Starting phenix.real_space_refine on Fri Feb 16 17:22:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/02_2024/8em7_28241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/02_2024/8em7_28241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/02_2024/8em7_28241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/02_2024/8em7_28241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/02_2024/8em7_28241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/02_2024/8em7_28241_updated.pdb" } resolution = 2.97 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= 0.001 sd= 0.045 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 Ca 88 9.91 5 S 764 5.16 5 C 41716 2.51 5 N 11682 2.21 5 O 13302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2169": "OE1" <-> "OE2" Residue "A PHE 3000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2169": "OE1" <-> "OE2" Residue "B PHE 3000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67552 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 32850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4378, 32850 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 406} Link IDs: {'PCIS': 5, 'PTRANS': 213, 'TRANS': 4159} Chain breaks: 1 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1631 Unresolved non-hydrogen dihedrals: 1031 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 33, 'ASP:plan': 61, 'TYR:plan': 2, 'ASN:plan1': 32, 'HIS:plan': 12, 'PHE:plan': 1, 'GLU:plan': 55, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 901 Chain: "B" Number of atoms: 32850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4378, 32850 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 406} Link IDs: {'PCIS': 5, 'PTRANS': 213, 'TRANS': 4159} Chain breaks: 1 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1631 Unresolved non-hydrogen dihedrals: 1031 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 33, 'ASP:plan': 61, 'TYR:plan': 2, 'ASN:plan1': 32, 'HIS:plan': 12, 'PHE:plan': 1, 'GLU:plan': 55, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 901 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 898 Unusual residues: {' CA': 44, 'NAG': 39, 'NGA': 22} Classifications: {'undetermined': 105} Link IDs: {None: 104} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 61 Chain: "B" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 898 Unusual residues: {' CA': 44, 'NAG': 39, 'NGA': 22} Classifications: {'undetermined': 105} Link IDs: {None: 104} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 61 Time building chain proxies: 26.00, per 1000 atoms: 0.38 Number of scatterers: 67552 At special positions: 0 Unit cell: (158.53, 219.95, 241.53, 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) Ca 88 19.99 S 764 16.00 O 13302 8.00 N 11682 7.00 C 41716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=322, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 40 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 80 " distance=2.04 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 93 " distance=2.02 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 103 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 120 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 179 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 208 " distance=2.04 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 217 " distance=2.02 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 306 " distance=2.04 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " distance=2.02 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.04 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 703 " distance=2.04 Simple disulfide: pdb=" SG CYS A 973 " - pdb=" SG CYS A 987 " distance=2.04 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.04 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.02 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.02 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.03 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.04 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.04 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.05 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1135 " distance=2.04 Simple disulfide: pdb=" SG CYS A1129 " - pdb=" SG CYS A1144 " distance=2.04 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS A1162 " distance=2.02 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.04 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.04 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.04 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A1272 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1297 " distance=2.03 Simple disulfide: pdb=" SG CYS A1291 " - pdb=" SG CYS A1306 " distance=2.03 Simple disulfide: pdb=" SG CYS A1313 " - pdb=" SG CYS A1326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1339 " distance=2.05 Simple disulfide: pdb=" SG CYS A1333 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1354 " - pdb=" SG CYS A1365 " distance=2.04 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1374 " distance=2.02 Simple disulfide: pdb=" SG CYS A1376 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1401 " - pdb=" SG CYS A1414 " distance=2.03 Simple disulfide: pdb=" SG CYS A1416 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1705 " - pdb=" SG CYS A1714 " distance=2.04 Simple disulfide: pdb=" SG CYS A1710 " - pdb=" SG CYS A1726 " distance=2.02 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1741 " distance=2.03 Simple disulfide: pdb=" SG CYS A2023 " - pdb=" SG CYS A2034 " distance=2.04 Simple disulfide: pdb=" SG CYS A2030 " - pdb=" SG CYS A2044 " distance=2.03 Simple disulfide: pdb=" SG CYS A2046 " - pdb=" SG CYS A2059 " distance=2.03 Simple disulfide: pdb=" SG CYS A2347 " - pdb=" SG CYS A2358 " distance=2.04 Simple disulfide: pdb=" SG CYS A2354 " - pdb=" SG CYS A2369 " distance=2.04 Simple disulfide: pdb=" SG CYS A2371 " - pdb=" SG CYS A2383 " distance=2.03 Simple disulfide: pdb=" SG CYS A2518 " - pdb=" SG CYS A2652 " distance=2.04 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2667 " distance=2.04 Simple disulfide: pdb=" SG CYS A2663 " - pdb=" SG CYS A2676 " distance=2.03 Simple disulfide: pdb=" SG CYS A2678 " - pdb=" SG CYS A2693 " distance=2.05 Simple disulfide: pdb=" SG CYS A2701 " - pdb=" SG CYS A2713 " distance=2.04 Simple disulfide: pdb=" SG CYS A2708 " - pdb=" SG CYS A2726 " distance=2.03 Simple disulfide: pdb=" SG CYS A2720 " - pdb=" SG CYS A2737 " distance=2.04 Simple disulfide: pdb=" SG CYS A2742 " - pdb=" SG CYS A2754 " distance=2.03 Simple disulfide: pdb=" SG CYS A2749 " - pdb=" SG CYS A2767 " distance=2.03 Simple disulfide: pdb=" SG CYS A2761 " - pdb=" SG CYS A2776 " distance=2.02 Simple disulfide: pdb=" SG CYS A2781 " - pdb=" SG CYS A2794 " distance=2.04 Simple disulfide: pdb=" SG CYS A2789 " - pdb=" SG CYS A2807 " distance=2.03 Simple disulfide: pdb=" SG CYS A2801 " - pdb=" SG CYS A2818 " distance=2.03 Simple disulfide: pdb=" SG CYS A2823 " - pdb=" SG CYS A2836 " distance=2.04 Simple disulfide: pdb=" SG CYS A2830 " - pdb=" SG CYS A2849 " distance=2.04 Simple disulfide: pdb=" SG CYS A2843 " - pdb=" SG CYS A2860 " distance=2.03 Simple disulfide: pdb=" SG CYS A2865 " - pdb=" SG CYS A2878 " distance=2.04 Simple disulfide: pdb=" SG CYS A2872 " - pdb=" SG CYS A2891 " distance=2.03 Simple disulfide: pdb=" SG CYS A2885 " - pdb=" SG CYS A2901 " distance=2.04 Simple disulfide: pdb=" SG CYS A2908 " - pdb=" SG CYS A2920 " distance=2.03 Simple disulfide: pdb=" SG CYS A2915 " - pdb=" SG CYS A2933 " distance=2.03 Simple disulfide: pdb=" SG CYS A2927 " - pdb=" SG CYS A2945 " distance=2.03 Simple disulfide: pdb=" SG CYS A2950 " - pdb=" SG CYS A2967 " distance=2.04 Simple disulfide: pdb=" SG CYS A2957 " - pdb=" SG CYS A2980 " distance=2.04 Simple disulfide: pdb=" SG CYS A2974 " - pdb=" SG CYS A2990 " distance=2.03 Simple disulfide: pdb=" SG CYS A2995 " - pdb=" SG CYS A3007 " distance=2.04 Simple disulfide: pdb=" SG CYS A3002 " - pdb=" SG CYS A3020 " distance=2.03 Simple disulfide: pdb=" SG CYS A3014 " - pdb=" SG CYS A3029 " distance=2.04 Simple disulfide: pdb=" SG CYS A3034 " - pdb=" SG CYS A3046 " distance=2.03 Simple disulfide: pdb=" SG CYS A3041 " - pdb=" SG CYS A3059 " distance=2.02 Simple disulfide: pdb=" SG CYS A3053 " - pdb=" SG CYS A3070 " distance=2.04 Simple disulfide: pdb=" SG CYS A3077 " - pdb=" SG CYS A3089 " distance=2.03 Simple disulfide: pdb=" SG CYS A3084 " - pdb=" SG CYS A3102 " distance=2.03 Simple disulfide: pdb=" SG CYS A3096 " - pdb=" SG CYS A3111 " distance=2.03 Simple disulfide: pdb=" SG CYS A3116 " - pdb=" SG CYS A3128 " distance=2.04 Simple disulfide: pdb=" SG CYS A3124 " - pdb=" SG CYS A3137 " distance=2.03 Simple disulfide: pdb=" SG CYS A3139 " - pdb=" SG CYS A3152 " distance=2.03 Simple disulfide: pdb=" SG CYS A3158 " - pdb=" SG CYS A3169 " distance=2.03 Simple disulfide: pdb=" SG CYS A3165 " - pdb=" SG CYS A3178 " distance=2.04 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.04 Simple disulfide: pdb=" SG CYS A3313 " - pdb=" SG CYS A3321 " distance=2.03 Simple disulfide: pdb=" SG CYS A3471 " - pdb=" SG CYS A3482 " distance=2.04 Simple disulfide: pdb=" SG CYS A3478 " - pdb=" SG CYS A3493 " distance=2.03 Simple disulfide: pdb=" SG CYS A3495 " - pdb=" SG CYS A3510 " distance=2.03 Simple disulfide: pdb=" SG CYS A3514 " - pdb=" SG CYS A3527 " distance=2.03 Simple disulfide: pdb=" SG CYS A3521 " - pdb=" SG CYS A3540 " distance=2.03 Simple disulfide: pdb=" SG CYS A3534 " - pdb=" SG CYS A3550 " distance=2.04 Simple disulfide: pdb=" SG CYS A3555 " - pdb=" SG CYS A3567 " distance=2.02 Simple disulfide: pdb=" SG CYS A3562 " - pdb=" SG CYS A3580 " distance=2.04 Simple disulfide: pdb=" SG CYS A3574 " - pdb=" SG CYS A3591 " distance=2.04 Simple disulfide: pdb=" SG CYS A3596 " - pdb=" SG CYS A3608 " distance=2.03 Simple disulfide: pdb=" SG CYS A3603 " - pdb=" SG CYS A3621 " distance=2.03 Simple disulfide: pdb=" SG CYS A3615 " - pdb=" SG CYS A3632 " distance=2.03 Simple disulfide: pdb=" SG CYS A3637 " - pdb=" SG CYS A3649 " distance=2.04 Simple disulfide: pdb=" SG CYS A3644 " - pdb=" SG CYS A3662 " distance=2.03 Simple disulfide: pdb=" SG CYS A3656 " - pdb=" SG CYS A3673 " distance=2.04 Simple disulfide: pdb=" SG CYS A3680 " - pdb=" SG CYS A3694 " distance=2.02 Simple disulfide: pdb=" SG CYS A3688 " - pdb=" SG CYS A3707 " distance=2.04 Simple disulfide: pdb=" SG CYS A3701 " - pdb=" SG CYS A3716 " distance=2.04 Simple disulfide: pdb=" SG CYS A3721 " - pdb=" SG CYS A3734 " distance=2.03 Simple disulfide: pdb=" SG CYS A3729 " - pdb=" SG CYS A3747 " distance=2.03 Simple disulfide: pdb=" SG CYS A3741 " - pdb=" SG CYS A3756 " distance=2.04 Simple disulfide: pdb=" SG CYS A3761 " - pdb=" SG CYS A3773 " distance=2.03 Simple disulfide: pdb=" SG CYS A3768 " - pdb=" SG CYS A3786 " distance=2.04 Simple disulfide: pdb=" SG CYS A3780 " - pdb=" SG CYS A3795 " distance=2.03 Simple disulfide: pdb=" SG CYS A3800 " - pdb=" SG CYS A3812 " distance=2.03 Simple disulfide: pdb=" SG CYS A3807 " - pdb=" SG CYS A3825 " distance=2.04 Simple disulfide: pdb=" SG CYS A3819 " - pdb=" SG CYS A3834 " distance=2.03 Simple disulfide: pdb=" SG CYS A3844 " - pdb=" SG CYS A3856 " distance=2.01 Simple disulfide: pdb=" SG CYS A3851 " - pdb=" SG CYS A3869 " distance=2.03 Simple disulfide: pdb=" SG CYS A3863 " - pdb=" SG CYS A3880 " distance=2.04 Simple disulfide: pdb=" SG CYS A3885 " - pdb=" SG CYS A3898 " distance=2.03 Simple disulfide: pdb=" SG CYS A3893 " - pdb=" SG CYS A3911 " distance=2.05 Simple disulfide: pdb=" SG CYS A3905 " - pdb=" SG CYS A3922 " distance=2.04 Simple disulfide: pdb=" SG CYS A3930 " - pdb=" SG CYS A3942 " distance=2.03 Simple disulfide: pdb=" SG CYS A3937 " - pdb=" SG CYS A3955 " distance=2.04 Simple disulfide: pdb=" SG CYS A3949 " - pdb=" SG CYS A3964 " distance=2.04 Simple disulfide: pdb=" SG CYS A3972 " - pdb=" SG CYS A3981 " distance=2.04 Simple disulfide: pdb=" SG CYS A3977 " - pdb=" SG CYS A3991 " distance=2.02 Simple disulfide: pdb=" SG CYS A3993 " - pdb=" SG CYS A4007 " distance=2.03 Simple disulfide: pdb=" SG CYS A4013 " - pdb=" SG CYS A4023 " distance=2.03 Simple disulfide: pdb=" SG CYS A4019 " - pdb=" SG CYS A4032 " distance=2.04 Simple disulfide: pdb=" SG CYS A4034 " - pdb=" SG CYS A4049 " distance=2.03 Simple disulfide: pdb=" SG CYS A4336 " - pdb=" SG CYS A4344 " distance=2.03 Simple disulfide: pdb=" SG CYS A4340 " - pdb=" SG CYS A4353 " distance=2.04 Simple disulfide: pdb=" SG CYS A4355 " - pdb=" SG CYS A4369 " distance=2.04 Simple disulfide: pdb=" SG CYS A4383 " - pdb=" SG CYS A4391 " distance=2.04 Simple disulfide: pdb=" SG CYS A4385 " - pdb=" SG CYS A4401 " distance=2.03 Simple disulfide: pdb=" SG CYS A4403 " - pdb=" SG CYS A4412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 62 " distance=2.04 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 80 " distance=2.04 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 93 " distance=2.02 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 103 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 179 " distance=2.04 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 217 " distance=2.02 Simple disulfide: pdb=" SG CYS B 222 