (ppp) cc_final: 0.7996 (ppp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.5771 time to fit residues: 143.6873 Evaluate side-chains 132 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 6.571 ------------------------------------------------------------------------------- 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: 9.9990 chunk 515 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 446 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 484 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 497 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 0.0010 overall best weight: 0.9790 ------------------------------------------------------------------------------- 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** A2985 ASN ** D1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2985 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.037250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029029 restraints weight = 508425.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.030092 restraints weight = 278932.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.030679 restraints weight = 168037.439| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 50662 Z= 0.119 Angle : 0.438 10.457 68578 Z= 0.228 Chirality : 0.039 0.192 7754 Planarity : 0.003 0.043 8594 Dihedral : 6.102 86.901 6744 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.91 (0.11), residues: 6034 helix: 2.64 (0.10), residues: 2784 sheet: 1.06 (0.16), residues: 978 loop : -0.39 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 282 HIS 0.004 0.001 HIS A2400 PHE 0.026 0.001 PHE D3635 TYR 0.023 0.001 TYR A2574 ARG 0.002 0.000 ARG A3273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6439.10 seconds wall clock time: 122 minutes 12.92 seconds (7332.92 seconds total)