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 229 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 306 " distance=2.04 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 320 " distance=2.02 Simple disulfide: pdb=" SG CYS B 316 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 351 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 384 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 673 " distance=2.04 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 688 " distance=2.03 Simple disulfide: pdb=" SG CYS B 690 " - pdb=" SG CYS B 703 " distance=2.04 Simple disulfide: pdb=" SG CYS B 973 " - pdb=" SG CYS B 987 " distance=2.04 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 997 " distance=2.04 Simple disulfide: pdb=" SG CYS B 999 " - pdb=" SG CYS B1012 " distance=2.02 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1037 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1050 " distance=2.02 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1059 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1079 " distance=2.03 Simple disulfide: pdb=" SG CYS B1073 " - pdb=" SG CYS B1092 " distance=2.04 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1101 " distance=2.04 Simple disulfide: pdb=" SG CYS B1110 " - pdb=" SG CYS B1122 " distance=2.05 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1135 " distance=2.04 Simple disulfide: pdb=" SG CYS B1129 " - pdb=" SG CYS B1144 " distance=2.04 Simple disulfide: pdb=" SG CYS B1150 " - pdb=" SG CYS B1162 " distance=2.02 Simple disulfide: pdb=" SG CYS B1157 " - pdb=" SG CYS B1175 " distance=2.04 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1184 " distance=2.04 Simple disulfide: pdb=" SG CYS B1188 " - pdb=" SG CYS B1201 " distance=2.03 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG CYS B1214 " distance=2.03 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1223 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B1238 " - pdb=" SG CYS B1257 " distance=2.04 Simple disulfide: pdb=" SG CYS B1251 " - pdb=" SG CYS B1267 " distance=2.03 Simple disulfide: pdb=" SG CYS B1272 " - pdb=" SG CYS B1284 " distance=2.03 Simple disulfide: pdb=" SG CYS B1279 " - pdb=" SG CYS B1297 " distance=2.03 Simple disulfide: pdb=" SG CYS B1291 " - pdb=" SG CYS B1306 " distance=2.03 Simple disulfide: pdb=" SG CYS B1313 " - pdb=" SG CYS B1326 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1339 " distance=2.05 Simple disulfide: pdb=" SG CYS B1333 " - pdb=" SG CYS B1349 " distance=2.03 Simple disulfide: pdb=" SG CYS B1354 " - pdb=" SG CYS B1365 " distance=2.04 Simple disulfide: pdb=" SG CYS B1361 " - pdb=" SG CYS B1374 " distance=2.02 Simple disulfide: pdb=" SG CYS B1376 " - pdb=" SG CYS B1389 " distance=2.03 Simple disulfide: pdb=" SG CYS B1395 " - pdb=" SG CYS B1405 " distance=2.03 Simple disulfide: pdb=" SG CYS B1401 " - pdb=" SG CYS B1414 " distance=2.03 Simple disulfide: pdb=" SG CYS B1416 " - pdb=" SG CYS B1429 " distance=2.03 Simple disulfide: pdb=" SG CYS B1705 " - pdb=" SG CYS B1714 " distance=2.04 Simple disulfide: pdb=" SG CYS B1710 " - pdb=" SG CYS B1726 " distance=2.02 Simple disulfide: pdb=" SG CYS B1728 " - pdb=" SG CYS B1741 " distance=2.03 Simple disulfide: pdb=" SG CYS B2023 " - pdb=" SG CYS B2034 " distance=2.04 Simple disulfide: pdb=" SG CYS B2030 " - pdb=" SG CYS B2044 " distance=2.03 Simple disulfide: pdb=" SG CYS B2046 " - pdb=" SG CYS B2059 " distance=2.03 Simple disulfide: pdb=" SG CYS B2347 " - pdb=" SG CYS B2358 " distance=2.04 Simple disulfide: pdb=" SG CYS B2354 " - pdb=" SG CYS B2369 " distance=2.04 Simple disulfide: pdb=" SG CYS B2371 " - pdb=" SG CYS B2383 " distance=2.03 Simple disulfide: pdb=" SG CYS B2518 " - pdb=" SG CYS B2652 " distance=2.04 Simple disulfide: pdb=" SG CYS B2656 " - pdb=" SG CYS B2667 " distance=2.04 Simple disulfide: pdb=" SG CYS B2663 " - pdb=" SG CYS B2676 " distance=2.03 Simple disulfide: pdb=" SG CYS B2678 " - pdb=" SG CYS B2693 " distance=2.05 Simple disulfide: pdb=" SG CYS B2701 " - pdb=" SG CYS B2713 " distance=2.04 Simple disulfide: pdb=" SG CYS B2708 " - pdb=" SG CYS B2726 " distance=2.03 Simple disulfide: pdb=" SG CYS B2720 " - pdb=" SG CYS B2737 " distance=2.04 Simple disulfide: pdb=" SG CYS B2742 " - pdb=" SG CYS B2754 " distance=2.03 Simple disulfide: pdb=" SG CYS B2749 " - pdb=" SG CYS B2767 " distance=2.03 Simple disulfide: pdb=" SG CYS B2761 " - pdb=" SG CYS B2776 " distance=2.02 Simple disulfide: pdb=" SG CYS B2781 " - pdb=" SG CYS B2794 " distance=2.04 Simple disulfide: pdb=" SG CYS B2789 " - pdb=" SG CYS B2807 " distance=2.03 Simple disulfide: pdb=" SG CYS B2801 " - pdb=" SG CYS B2818 " distance=2.03 Simple disulfide: pdb=" SG CYS B2823 " - pdb=" SG CYS B2836 " distance=2.04 Simple disulfide: pdb=" SG CYS B2830 " - pdb=" SG CYS B2849 " distance=2.04 Simple disulfide: pdb=" SG CYS B2843 " - pdb=" SG CYS B2860 " distance=2.03 Simple disulfide: pdb=" SG CYS B2865 " - pdb=" SG CYS B2878 " distance=2.04 Simple disulfide: pdb=" SG CYS B2872 " - pdb=" SG CYS B2891 " distance=2.03 Simple disulfide: pdb=" SG CYS B2885 " - pdb=" SG CYS B2901 " distance=2.04 Simple disulfide: pdb=" SG CYS B2908 " - pdb=" SG CYS B2920 " distance=2.03 Simple disulfide: pdb=" SG CYS B2915 " - pdb=" SG CYS B2933 " distance=2.03 Simple disulfide: pdb=" SG CYS B2927 " - pdb=" SG CYS B2945 " distance=2.03 Simple disulfide: pdb=" SG CYS B2950 " - pdb=" SG CYS B2967 " distance=2.04 Simple disulfide: pdb=" SG CYS B2957 " - pdb=" SG CYS B2980 " distance=2.04 Simple disulfide: pdb=" SG CYS B2974 " - pdb=" SG CYS B2990 " distance=2.03 Simple disulfide: pdb=" SG CYS B2995 " - pdb=" SG CYS B3007 " distance=2.04 Simple disulfide: pdb=" SG CYS B3002 " - pdb=" SG CYS B3020 " distance=2.03 Simple disulfide: pdb=" SG CYS B3014 " - pdb=" SG CYS B3029 " distance=2.04 Simple disulfide: pdb=" SG CYS B3034 " - pdb=" SG CYS B3046 " distance=2.03 Simple disulfide: pdb=" SG CYS B3041 " - pdb=" SG CYS B3059 " distance=2.02 Simple disulfide: pdb=" SG CYS B3053 " - pdb=" SG CYS B3070 " distance=2.04 Simple disulfide: pdb=" SG CYS B3077 " - pdb=" SG CYS B3089 " distance=2.03 Simple disulfide: pdb=" SG CYS B3084 " - pdb=" SG CYS B3102 " distance=2.03 Simple disulfide: pdb=" SG CYS B3096 " - pdb=" SG CYS B3111 " distance=2.03 Simple disulfide: pdb=" SG CYS B3116 " - pdb=" SG CYS B3128 " distance=2.04 Simple disulfide: pdb=" SG CYS B3124 " - pdb=" SG CYS B3137 " distance=2.03 Simple disulfide: pdb=" SG CYS B3139 " - pdb=" SG CYS B3152 " distance=2.03 Simple disulfide: pdb=" SG CYS B3158 " - pdb=" SG CYS B3169 " distance=2.03 Simple disulfide: pdb=" SG CYS B3165 " - pdb=" SG CYS B3178 " distance=2.04 Simple disulfide: pdb=" SG CYS B3180 " - pdb=" SG CYS B3193 " distance=2.04 Simple disulfide: pdb=" SG CYS B3313 " - pdb=" SG CYS B3321 " distance=2.03 Simple disulfide: pdb=" SG CYS B3471 " - pdb=" SG CYS B3482 " distance=2.04 Simple disulfide: pdb=" SG CYS B3478 " - pdb=" SG CYS B3493 " distance=2.03 Simple disulfide: pdb=" SG CYS B3495 " - pdb=" SG CYS B3510 " distance=2.03 Simple disulfide: pdb=" SG CYS B3514 " - pdb=" SG CYS B3527 " distance=2.03 Simple disulfide: pdb=" SG CYS B3521 " - pdb=" SG CYS B3540 " distance=2.03 Simple disulfide: pdb=" SG CYS B3534 " - pdb=" SG CYS B3550 " distance=2.04 Simple disulfide: pdb=" SG CYS B3555 " - pdb=" SG CYS B3567 " distance=2.02 Simple disulfide: pdb=" SG CYS B3562 " - pdb=" SG CYS B3580 " distance=2.04 Simple disulfide: pdb=" SG CYS B3574 " - pdb=" SG CYS B3591 " distance=2.04 Simple disulfide: pdb=" SG CYS B3596 " - pdb=" SG CYS B3608 " distance=2.03 Simple disulfide: pdb=" SG CYS B3603 " - pdb=" SG CYS B3621 " distance=2.03 Simple disulfide: pdb=" SG CYS B3615 " - pdb=" SG CYS B3632 " distance=2.03 Simple disulfide: pdb=" SG CYS B3637 " - pdb=" SG CYS B3649 " distance=2.04 Simple disulfide: pdb=" SG CYS B3644 " - pdb=" SG CYS B3662 " distance=2.03 Simple disulfide: pdb=" SG CYS B3656 " - pdb=" SG CYS B3673 " distance=2.04 Simple disulfide: pdb=" SG CYS B3680 " - pdb=" SG CYS B3694 " distance=2.02 Simple disulfide: pdb=" SG CYS B3688 " - pdb=" SG CYS B3707 " distance=2.04 Simple disulfide: pdb=" SG CYS B3701 " - pdb=" SG CYS B3716 " distance=2.04 Simple disulfide: pdb=" SG CYS B3721 " - pdb=" SG CYS B3734 " distance=2.03 Simple disulfide: pdb=" SG CYS B3729 " - pdb=" SG CYS B3747 " distance=2.03 Simple disulfide: pdb=" SG CYS B3741 " - pdb=" SG CYS B3756 " distance=2.04 Simple disulfide: pdb=" SG CYS B3761 " - pdb=" SG CYS B3773 " distance=2.03 Simple disulfide: pdb=" SG CYS B3768 " - pdb=" SG CYS B3786 " distance=2.04 Simple disulfide: pdb=" SG CYS B3780 " - pdb=" SG CYS B3795 " distance=2.03 Simple disulfide: pdb=" SG CYS B3800 " - pdb=" SG CYS B3812 " distance=2.03 Simple disulfide: pdb=" SG CYS B3807 " - pdb=" SG CYS B3825 " distance=2.04 Simple disulfide: pdb=" SG CYS B3819 " - pdb=" SG CYS B3834 " distance=2.03 Simple disulfide: pdb=" SG CYS B3844 " - pdb=" SG CYS B3856 " distance=2.01 Simple disulfide: pdb=" SG CYS B3851 " - pdb=" SG CYS B3869 " distance=2.03 Simple disulfide: pdb=" SG CYS B3863 " - pdb=" SG CYS B3880 " distance=2.04 Simple disulfide: pdb=" SG CYS B3885 " - pdb=" SG CYS B3898 " distance=2.03 Simple disulfide: pdb=" SG CYS B3893 " - pdb=" SG CYS B3911 " distance=2.05 Simple disulfide: pdb=" SG CYS B3905 " - pdb=" SG CYS B3922 " distance=2.04 Simple disulfide: pdb=" SG CYS B3930 " - pdb=" SG CYS B3942 " distance=2.03 Simple disulfide: pdb=" SG CYS B3937 " - pdb=" SG CYS B3955 " distance=2.04 Simple disulfide: pdb=" SG CYS B3949 " - pdb=" SG CYS B3964 " distance=2.04 Simple disulfide: pdb=" SG CYS B3972 " - pdb=" SG CYS B3981 " distance=2.04 Simple disulfide: pdb=" SG CYS B3977 " - pdb=" SG CYS B3991 " distance=2.02 Simple disulfide: pdb=" SG CYS B3993 " - pdb=" SG CYS B4007 " distance=2.03 Simple disulfide: pdb=" SG CYS B4013 " - pdb=" SG CYS B4023 " distance=2.03 Simple disulfide: pdb=" SG CYS B4019 " - pdb=" SG CYS B4032 " distance=2.04 Simple disulfide: pdb=" SG CYS B4034 " - pdb=" SG CYS B4049 " distance=2.03 Simple disulfide: pdb=" SG CYS B4336 " - pdb=" SG CYS B4344 " distance=2.03 Simple disulfide: pdb=" SG CYS B4340 " - pdb=" SG CYS B4353 " distance=2.04 Simple disulfide: pdb=" SG CYS B4355 " - pdb=" SG CYS B4369 " distance=2.04 Simple disulfide: pdb=" SG CYS B4383 " - pdb=" SG CYS B4391 " distance=2.04 Simple disulfide: pdb=" SG CYS B4385 " - pdb=" SG CYS B4401 " distance=2.03 Simple disulfide: pdb=" SG CYS B4403 " - pdb=" SG CYS B4412 " distance=2.04 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=44, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A4701 " - " ASN A 340 " " NAG A4702 " - " ASN A 387 " " NAG A4703 " - " ASN A 657 " " NAG A4704 " - " ASN A 865 " " NAG A4705 " - " ASN A1187 " " NAG A4706 " - " ASN A1328 " " NAG A4707 " - " ASN A1341 " " NAG A4708 " - " ASN A1384 " " NAG A4709 " - " ASN A1451 " " NAG A4710 " - " ASN A1497 " " NAG A4711 " - " ASN A1551 " " NAG A4712 " - " ASN A1676 " " NAG A4713 " - " ASN A1733 " " NAG A4714 " - " ASN A1811 " " NAG A4715 " - " ASN A2134 " " NAG A4716 " - " ASN A2225 " " NAG A4717 " - " ASN A2396 " " NAG A4718 " - " ASN A2488 " " NAG A4719 " - " ASN A2548 " " NAG A4720 " - " ASN A2782 " " NAG A4721 " - " ASN A2810 " " NAG A4722 " - " ASN A2949 " " NAG A4723 " - " ASN A2989 " " NAG A4724 " - " ASN A3127 " " NAG A4725 " - " ASN A3213 " " NAG A4726 " - " ASN A3259 " " NAG A4727 " - " ASN A3317 " " NAG A4728 " - " ASN A3357 " " NAG A4729 " - " ASN A3448 " " NAG A4730 " - " ASN A3566 " " NAG A4731 " - " ASN A3682 " " NAG A4732 " - " ASN A3840 " " NAG A4733 " - " ASN A3969 " " NAG A4734 " - " ASN A3980 " " NAG A4735 " - " ASN A4070 " " NAG A4736 " - " ASN A4329 " " NAG A4739 " - " ASN A 178 " " NAG A4804 " - " ASN A 159 " " NAG A4805 " - " ASN A 462 " " NAG B4701 " - " ASN B 340 " " NAG B4702 " - " ASN B 387 " " NAG B4703 " - " ASN B 657 " " NAG B4704 " - " ASN B 865 " " NAG B4705 " - " ASN B1187 " " NAG B4706 " - " ASN B1328 " " NAG B4707 " - " ASN B1341 " " NAG B4708 " - " ASN B1384 " " NAG B4709 " - " ASN B1451 " " NAG B4710 " - " ASN B1497 " " NAG B4711 " - " ASN B1551 " " NAG B4712 " - " ASN B1676 " " NAG B4713 " - " ASN B1733 " " NAG B4714 " - " ASN B1811 " " NAG B4715 " - " ASN B2134 " " NAG B4716 " - " ASN B2225 " " NAG B4717 " - " ASN B2396 " " NAG B4718 " - " ASN B2488 " " NAG B4719 " - " ASN B2548 " " NAG B4720 " - " ASN B2782 " " NAG B4721 " - " ASN B2810 " " NAG B4722 " - " ASN B2949 " " NAG B4723 " - " ASN B2989 " " NAG B4724 " - " ASN B3127 " " NAG B4725 " - " ASN B3213 " " NAG B4726 " - " ASN B3259 " " NAG B4727 " - " ASN B3317 " " NAG B4728 " - " ASN B3357 " " NAG B4729 " - " ASN B3448 " " NAG B4730 " - " ASN B3566 " " NAG B4731 " - " ASN B3682 " " NAG B4732 " - " ASN B3840 " " NAG B4733 " - " ASN B3969 " " NAG B4734 " - " ASN B3980 " " NAG B4735 " - " ASN B4070 " " NAG B4736 " - " ASN B4329 " " NAG B4739 " - " ASN B 178 " " NAG B4804 " - " ASN B 159 " " NAG B4805 " - " ASN B 462 " " NAG C 1 " - " ASN A2178 " " NAG D 1 " - " ASN B2178 " Number of additional bonds: simple=44, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.63 Conformation dependent library (CDL) restraints added in 9.1 seconds 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 214 sheets defined 7.9% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 36.06 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 97 through 100 No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.097A pdb=" N CYS A 127 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.784A pdb=" N CYS A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.076A pdb=" N ILE A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 597 through 600 No H-bonds generated for 'chain 'A' and resid 597 through 600' Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 665 through 668 Processing helix chain 'A' and resid 976 through 982 Proline residue: A 979 - end of helix Processing helix chain 'A' and resid 1040 through 1044 removed outlier: 3.855A pdb=" N CYS A1044 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1096 through 1100 removed outlier: 4.012A pdb=" N ASN A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1100' Processing helix chain 'A' and resid 1125 through 1128 Processing helix chain 'A' and resid 1139 through 1143 removed outlier: 4.326A pdb=" N ASN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1143' Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 4.133A pdb=" N GLY A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1179 through 1183' Processing helix chain 'A' and resid 1204 through 1208 removed outlier: 4.361A pdb=" N CYS A1208 " --> pdb=" O ARG A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1222 No H-bonds generated for 'chain 'A' and resid 1220 through 1222' Processing helix chain 'A' and resid 1228 through 1230 No H-bonds generated for 'chain 'A' and resid 1228 through 1230' Processing helix chain 'A' and resid 1247 through 1249 No H-bonds generated for 'chain 'A' and resid 1247 through 1249' Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 4.050A pdb=" N CYS A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1329 through 1331 No H-bonds generated for 'chain 'A' and resid 1329 through 1331' Processing helix chain 'A' and resid 1347 through 1350 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1394 through 1396 No H-bonds generated for 'chain 'A' and resid 1394 through 1396' Processing helix chain 'A' and resid 1695 through 1697 No H-bonds generated for 'chain 'A' and resid 1695 through 1697' Processing helix chain 'A' and resid 1705 through 1707 No H-bonds generated for 'chain 'A' and resid 1705 through 1707' Processing helix chain 'A' and resid 2022 through 2025 No H-bonds generated for 'chain 'A' and resid 2022 through 2025' Processing helix chain 'A' and resid 2038 through 2040 No H-bonds generated for 'chain 'A' and resid 2038 through 2040' Processing helix chain 'A' and resid 2332 through 2334 No H-bonds generated for 'chain 'A' and resid 2332 through 2334' Processing helix chain 'A' and resid 2346 through 2348 No H-bonds generated for 'chain 'A' and resid 2346 through 2348' Processing helix chain 'A' and resid 2350 through 2353 Processing helix chain 'A' and resid 2655 through 2657 No H-bonds generated for 'chain 'A' and resid 2655 through 2657' Processing helix chain 'A' and resid 2660 through 2662 No H-bonds generated for 'chain 'A' and resid 2660 through 2662' Processing helix chain 'A' and resid 2716 through 2720 removed outlier: 4.334A pdb=" N CYS A2720 " --> pdb=" O ASP A2717 " (cutoff:3.500A) Processing helix chain 'A' and resid 2734 through 2737 No H-bonds generated for 'chain 'A' and resid 2734 through 2737' Processing helix chain 'A' and resid 2757 through 2759 No H-bonds generated for 'chain 'A' and resid 2757 through 2759' Processing helix chain 'A' and resid 2797 through 2799 No H-bonds generated for 'chain 'A' and resid 2797 through 2799' Processing helix chain 'A' and resid 2839 through 2843 removed outlier: 4.086A pdb=" N CYS A2843 " --> pdb=" O ALA A2840 " (cutoff:3.500A) Processing helix chain 'A' and resid 2857 through 2862 removed outlier: 5.002A pdb=" N SER A2862 " --> pdb=" O ILE A2858 " (cutoff:3.500A) Processing helix chain 'A' and resid 2881 through 2886 removed outlier: 4.030A pdb=" N CYS A2885 " --> pdb=" O TYR A2882 " (cutoff:3.500A) Processing helix chain 'A' and resid 2895 through 2897 No H-bonds generated for 'chain 'A' and resid 2895 through 2897' Processing helix chain 'A' and resid 2899 through 2901 No H-bonds generated for 'chain 'A' and resid 2899 through 2901' Processing helix chain 'A' and resid 2923 through 2925 No H-bonds generated for 'chain 'A' and resid 2923 through 2925' Processing helix chain 'A' and resid 2941 through 2943 No H-bonds generated for 'chain 'A' and resid 2941 through 2943' Processing helix chain 'A' and resid 2945 through 2947 No H-bonds generated for 'chain 'A' and resid 2945 through 2947' Processing helix chain 'A' and resid 2970 through 2973 No H-bonds generated for 'chain 'A' and resid 2970 through 2973' Processing helix chain 'A' and resid 2984 through 2986 No H-bonds generated for 'chain 'A' and resid 2984 through 2986' Processing helix chain 'A' and resid 3010 through 3012 No H-bonds generated for 'chain 'A' and resid 3010 through 3012' Processing helix chain 'A' and resid 3049 through 3053 removed outlier: 4.019A pdb=" N CYS A3053 " --> pdb=" O LEU A3050 " (cutoff:3.500A) Processing helix chain 'A' and resid 3067 through 3070 No H-bonds generated for 'chain 'A' and resid 3067 through 3070' Processing helix chain 'A' and resid 3092 through 3096 removed outlier: 3.860A pdb=" N CYS A3096 " --> pdb=" O GLY A3093 " (cutoff:3.500A) Processing helix chain 'A' and resid 3106 through 3109 No H-bonds generated for 'chain 'A' and resid 3106 through 3109' Processing helix chain 'A' and resid 3115 through 3117 No H-bonds generated for 'chain 'A' and resid 3115 through 3117' Processing helix chain 'A' and resid 3157 through 3160 No H-bonds generated for 'chain 'A' and resid 3157 through 3160' Processing helix chain 'A' and resid 3162 through 3164 No H-bonds generated for 'chain 'A' and resid 3162 through 3164' Processing helix chain 'A' and resid 3461 through 3463 No H-bonds generated for 'chain 'A' and resid 3461 through 3463' Processing helix chain 'A' and resid 3475 through 3477 No H-bonds generated for 'chain 'A' and resid 3475 through 3477' Processing helix chain 'A' and resid 3522 through 3524 No H-bonds generated for 'chain 'A' and resid 3522 through 3524' Processing helix chain 'A' and resid 3530 through 3532 No H-bonds generated for 'chain 'A' and resid 3530 through 3532' Processing helix chain 'A' and resid 3570 through 3574 removed outlier: 4.484A pdb=" N CYS A3574 " --> pdb=" O GLN A3571 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3591 No H-bonds generated for 'chain 'A' and resid 3588 through 3591' Processing helix chain 'A' and resid 3611 through 3613 No H-bonds generated for 'chain 'A' and resid 3611 through 3613' Processing helix chain 'A' and resid 3624 through 3626 No H-bonds generated for 'chain 'A' and resid 3624 through 3626' Processing helix chain 'A' and resid 3629 through 3632 No H-bonds generated for 'chain 'A' and resid 3629 through 3632' Processing helix chain 'A' and resid 3652 through 3654 No H-bonds generated for 'chain 'A' and resid 3652 through 3654' Processing helix chain 'A' and resid 3670 through 3673 No H-bonds generated for 'chain 'A' and resid 3670 through 3673' Processing helix chain 'A' and resid 3676 through 3678 No H-bonds generated for 'chain 'A' and resid 3676 through 3678' Processing helix chain 'A' and resid 3697 through 3700 Processing helix chain 'A' and resid 3713 through 3715 No H-bonds generated for 'chain 'A' and resid 3713 through 3715' Processing helix chain 'A' and resid 3737 through 3741 removed outlier: 3.937A pdb=" N CYS A3741 " --> pdb=" O ARG A3738 " (cutoff:3.500A) Processing helix chain 'A' and resid 3751 through 3754 No H-bonds generated for 'chain 'A' and resid 3751 through 3754' Processing helix chain 'A' and resid 3776 through 3780 removed outlier: 3.929A pdb=" N CYS A3780 " --> pdb=" O ARG A3777 " (cutoff:3.500A) Processing helix chain 'A' and resid 3815 through 3817 No H-bonds generated for 'chain 'A' and resid 3815 through 3817' Processing helix chain 'A' and resid 3831 through 3833 No H-bonds generated for 'chain 'A' and resid 3831 through 3833' Processing helix chain 'A' and resid 3859 through 3861 No H-bonds generated for 'chain 'A' and resid 3859 through 3861' Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 3877 through 3882 removed outlier: 3.907A pdb=" N PHE A3881 " --> pdb=" O HIS A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3905 removed outlier: 3.719A pdb=" N CYS A3905 " --> pdb=" O HIS A3902 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3902 through 3905' Processing helix chain 'A' and resid 3919 through 3922 No H-bonds generated for 'chain 'A' and resid 3919 through 3922' Processing helix chain 'A' and resid 3946 through 3949 removed outlier: 3.753A pdb=" N CYS A3949 " --> pdb=" O HIS A3946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3946 through 3949' Processing helix chain 'A' and resid 3972 through 3974 No H-bonds generated for 'chain 'A' and resid 3972 through 3974' Processing helix chain 'A' and resid 4012 through 4014 No H-bonds generated for 'chain 'A' and resid 4012 through 4014' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 83 through 86 No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 97 through 100 No H-bonds generated for 'chain 'B' and resid 97 through 100' Processing helix chain 'B' and resid 123 through 127 removed outlier: 4.097A pdb=" N CYS B 127 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.784A pdb=" N CYS B 164 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.076A pdb=" N ILE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 597 through 600 No H-bonds generated for 'chain 'B' and resid 597 through 600' Processing helix chain 'B' and resid 652 through 655 Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 665 through 668 Processing helix chain 'B' and resid 976 through 982 Proline residue: B 979 - end of helix Processing helix chain 'B' and resid 1040 through 1044 removed outlier: 3.855A pdb=" N CYS B1044 " --> pdb=" O ILE B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1086 No H-bonds generated for 'chain 'B' and resid 1084 through 1086' Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 4.012A pdb=" N ASN B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1096 through 1100' Processing helix chain 'B' and resid 1125 through 1128 Processing helix chain 'B' and resid 1139 through 1143 removed outlier: 4.326A pdb=" N ASN B1143 " --> pdb=" O SER B1139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1143' Processing helix chain 'B' and resid 1165 through 1168 Processing helix chain 'B' and resid 1179 through 1183 removed outlier: 4.133A pdb=" N GLY B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1179 through 1183' Processing helix chain 'B' and resid 1204 through 1208 removed outlier: 4.361A pdb=" N CYS B1208 " --> pdb=" O ARG B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1222 No H-bonds generated for 'chain 'B' and resid 1220 through 1222' Processing helix chain 'B' and resid 1228 through 1230 No H-bonds generated for 'chain 'B' and resid 1228 through 1230' Processing helix chain 'B' and resid 1247 through 1249 No H-bonds generated for 'chain 'B' and resid 1247 through 1249' Processing helix chain 'B' and resid 1287 through 1291 removed outlier: 4.050A pdb=" N CYS B1291 " --> pdb=" O SER B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1304 No H-bonds generated for 'chain 'B' and resid 1302 through 1304' Processing helix chain 'B' and resid 1329 through 1331 No H-bonds generated for 'chain 'B' and resid 1329 through 1331' Processing helix chain 'B' and resid 1347 through 1350 Processing helix chain 'B' and resid 1354 through 1356 No H-bonds generated for 'chain 'B' and resid 1354 through 1356' Processing helix chain 'B' and resid 1358 through 1360 No H-bonds generated for 'chain 'B' and resid 1358 through 1360' Processing helix chain 'B' and resid 1394 through 1396 No H-bonds generated for 'chain 'B' and resid 1394 through 1396' Processing helix chain 'B' and resid 1695 through 1697 No H-bonds generated for 'chain 'B' and resid 1695 through 1697' Processing helix chain 'B' and resid 1705 through 1707 No H-bonds generated for 'chain 'B' and resid 1705 through 1707' Processing helix chain 'B' and resid 2022 through 2025 No H-bonds generated for 'chain 'B' and resid 2022 through 2025' Processing helix chain 'B' and resid 2038 through 2040 No H-bonds generated for 'chain 'B' and resid 2038 through 2040' Processing helix chain 'B' and resid 2332 through 2334 No H-bonds generated for 'chain 'B' and resid 2332 through 2334' Processing helix chain 'B' and resid 2346 through 2348 No H-bonds generated for 'chain 'B' and resid 2346 through 2348' Processing helix chain 'B' and resid 2350 through 2353 Processing helix chain 'B' and resid 2655 through 2657 No H-bonds generated for 'chain 'B' and resid 2655 through 2657' Processing helix chain 'B' and resid 2660 through 2662 No H-bonds generated for 'chain 'B' and resid 2660 through 2662' Processing helix chain 'B' and resid 2716 through 2720 removed outlier: 4.334A pdb=" N CYS B2720 " --> pdb=" O ASP B2717 " (cutoff:3.500A) Processing helix chain 'B' and resid 2734 through 2737 No H-bonds generated for 'chain 'B' and resid 2734 through 2737' Processing helix chain 'B' and resid 2757 through 2759 No H-bonds generated for 'chain 'B' and resid 2757 through 2759' Processing helix chain 'B' and resid 2797 through 2799 No H-bonds generated for 'chain 'B' and resid 2797 through 2799' Processing helix chain 'B' and resid 2839 through 2843 removed outlier: 4.086A pdb=" N CYS B2843 " --> pdb=" O ALA B2840 " (cutoff:3.500A) Processing helix chain 'B' and resid 2857 through 2862 removed outlier: 5.002A pdb=" N SER B2862 " --> pdb=" O ILE B2858 " (cutoff:3.500A) Processing helix chain 'B' and resid 2881 through 2886 removed outlier: 4.030A pdb=" N CYS B2885 " --> pdb=" O TYR B2882 " (cutoff:3.500A) Processing helix chain 'B' and resid 2895 through 2897 No H-bonds generated for 'chain 'B' and resid 2895 through 2897' Processing helix chain 'B' and resid 2899 through 2901 No H-bonds generated for 'chain 'B' and resid 2899 through 2901' Processing helix chain 'B' and resid 2923 through 2925 No H-bonds generated for 'chain 'B' and resid 2923 through 2925' Processing helix chain 'B' and resid 2941 through 2943 No H-bonds generated for 'chain 'B' and resid 2941 through 2943' Processing helix chain 'B' and resid 2945 through 2947 No H-bonds generated for 'chain 'B' and resid 2945 through 2947' Processing helix chain 'B' and resid 2970 through 2973 No H-bonds generated for 'chain 'B' and resid 2970 through 2973' Processing helix chain 'B' and resid 2984 through 2986 No H-bonds generated for 'chain 'B' and resid 2984 through 2986' Processing helix chain 'B' and resid 3010 through 3012 No H-bonds generated for 'chain 'B' and resid 3010 through 3012' Processing helix chain 'B' and resid 3049 through 3053 removed outlier: 4.019A pdb=" N CYS B3053 " --> pdb=" O LEU B3050 " (cutoff:3.500A) Processing helix chain 'B' and resid 3067 through 3070 No H-bonds generated for 'chain 'B' and resid 3067 through 3070' Processing helix chain 'B' and resid 3092 through 3096 removed outlier: 3.860A pdb=" N CYS B3096 " --> pdb=" O GLY B3093 " (cutoff:3.500A) Processing helix chain 'B' and resid 3106 through 3109 No H-bonds generated for 'chain 'B' and resid 3106 through 3109' Processing helix chain 'B' and resid 3115 through 3117 No H-bonds generated for 'chain 'B' and resid 3115 through 3117' Processing helix chain 'B' and resid 3157 through 3160 No H-bonds generated for 'chain 'B' and resid 3157 through 3160' Processing helix chain 'B' and resid 3162 through 3164 No H-bonds generated for 'chain 'B' and resid 3162 through 3164' Processing helix chain 'B' and resid 3461 through 3463 No H-bonds generated for 'chain 'B' and resid 3461 through 3463' Processing helix chain 'B' and resid 3475 through 3477 No H-bonds generated for 'chain 'B' and resid 3475 through 3477' Processing helix chain 'B' and resid 3522 through 3524 No H-bonds generated for 'chain 'B' and resid 3522 through 3524' Processing helix chain 'B' and resid 3530 through 3532 No H-bonds generated for 'chain 'B' and resid 3530 through 3532' Processing helix chain 'B' and resid 3570 through 3574 removed outlier: 4.484A pdb=" N CYS B3574 " --> pdb=" O GLN B3571 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3591 No H-bonds generated for 'chain 'B' and resid 3588 through 3591' Processing helix chain 'B' and resid 3611 through 3613 No H-bonds generated for 'chain 'B' and resid 3611 through 3613' Processing helix chain 'B' and resid 3624 through 3626 No H-bonds generated for 'chain 'B' and resid 3624 through 3626' Processing helix chain 'B' and resid 3629 through 3632 No H-bonds generated for 'chain 'B' and resid 3629 through 3632' Processing helix chain 'B' and resid 3652 through 3654 No H-bonds generated for 'chain 'B' and resid 3652 through 3654' Processing helix chain 'B' and resid 3670 through 3673 No H-bonds generated for 'chain 'B' and resid 3670 through 3673' Processing helix chain 'B' and resid 3676 through 3678 No H-bonds generated for 'chain 'B' and resid 3676 through 3678' Processing helix chain 'B' and resid 3697 through 3700 Processing helix chain 'B' and resid 3713 through 3715 No H-bonds generated for 'chain 'B' and resid 3713 through 3715' Processing helix chain 'B' and resid 3737 through 3741 removed outlier: 3.937A pdb=" N CYS B3741 " --> pdb=" O ARG B3738 " (cutoff:3.500A) Processing helix chain 'B' and resid 3751 through 3754 No H-bonds generated for 'chain 'B' and resid 3751 through 3754' Processing helix chain 'B' and resid 3776 through 3780 removed outlier: 3.929A pdb=" N CYS B3780 " --> pdb=" O ARG B3777 " (cutoff:3.500A) Processing helix chain 'B' and resid 3815 through 3817 No H-bonds generated for 'chain 'B' and resid 3815 through 3817' Processing helix chain 'B' and resid 3831 through 3833 No H-bonds generated for 'chain 'B' and resid 3831 through 3833' Processing helix chain 'B' and resid 3859 through 3861 No H-bonds generated for 'chain 'B' and resid 3859 through 3861' Processing helix chain 'B' and resid 3873 through 3875 No H-bonds generated for 'chain 'B' and resid 3873 through 3875' Processing helix chain 'B' and resid 3877 through 3882 removed outlier: 3.907A pdb=" N PHE B3881 " --> pdb=" O HIS B3878 " (cutoff:3.500A) Processing helix chain 'B' and resid 3902 through 3905 removed outlier: 3.719A pdb=" N CYS B3905 " --> pdb=" O HIS B3902 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3902 through 3905' Processing helix chain 'B' and resid 3919 through 3922 No H-bonds generated for 'chain 'B' and resid 3919 through 3922' Processing helix chain 'B' and resid 3946 through 3949 removed outlier: 3.753A pdb=" N CYS B3949 " --> pdb=" O HIS B3946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3946 through 3949' Processing helix chain 'B' and resid 3972 through 3974 No H-bonds generated for 'chain 'B' and resid 3972 through 3974' Processing helix chain 'B' and resid 4012 through 4014 No H-bonds generated for 'chain 'B' and resid 4012 through 4014' Processing sheet with id= A, first strand: chain 'A' and resid 71 through 73 Processing sheet with id= B, first strand: chain 'A' and resid 112 through 115 removed outlier: 3.565A pdb=" N CYS A 115 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 190 Processing sheet with id= D, first strand: chain 'A' and resid 226 through 229 Processing sheet with id= E, first strand: chain 'A' and resid 269 through 271 Processing sheet with id= F, first strand: chain 'A' and resid 320 through 322 Processing sheet with id= G, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= H, first strand: chain 'A' and resid 360 through 362 Processing sheet with id= I, first strand: chain 'A' and resid 376 through 379 Processing sheet with id= J, first strand: chain 'A' and resid 647 through 650 Processing sheet with id= K, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.801A pdb=" N GLY A 427 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 468 through 474 removed outlier: 6.633A pdb=" N VAL A 483 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 471 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR A 481 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL A 473 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS A 479 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 492 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR A 502 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN A 494 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ARG A 500 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.062A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG A 539 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP A 549 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE A 541 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG A 547 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 561 through 564 removed outlier: 3.610A pdb=" N ALA A 594 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 582 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR A 592 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR A 584 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ARG A 590 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 603 through 609 removed outlier: 6.390A pdb=" N THR A 616 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 606 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 614 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 608 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS A 625 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL A 636 " --> pdb=" O LYS A 625 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 672 through 677 Processing sheet with id= Q, first strand: chain 'A' and resid 694 through 696 Processing sheet with id= R, first strand: chain 'A' and resid 718 through 721 removed outlier: 3.647A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 745 through 748 removed outlier: 3.684A pdb=" N THR A 778 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN A 766 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 776 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS A 768 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS A 774 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 785 through 791 removed outlier: 6.592A pdb=" N THR A 800 " --> pdb=" O GLU A 786 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 788 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR A 798 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A 790 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A 796 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 809 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 819 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS A 811 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG A 817 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 827 through 833 removed outlier: 6.712A pdb=" N SER A 842 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 830 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 840 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL A 832 " --> pdb=" O TYR A 838 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 838 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG A 852 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TRP A 854 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 860 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 874 through 877 Processing sheet with id= W, first strand: chain 'A' and resid 915 through 921 removed outlier: 6.633A pdb=" N THR A 928 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 918 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 926 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 920 " --> pdb=" O ASN A 924 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASN A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 950 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 937 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A 948 " --> pdb=" O ARG A 937 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 986 through 990 Processing sheet with id= Y, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id= Z, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id= AA, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id= AB, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 3.551A pdb=" N MET A1121 " --> pdb=" O CYS A1117 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 1154 through 1157 removed outlier: 3.965A pdb=" N ARG A1161 " --> pdb=" O CYS A1157 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS A1457 " --> pdb=" O CYS A1162 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER A1164 " --> pdb=" O HIS A1457 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A1459 " --> pdb=" O SER A1164 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1438 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A1689 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id= AE, first strand: chain 'A' and resid 1276 through 1278 Processing sheet with id= AF, first strand: chain 'A' and resid 1317 through 1320 removed outlier: 4.293A pdb=" N ILE A1325 " --> pdb=" O CYS A1320 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 1364 through 1368 Processing sheet with id= AH, first strand: chain 'A' and resid 1380 through 1382 Processing sheet with id= AI, first strand: chain 'A' and resid 1404 through 1408 Processing sheet with id= AJ, first strand: chain 'A' and resid 1420 through 1422 Processing sheet with id= AK, first strand: chain 'A' and resid 1472 through 1475 removed outlier: 3.614A pdb=" N LYS A1490 " --> pdb=" O ASP A1485 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A1505 " --> pdb=" O THR A1491 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A1493 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL A1503 " --> pdb=" O SER A1493 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 1515 through 1517 removed outlier: 6.066A pdb=" N VAL A1536 " --> pdb=" O VAL A1546 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A1546 " --> pdb=" O VAL A1536 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS A1538 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A1544 " --> pdb=" O LYS A1538 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A' and resid 1555 through 1561 removed outlier: 5.959A pdb=" N SER A1572 " --> pdb=" O ARG A1556 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A1558 " --> pdb=" O PHE A1570 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A1570 " --> pdb=" O LEU A1558 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU A1560 " --> pdb=" O VAL A1568 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A1568 " --> pdb=" O LEU A1560 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG A1582 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL A1592 " --> pdb=" O ARG A1582 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER A1584 " --> pdb=" O ARG A1590 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A1590 " --> pdb=" O SER A1584 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 1601 through 1607 removed outlier: 5.783A pdb=" N MET A1616 " --> pdb=" O CYS A1602 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A1604 " --> pdb=" O TYR A1614 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR A1614 " --> pdb=" O LEU A1604 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A1606 " --> pdb=" O LEU A1612 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A1612 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE A1625 " --> pdb=" O GLN A1635 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLN A1635 " --> pdb=" O PHE A1625 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP A1627 " --> pdb=" O ARG A1633 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A1633 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 1646 through 1652 removed outlier: 6.649A pdb=" N THR A1659 " --> pdb=" O HIS A1647 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A1649 " --> pdb=" O PHE A1657 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A1657 " --> pdb=" O LEU A1649 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A1651 " --> pdb=" O SER A1655 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A1681 " --> pdb=" O VAL A1666 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN A1668 " --> pdb=" O VAL A1679 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL A1679 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASN A1670 " --> pdb=" O GLN A1677 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN A1677 " --> pdb=" O ASN A1670 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'A' and resid 1713 through 1716 Processing sheet with id= AQ, first strand: chain 'A' and resid 1732 through 1734 Processing sheet with id= AR, first strand: chain 'A' and resid 1756 through 1761 Processing sheet with id= AS, first strand: chain 'A' and resid 1784 through 1787 Processing sheet with id= AT, first strand: chain 'A' and resid 1824 through 1830 removed outlier: 6.600A pdb=" N THR A1839 " --> pdb=" O LEU A1825 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A1827 " --> pdb=" O TYR A1837 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR A1837 " --> pdb=" O LEU A1827 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A1829 " --> pdb=" O ASN A1835 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A1835 " --> pdb=" O LEU A1829 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A1848 " --> pdb=" O THR A1860 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR A1860 " --> pdb=" O VAL A1848 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR A1850 " --> pdb=" O GLY A1858 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY A1858 " --> pdb=" O THR A1850 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 1874 through 1880 removed outlier: 6.377A pdb=" N SER A1889 " --> pdb=" O VAL A1875 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A1877 " --> pdb=" O TYR A1887 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR A1887 " --> pdb=" O ILE A1877 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL A1879 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS A1885 " --> pdb=" O VAL A1879 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER A1903 " --> pdb=" O ILE A1913 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE A1913 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN A1905 " --> pdb=" O LEU A1911 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A1911 " --> pdb=" O ASN A1905 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'A' and resid 1922 through 1928 removed outlier: 3.680A pdb=" N GLU A1923 " --> pdb=" O ALA A1937 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA A1937 " --> pdb=" O GLU A1923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A1925 " --> pdb=" O TYR A1935 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A1935 " --> pdb=" O VAL A1925 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A1927 " --> pdb=" O LYS A1933 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A1933 " --> pdb=" O LEU A1927 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A1946 " --> pdb=" O ILE A1956 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE A1956 " --> pdb=" O ARG A1946 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASN A1948 " --> pdb=" O ARG A1954 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG A1954 " --> pdb=" O ASN A1948 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'A' and resid 1967 through 1970 removed outlier: 6.565A pdb=" N ARG A1986 " --> pdb=" O VAL A1997 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A1997 " --> pdb=" O ARG A1986 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP A1988 " --> pdb=" O LYS A1995 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS A1995 " --> pdb=" O ASP A1988 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'A' and resid 2033 through 2036 Processing sheet with id= AY, first strand: chain 'A' and resid 2050 through 2052 Processing sheet with id= AZ, first strand: chain 'A' and resid 2073 through 2078 Processing sheet with id= BA, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.886A pdb=" N CYS A2113 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA A2101 " --> pdb=" O TYR A2111 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A2111 " --> pdb=" O ALA A2101 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A2103 " --> pdb=" O PHE A2109 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE A2109 " --> pdb=" O VAL A2103 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG A2127 " --> pdb=" O ASN A2137 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN A2137 " --> pdb=" O ARG A2127 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'A' and resid 2147 through 2154 removed outlier: 6.319A pdb=" N THR A2163 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A2151 " --> pdb=" O TYR A2161 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR A2161 " --> pdb=" O VAL A2151 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL A2153 " --> pdb=" O ASN A2159 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A2159 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A2174 " --> pdb=" O VAL A2184 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL A2184 " --> pdb=" O VAL A2174 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG A2176 " --> pdb=" O ARG A2182 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG A2182 " --> pdb=" O ARG A2176 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'A' and resid 2196 through 2199 removed outlier: 3.524A pdb=" N VAL A2230 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG A2218 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL A2228 " --> pdb=" O ARG A2218 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'A' and resid 2270 through 2272 removed outlier: 3.613A pdb=" N TYR A2248 " --> pdb=" O ASP A2243 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A2239 " --> pdb=" O VAL A2252 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 6.652A pdb=" N VAL A2294 " --> pdb=" O TYR A2282 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A2284 " --> pdb=" O ILE A2292 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A2292 " --> pdb=" O ILE A2284 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A2286 " --> pdb=" O SER A2290 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER A2290 " --> pdb=" O VAL A2286 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A2300 " --> pdb=" O ASP A2295 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A2318 " --> pdb=" O VAL A2301 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLN A2303 " --> pdb=" O VAL A2316 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL A2316 " --> pdb=" O GLN A2303 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'A' and resid 2641 through 2644 Processing sheet with id= BG, first strand: chain 'A' and resid 2469 through 2475 removed outlier: 6.805A pdb=" N SER A2484 " --> pdb=" O ASP A2470 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A2472 " --> pdb=" O TYR A2482 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR A2482 " --> pdb=" O ILE A2472 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE A2474 " --> pdb=" O ARG A2480 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A2480 " --> pdb=" O PHE A2474 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER A2493 " --> pdb=" O VAL A2503 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL A2503 " --> pdb=" O SER A2493 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA A2495 " --> pdb=" O ARG A2501 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG A2501 " --> pdb=" O ALA A2495 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'A' and resid 2513 through 2516 removed outlier: 6.157A pdb=" N ARG A2535 " --> pdb=" O PRO A2545 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR A2537 " --> pdb=" O ARG A2543 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG A2543 " --> pdb=" O THR A2537 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'A' and resid 2554 through 2560 removed outlier: 6.478A pdb=" N ALA A2569 " --> pdb=" O ASN A2555 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A2557 " --> pdb=" O TYR A2567 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A2567 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU A2559 " --> pdb=" O LEU A2565 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A2565 " --> pdb=" O LEU A2559 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A2590 " --> pdb=" O ILE A2576 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG A2578 " --> pdb=" O VAL A2588 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL A2588 " --> pdb=" O ARG A2578 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR A2580 " --> pdb=" O ARG A2586 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG A2586 " --> pdb=" O THR A2580 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'A' and resid 2599 through 2602 Processing sheet with id= BK, first strand: chain 'A' and resid 2705 through 2707 Processing sheet with id= BL, first strand: chain 'A' and resid 2747 through 2749 removed outlier: 3.624A pdb=" N VAL A2755 " --> pdb=" O PHE A2747 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A2753 " --> pdb=" O CYS A2749 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'A' and resid 2786 through 2788 Processing sheet with id= BN, first strand: chain 'A' and resid 2827 through 2829 Processing sheet with id= BO, first strand: chain 'A' and resid 2912 through 2914 Processing sheet with id= BP, first strand: chain 'A' and resid 2954 through 2956 Processing sheet with id= BQ, first strand: chain 'A' and resid 2999 through 3002 removed outlier: 3.587A pdb=" N ARG A3006 " --> pdb=" O CYS A3002 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'A' and resid 3038 through 3041 removed outlier: 3.717A pdb=" N GLN A3045 " --> pdb=" O CYS A3041 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'A' and resid 3081 through 3083 Processing sheet with id= BT, first strand: chain 'A' and resid 3127 through 3130 Processing sheet with id= BU, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id= BV, first strand: chain 'A' and resid 3168 through 3172 Processing sheet with id= BW, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id= BX, first strand: chain 'A' and resid 3455 through 3459 removed outlier: 3.554A pdb=" N ASP A3455 " --> pdb=" O SER A3206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A3225 " --> pdb=" O ILE A3211 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN A3213 " --> pdb=" O LEU A3223 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A3223 " --> pdb=" O ASN A3213 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR A3215 " --> pdb=" O TYR A3221 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A3221 " --> pdb=" O THR A3215 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'A' and resid 3231 through 3237 removed outlier: 6.729A pdb=" N ILE A3246 " --> pdb=" O VAL A3232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A3234 " --> pdb=" O TYR A3244 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A3244 " --> pdb=" O LEU A3234 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A3236 " --> pdb=" O ARG A3242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG A3242 " --> pdb=" O PHE A3236 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG A3255 " --> pdb=" O THR A3265 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR A3265 " --> pdb=" O ARG A3255 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N PHE A3257 " --> pdb=" O GLN A3263 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN A3263 " --> pdb=" O PHE A3257 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 6.671A pdb=" N LEU A3289 " --> pdb=" O GLU A3275 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU A3277 " --> pdb=" O TYR A3287 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A3287 " --> pdb=" O LEU A3277 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL A3279 " --> pdb=" O LYS A3285 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A3285 " --> pdb=" O VAL A3279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A3310 " --> pdb=" O LEU A3296 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A3298 " --> pdb=" O MET A3308 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N MET A3308 " --> pdb=" O VAL A3298 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP A3300 " --> pdb=" O ARG A3306 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG A3306 " --> pdb=" O ASP A3300 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 5.731A pdb=" N ALA A3340 " --> pdb=" O ARG A3326 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A3328 " --> pdb=" O TYR A3338 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A3338 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU A3330 " --> pdb=" O TYR A3336 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR A3336 " --> pdb=" O LEU A3330 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG A3350 " --> pdb=" O VAL A3360 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL A3360 " --> pdb=" O ARG A3350 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'A' and resid 3372 through 3375 removed outlier: 3.660A pdb=" N TYR A3405 " --> pdb=" O ILE A3391 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A3393 " --> pdb=" O THR A3403 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR A3403 " --> pdb=" O PHE A3393 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASP A3395 " --> pdb=" O ARG A3401 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG A3401 " --> pdb=" O ASP A3395 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'A' and resid 3415 through 3418 removed outlier: 6.765A pdb=" N LYS A3434 " --> pdb=" O VAL A3445 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL A3445 " --> pdb=" O LYS A3434 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A3436 " --> pdb=" O ARG A3443 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG A3443 " --> pdb=" O ASN A3436 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'A' and resid 3481 through 3484 Processing sheet with id= CE, first strand: chain 'A' and resid 3499 through 3503 Processing sheet with id= CF, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id= CG, first strand: chain 'A' and resid 3560 through 3562 removed outlier: 3.761A pdb=" N ASN A3566 " --> pdb=" O CYS A3562 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'A' and resid 3600 through 3603 removed outlier: 3.721A pdb=" N ARG A3607 " --> pdb=" O CYS A3603 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'A' and resid 3641 through 3644 removed outlier: 3.757A pdb=" N ARG A3648 " --> pdb=" O CYS A3644 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'A' and resid 3726 through 3729 removed outlier: 3.596A pdb=" N HIS A3733 " --> pdb=" O CYS A3729 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'A' and resid 3765 through 3767 Processing sheet with id= CL, first strand: chain 'A' and resid 3804 through 3807 Processing sheet with id= CM, first strand: chain 'A' and resid 3849 through 3851 removed outlier: 3.688A pdb=" N VAL A3855 " --> pdb=" O CYS A3851 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'A' and resid 3890 through 3892 Processing sheet with id= CO, first strand: chain 'A' and resid 3934 through 3937 removed outlier: 3.801A pdb=" N ASN A3941 " --> pdb=" O CYS A3937 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'A' and resid 3981 through 3983 Processing sheet with id= CQ, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id= CR, first strand: chain 'A' and resid 4022 through 4026 Processing sheet with id= CS, first strand: chain 'A' and resid 4038 through 4040 Processing sheet with id= CT, first strand: chain 'A' and resid 4321 through 4323 removed outlier: 6.277A pdb=" N LYS A4068 " --> pdb=" O GLU A4078 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A4078 " --> pdb=" O LYS A4068 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A4070 " --> pdb=" O PHE A4076 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE A4076 " --> pdb=" O ASN A4070 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'A' and resid 4089 through 4092 Processing sheet with id= CV, first strand: chain 'A' and resid 4146 through 4152 removed outlier: 6.536A pdb=" N SER A4161 " --> pdb=" O ASP A4147 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A4149 " --> pdb=" O TYR A4159 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR A4159 " --> pdb=" O LEU A4149 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A4151 " --> pdb=" O HIS A4157 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS A4157 " --> pdb=" O VAL A4151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A4182 " --> pdb=" O ILE A4168 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A4170 " --> pdb=" O TRP A4180 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP A4180 " --> pdb=" O VAL A4170 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A4172 " --> pdb=" O ARG A4178 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG A4178 " --> pdb=" O THR A4172 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 6.503A pdb=" N THR A4204 " --> pdb=" O ALA A4190 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A4192 " --> pdb=" O PHE A4202 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A4202 " --> pdb=" O ILE A4192 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL A4194 " --> pdb=" O LEU A4200 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A4200 " --> pdb=" O VAL A4194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER A4214 " --> pdb=" O VAL A4224 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL A4224 " --> pdb=" O SER A4214 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TRP A4216 " --> pdb=" O ARG A4222 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG A4222 " --> pdb=" O TRP A4216 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'A' and resid 4233 through 4238 removed outlier: 6.579A pdb=" N SER A4249 " --> pdb=" O ASN A4234 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A4236 " --> pdb=" O TYR A4247 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR A4247 " --> pdb=" O LEU A4236 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER A4258 " --> pdb=" O LEU A4268 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU A4268 " --> pdb=" O SER A4258 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'A' and resid 4279 through 4282 removed outlier: 3.969A pdb=" N GLU A4295 " --> pdb=" O ALA A4290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A4311 " --> pdb=" O VAL A4296 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A4298 " --> pdb=" O LYS A4309 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS A4309 " --> pdb=" O ARG A4298 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id= DA, first strand: chain 'A' and resid 4390 through 4393 Processing sheet with id= DB, first strand: chain 'A' and resid 2421 through 2428 removed outlier: 6.448A pdb=" N THR A2437 " --> pdb=" O ILE A2423 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A2425 " --> pdb=" O PHE A2435 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE A2435 " --> pdb=" O LEU A2425 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR A2427 " --> pdb=" O ARG A2433 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG A2433 " --> pdb=" O TYR A2427 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG A2444 " --> pdb=" O LEU A2440 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A2449 " --> pdb=" O ILE A2461 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE A2461 " --> pdb=" O TYR A2449 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'A' and resid 3685 through 3688 removed outlier: 3.552A pdb=" N CYS A3688 " --> pdb=" O ARG A3693 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG A3693 " --> pdb=" O CYS A3688 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'B' and resid 71 through 73 Processing sheet with id= DE, first strand: chain 'B' and resid 112 through 115 removed outlier: 3.565A pdb=" N CYS B 115 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'B' and resid 187 through 190 Processing sheet with id= DG, first strand: chain 'B' and resid 226 through 229 Processing sheet with id= DH, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= DI, first strand: chain 'B' and resid 320 through 322 Processing sheet with id= DJ, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= DK, first strand: chain 'B' and resid 360 through 362 Processing sheet with id= DL, first strand: chain 'B' and resid 376 through 379 Processing sheet with id= DM, first strand: chain 'B' and resid 647 through 650 Processing sheet with id= DN, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.801A pdb=" N GLY B 427 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'B' and resid 468 through 474 removed outlier: 6.633A pdb=" N VAL B 483 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 471 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR B 481 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL B 473 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS B 479 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 492 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR B 502 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN B 494 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ARG B 500 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'B' and resid 513 through 517 removed outlier: 4.062A pdb=" N GLY B 513 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 539 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP B 549 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE B 541 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B 547 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'B' and resid 561 through 564 removed outlier: 3.610A pdb=" N ALA B 594 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 582 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR B 592 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 584 " --> pdb=" O ARG B 590 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ARG B 590 " --> pdb=" O THR B 584 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'B' and resid 603 through 609 removed outlier: 6.390A pdb=" N THR B 616 " --> pdb=" O PHE B 604 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 606 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 614 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU B 608 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS B 625 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL B 636 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'B' and resid 672 through 677 Processing sheet with id= DT, first strand: chain 'B' and resid 694 through 696 Processing sheet with id= DU, first strand: chain 'B' and resid 718 through 721 removed outlier: 3.647A pdb=" N HIS B 958 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing sheet with id= DV, first strand: chain 'B' and resid 745 through 748 removed outlier: 3.684A pdb=" N THR B 778 " --> pdb=" O ILE B 764 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN B 766 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL B 776 " --> pdb=" O GLN B 766 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS B 768 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 774 " --> pdb=" O LYS B 768 " (cutoff:3.500A) Processing sheet with id= DW, first strand: chain 'B' and resid 785 through 791 removed outlier: 6.592A pdb=" N THR B 800 " --> pdb=" O GLU B 786 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 788 " --> pdb=" O TYR B 798 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 798 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE B 790 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 796 " --> pdb=" O PHE B 790 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 809 " --> pdb=" O GLN B 819 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN B 819 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS B 811 " --> pdb=" O ARG B 817 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG B 817 " --> pdb=" O LYS B 811 " (cutoff:3.500A) Processing sheet with id= DX, first strand: chain 'B' and resid 827 through 833 removed outlier: 6.712A pdb=" N SER B 842 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 830 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 840 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL B 832 " --> pdb=" O TYR B 838 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 838 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG B 852 " --> pdb=" O PRO B 862 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TRP B 854 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 860 " --> pdb=" O TRP B 854 " (cutoff:3.500A) Processing sheet with id= DY, first strand: chain 'B' and resid 874 through 877 Processing sheet with id= DZ, first strand: chain 'B' and resid 915 through 921 removed outlier: 6.633A pdb=" N THR B 928 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 918 " --> pdb=" O PHE B 926 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 926 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL B 920 " --> pdb=" O ASN B 924 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASN B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 950 " --> pdb=" O ILE B 935 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG B 937 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL B 948 " --> pdb=" O ARG B 937 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'B' and resid 986 through 990 Processing sheet with id= EB, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id= EC, first strand: chain 'B' and resid 1029 through 1031 Processing sheet with id= ED, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id= EE, first strand: chain 'B' and resid 1114 through 1117 removed outlier: 3.551A pdb=" N MET B1121 " --> pdb=" O CYS B1117 " (cutoff:3.500A) Processing sheet with id= EF, first strand: chain 'B' and resid 1154 through 1157 removed outlier: 3.965A pdb=" N ARG B1161 " --> pdb=" O CYS B1157 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS B1457 " --> pdb=" O CYS B1162 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER B1164 " --> pdb=" O HIS B1457 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE B1459 " --> pdb=" O SER B1164 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B1438 " --> pdb=" O ILE B1693 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B1689 " --> pdb=" O ALA B1442 " (cutoff:3.500A) Processing sheet with id= EG, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id= EH, first strand: chain 'B' and resid 1276 through 1278 Processing sheet with id= EI, first strand: chain 'B' and resid 1317 through 1320 removed outlier: 4.293A pdb=" N ILE B1325 " --> pdb=" O CYS B1320 " (cutoff:3.500A) Processing sheet with id= EJ, first strand: chain 'B' and resid 1364 through 1368 Processing sheet with id= EK, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id= EL, first strand: chain 'B' and resid 1404 through 1408 Processing sheet with id= EM, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id= EN, first strand: chain 'B' and resid 1472 through 1475 removed outlier: 3.614A pdb=" N LYS B1490 " --> pdb=" O ASP B1485 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B1505 " --> pdb=" O THR B1491 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER B1493 " --> pdb=" O VAL B1503 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL B1503 " --> pdb=" O SER B1493 " (cutoff:3.500A) Processing sheet with id= EO, first strand: chain 'B' and resid 1515 through 1517 removed outlier: 6.066A pdb=" N VAL B1536 " --> pdb=" O VAL B1546 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL B1546 " --> pdb=" O VAL B1536 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS B1538 " --> pdb=" O ARG B1544 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B1544 " --> pdb=" O LYS B1538 " (cutoff:3.500A) Processing sheet with id= EP, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 5.959A pdb=" N SER B1572 " --> pdb=" O ARG B1556 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B1558 " --> pdb=" O PHE B1570 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE B1570 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B1560 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B1568 " --> pdb=" O LEU B1560 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG B1582 " --> pdb=" O VAL B1592 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL B1592 " --> pdb=" O ARG B1582 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER B1584 " --> pdb=" O ARG B1590 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG B1590 " --> pdb=" O SER B1584 " (cutoff:3.500A) Processing sheet with id= EQ, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 5.783A pdb=" N MET B1616 " --> pdb=" O CYS B1602 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B1604 " --> pdb=" O TYR B1614 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B1614 " --> pdb=" O LEU B1604 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B1606 " --> pdb=" O LEU B1612 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B1612 " --> pdb=" O ILE B1606 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B1625 " --> pdb=" O GLN B1635 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLN B1635 " --> pdb=" O PHE B1625 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP B1627 " --> pdb=" O ARG B1633 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG B1633 " --> pdb=" O ASP B1627 " (cutoff:3.500A) Processing sheet with id= ER, first strand: chain 'B' and resid 1646 through 1652 removed outlier: 6.649A pdb=" N THR B1659 " --> pdb=" O HIS B1647 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B1649 " --> pdb=" O PHE B1657 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B1657 " --> pdb=" O LEU B1649 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU B1651 " --> pdb=" O SER B1655 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET B1681 " --> pdb=" O VAL B1666 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN B1668 " --> pdb=" O VAL B1679 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL B1679 " --> pdb=" O GLN B1668 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASN B1670 " --> pdb=" O GLN B1677 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN B1677 " --> pdb=" O ASN B1670 " (cutoff:3.500A) Processing sheet with id= ES, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id= ET, first strand: chain 'B' and resid 1732 through 1734 Processing sheet with id= EU, first strand: chain 'B' and resid 1756 through 1761 Processing sheet with id= EV, first strand: chain 'B' and resid 1784 through 1787 Processing sheet with id= EW, first strand: chain 'B' and resid 1824 through 1830 removed outlier: 6.600A pdb=" N THR B1839 " --> pdb=" O LEU B1825 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B1827 " --> pdb=" O TYR B1837 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR B1837 " --> pdb=" O LEU B1827 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU B1829 " --> pdb=" O ASN B1835 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN B1835 " --> pdb=" O LEU B1829 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B1848 " --> pdb=" O THR B1860 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR B1860 " --> pdb=" O VAL B1848 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR B1850 " --> pdb=" O GLY B1858 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY B1858 " --> pdb=" O THR B1850 " (cutoff:3.500A) Processing sheet with id= EX, first strand: chain 'B' and resid 1874 through 1880 removed outlier: 6.377A pdb=" N SER B1889 " --> pdb=" O VAL B1875 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B1877 " --> pdb=" O TYR B1887 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B1887 " --> pdb=" O ILE B1877 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL B1879 " --> pdb=" O LYS B1885 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS B1885 " --> pdb=" O VAL B1879 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER B1903 " --> pdb=" O ILE B1913 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE B1913 " --> pdb=" O SER B1903 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN B1905 " --> pdb=" O LEU B1911 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B1911 " --> pdb=" O ASN B1905 " (cutoff:3.500A) Processing sheet with id= EY, first strand: chain 'B' and resid 1922 through 1928 removed outlier: 3.680A pdb=" N GLU B1923 " --> pdb=" O ALA B1937 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B1937 " --> pdb=" O GLU B1923 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B1925 " --> pdb=" O TYR B1935 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B1935 " --> pdb=" O VAL B1925 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B1927 " --> pdb=" O LYS B1933 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS B1933 " --> pdb=" O LEU B1927 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG B1946 " --> pdb=" O ILE B1956 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE B1956 " --> pdb=" O ARG B1946 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASN B1948 " --> pdb=" O ARG B1954 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B1954 " --> pdb=" O ASN B1948 " (cutoff:3.500A) Processing sheet with id= EZ, first strand: chain 'B' and resid 1967 through 1970 removed outlier: 6.565A pdb=" N ARG B1986 " --> pdb=" O VAL B1997 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL B1997 " --> pdb=" O ARG B1986 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP B1988 " --> pdb=" O LYS B1995 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS B1995 " --> pdb=" O ASP B1988 " (cutoff:3.500A) Processing sheet with id= FA, first strand: chain 'B' and resid 2033 through 2036 Processing sheet with id= FB, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id= FC, first strand: chain 'B' and resid 2073 through 2078 Processing sheet with id= FD, first strand: chain 'B' and resid 2098 through 2104 removed outlier: 6.886A pdb=" N CYS B2113 " --> pdb=" O LEU B2099 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B2101 " --> pdb=" O TYR B2111 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR B2111 " --> pdb=" O ALA B2101 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B2103 " --> pdb=" O PHE B2109 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B2109 " --> pdb=" O VAL B2103 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG B2127 " --> pdb=" O ASN B2137 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN B2137 " --> pdb=" O ARG B2127 " (cutoff:3.500A) Processing sheet with id= FE, first strand: chain 'B' and resid 2147 through 2154 removed outlier: 6.319A pdb=" N THR B2163 " --> pdb=" O ARG B2149 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B2151 " --> pdb=" O TYR B2161 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR B2161 " --> pdb=" O VAL B2151 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL B2153 " --> pdb=" O ASN B2159 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN B2159 " --> pdb=" O VAL B2153 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B2174 " --> pdb=" O VAL B2184 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL B2184 " --> pdb=" O VAL B2174 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B2176 " --> pdb=" O ARG B2182 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B2182 " --> pdb=" O ARG B2176 " (cutoff:3.500A) Processing sheet with id= FF, first strand: chain 'B' and resid 2196 through 2199 removed outlier: 3.524A pdb=" N VAL B2230 " --> pdb=" O ILE B2216 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG B2218 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B2228 " --> pdb=" O ARG B2218 " (cutoff:3.500A) Processing sheet with id= FG, first strand: chain 'B' and resid 2270 through 2272 removed outlier: 3.613A pdb=" N TYR B2248 " --> pdb=" O ASP B2243 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B2239 " --> pdb=" O VAL B2252 " (cutoff:3.500A) Processing sheet with id= FH, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 6.652A pdb=" N VAL B2294 " --> pdb=" O TYR B2282 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B2284 " --> pdb=" O ILE B2292 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B2292 " --> pdb=" O ILE B2284 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL B2286 " --> pdb=" O SER B2290 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N SER B2290 " --> pdb=" O VAL B2286 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B2300 " --> pdb=" O ASP B2295 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B2318 " --> pdb=" O VAL B2301 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLN B2303 " --> pdb=" O VAL B2316 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL B2316 " --> pdb=" O GLN B2303 " (cutoff:3.500A) Processing sheet with id= FI, first strand: chain 'B' and resid 2641 through 2644 Processing sheet with id= FJ, first strand: chain 'B' and resid 2469 through 2475 removed outlier: 6.805A pdb=" N SER B2484 " --> pdb=" O ASP B2470 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B2472 " --> pdb=" O TYR B2482 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR B2482 " --> pdb=" O ILE B2472 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE B2474 " --> pdb=" O ARG B2480 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B2480 " --> pdb=" O PHE B2474 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B2493 " --> pdb=" O VAL B2503 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B2503 " --> pdb=" O SER B2493 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA B2495 " --> pdb=" O ARG B2501 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG B2501 " --> pdb=" O ALA B2495 " (cutoff:3.500A) Processing sheet with id= FK, first strand: chain 'B' and resid 2513 through 2516 removed outlier: 6.157A pdb=" N ARG B2535 " --> pdb=" O PRO B2545 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR B2537 " --> pdb=" O ARG B2543 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG B2543 " --> pdb=" O THR B2537 " (cutoff:3.500A) Processing sheet with id= FL, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 6.478A pdb=" N ALA B2569 " --> pdb=" O ASN B2555 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B2557 " --> pdb=" O TYR B2567 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR B2567 " --> pdb=" O LEU B2557 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU B2559 " --> pdb=" O LEU B2565 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B2565 " --> pdb=" O LEU B2559 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B2590 " --> pdb=" O ILE B2576 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B2578 " --> pdb=" O VAL B2588 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B2588 " --> pdb=" O ARG B2578 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR B2580 " --> pdb=" O ARG B2586 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG B2586 " --> pdb=" O THR B2580 " (cutoff:3.500A) Processing sheet with id= FM, first strand: chain 'B' and resid 2599 through 2602 Processing sheet with id= FN, first strand: chain 'B' and resid 2705 through 2707 Processing sheet with id= FO, first strand: chain 'B' and resid 2747 through 2749 removed outlier: 3.624A pdb=" N VAL B2755 " --> pdb=" O PHE B2747 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B2753 " --> pdb=" O CYS B2749 " (cutoff:3.500A) Processing sheet with id= FP, first strand: chain 'B' and resid 2786 through 2788 Processing sheet with id= FQ, first strand: chain 'B' and resid 2827 through 2829 Processing sheet with id= FR, first strand: chain 'B' and resid 2912 through 2914 Processing sheet with id= FS, first strand: chain 'B' and resid 2954 through 2956 Processing sheet with id= FT, first strand: chain 'B' and resid 2999 through 3002 removed outlier: 3.587A pdb=" N ARG B3006 " --> pdb=" O CYS B3002 " (cutoff:3.500A) Processing sheet with id= FU, first strand: chain 'B' and resid 3038 through 3041 removed outlier: 3.717A pdb=" N GLN B3045 " --> pdb=" O CYS B3041 " (cutoff:3.500A) Processing sheet with id= FV, first strand: chain 'B' and resid 3081 through 3083 Processing sheet with id= FW, first strand: chain 'B' and resid 3127 through 3130 Processing sheet with id= FX, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id= FY, first strand: chain 'B' and resid 3168 through 3172 Processing sheet with id= FZ, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id= GA, first strand: chain 'B' and resid 3455 through 3459 removed outlier: 3.554A pdb=" N ASP B3455 " --> pdb=" O SER B3206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B3225 " --> pdb=" O ILE B3211 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN B3213 " --> pdb=" O LEU B3223 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B3223 " --> pdb=" O ASN B3213 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR B3215 " --> pdb=" O TYR B3221 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B3221 " --> pdb=" O THR B3215 " (cutoff:3.500A) Processing sheet with id= GB, first strand: chain 'B' and resid 3231 through 3237 removed outlier: 6.729A pdb=" N ILE B3246 " --> pdb=" O VAL B3232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B3234 " --> pdb=" O TYR B3244 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR B3244 " --> pdb=" O LEU B3234 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE B3236 " --> pdb=" O ARG B3242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG B3242 " --> pdb=" O PHE B3236 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B3255 " --> pdb=" O THR B3265 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR B3265 " --> pdb=" O ARG B3255 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N PHE B3257 " --> pdb=" O GLN B3263 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN B3263 " --> pdb=" O PHE B3257 " (cutoff:3.500A) Processing sheet with id= GC, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 6.671A pdb=" N LEU B3289 " --> pdb=" O GLU B3275 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B3277 " --> pdb=" O TYR B3287 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B3287 " --> pdb=" O LEU B3277 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL B3279 " --> pdb=" O LYS B3285 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS B3285 " --> pdb=" O VAL B3279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B3310 " --> pdb=" O LEU B3296 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B3298 " --> pdb=" O MET B3308 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N MET B3308 " --> pdb=" O VAL B3298 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP B3300 " --> pdb=" O ARG B3306 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG B3306 " --> pdb=" O ASP B3300 " (cutoff:3.500A) Processing sheet with id= GD, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 5.731A pdb=" N ALA B3340 " --> pdb=" O ARG B3326 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B3328 " --> pdb=" O TYR B3338 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B3338 " --> pdb=" O ILE B3328 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU B3330 " --> pdb=" O TYR B3336 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR B3336 " --> pdb=" O LEU B3330 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG B3350 " --> pdb=" O VAL B3360 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL B3360 " --> pdb=" O ARG B3350 " (cutoff:3.500A) Processing sheet with id= GE, first strand: chain 'B' and resid 3372 through 3375 removed outlier: 3.660A pdb=" N TYR B3405 " --> pdb=" O ILE B3391 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE B3393 " --> pdb=" O THR B3403 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR B3403 " --> pdb=" O PHE B3393 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASP B3395 " --> pdb=" O ARG B3401 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG B3401 " --> pdb=" O ASP B3395 " (cutoff:3.500A) Processing sheet with id= GF, first strand: chain 'B' and resid 3415 through 3418 removed outlier: 6.765A pdb=" N LYS B3434 " --> pdb=" O VAL B3445 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL B3445 " --> pdb=" O LYS B3434 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN B3436 " --> pdb=" O ARG B3443 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG B3443 " --> pdb=" O ASN B3436 " (cutoff:3.500A) Processing sheet with id= GG, first strand: chain 'B' and resid 3481 through 3484 Processing sheet with id= GH, first strand: chain 'B' and resid 3499 through 3503 Processing sheet with id= GI, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id= GJ, first strand: chain 'B' and resid 3560 through 3562 removed outlier: 3.761A pdb=" N ASN B3566 " --> pdb=" O CYS B3562 " (cutoff:3.500A) Processing sheet with id= GK, first strand: chain 'B' and resid 3600 through 3603 removed outlier: 3.721A pdb=" N ARG B3607 " --> pdb=" O CYS B3603 " (cutoff:3.500A) Processing sheet with id= GL, first strand: chain 'B' and resid 3641 through 3644 removed outlier: 3.757A pdb=" N ARG B3648 " --> pdb=" O CYS B3644 " (cutoff:3.500A) Processing sheet with id= GM, first strand: chain 'B' and resid 3726 through 3729 removed outlier: 3.596A pdb=" N HIS B3733 " --> pdb=" O CYS B3729 " (cutoff:3.500A) Processing sheet with id= GN, first strand: chain 'B' and resid 3765 through 3767 Processing sheet with id= GO, first strand: chain 'B' and resid 3804 through 3807 Processing sheet with id= GP, first strand: chain 'B' and resid 3849 through 3851 removed outlier: 3.688A pdb=" N VAL B3855 " --> pdb=" O CYS B3851 " (cutoff:3.500A) Processing sheet with id= GQ, first strand: chain 'B' and resid 3890 through 3892 Processing sheet with id= GR, first strand: chain 'B' and resid 3934 through 3937 removed outlier: 3.801A pdb=" N ASN B3941 " --> pdb=" O CYS B3937 " (cutoff:3.500A) Processing sheet with id= GS, first strand: chain 'B' and resid 3981 through 3983 Processing sheet with id= GT, first strand: chain 'B' and resid 3997 through 3999 Processing sheet with id= GU, first strand: chain 'B' and resid 4022 through 4026 Processing sheet with id= GV, first strand: chain 'B' and resid 4038 through 4040 Processing sheet with id= GW, first strand: chain 'B' and resid 4321 through 4323 removed outlier: 6.277A pdb=" N LYS B4068 " --> pdb=" O GLU B4078 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU B4078 " --> pdb=" O LYS B4068 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B4070 " --> pdb=" O PHE B4076 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE B4076 " --> pdb=" O ASN B4070 " (cutoff:3.500A) Processing sheet with id= GX, first strand: chain 'B' and resid 4089 through 4092 Processing sheet with id= GY, first strand: chain 'B' and resid 4146 through 4152 removed outlier: 6.536A pdb=" N SER B4161 " --> pdb=" O ASP B4147 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B4149 " --> pdb=" O TYR B4159 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR B4159 " --> pdb=" O LEU B4149 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B4151 " --> pdb=" O HIS B4157 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS B4157 " --> pdb=" O VAL B4151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B4182 " --> pdb=" O ILE B4168 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B4170 " --> pdb=" O TRP B4180 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP B4180 " --> pdb=" O VAL B4170 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR B4172 " --> pdb=" O ARG B4178 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG B4178 " --> pdb=" O THR B4172 " (cutoff:3.500A) Processing sheet with id= GZ, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 6.503A pdb=" N THR B4204 " --> pdb=" O ALA B4190 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B4192 " --> pdb=" O PHE B4202 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE B4202 " --> pdb=" O ILE B4192 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B4194 " --> pdb=" O LEU B4200 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B4200 " --> pdb=" O VAL B4194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER B4214 " --> pdb=" O VAL B4224 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL B4224 " --> pdb=" O SER B4214 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TRP B4216 " --> pdb=" O ARG B4222 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG B4222 " --> pdb=" O TRP B4216 " (cutoff:3.500A) Processing sheet with id= HA, first strand: chain 'B' and resid 4233 through 4238 removed outlier: 6.579A pdb=" N SER B4249 " --> pdb=" O ASN B4234 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B4236 " --> pdb=" O TYR B4247 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B4247 " --> pdb=" O LEU B4236 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER B4258 " --> pdb=" O LEU B4268 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B4268 " --> pdb=" O SER B4258 " (cutoff:3.500A) Processing sheet with id= HB, first strand: chain 'B' and resid 4279 through 4282 removed outlier: 3.969A pdb=" N GLU B4295 " --> pdb=" O ALA B4290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B4311 " --> pdb=" O VAL B4296 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B4298 " --> pdb=" O LYS B4309 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS B4309 " --> pdb=" O ARG B4298 " (cutoff:3.500A) Processing sheet with id= HC, first strand: chain 'B' and resid 4343 through 4347 Processing sheet with id= HD, first strand: chain 'B' and resid 4390 through 4393 Processing sheet with id= HE, first strand: chain 'B' and resid 2421 through 2428 removed outlier: 6.448A pdb=" N THR B2437 " --> pdb=" O ILE B2423 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B2425 " --> pdb=" O PHE B2435 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B2435 " --> pdb=" O LEU B2425 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR B2427 " --> pdb=" O ARG B2433 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG B2433 " --> pdb=" O TYR B2427 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B2444 " --> pdb=" O LEU B2440 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B2449 " --> pdb=" O ILE B2461 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE B2461 " --> pdb=" O TYR B2449 " (cutoff:3.500A) Processing sheet with id= HF, first strand: chain 'B' and resid 3685 through 3688 removed outlier: 3.552A pdb=" N CYS B3688 " --> pdb=" O ARG B3693 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG B3693 " --> pdb=" O CYS B3688 " (cutoff:3.500A) 1386 hydrogen bonds defined for protein. 3462 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: 105.40 Time building geometry restraints manager: 23.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 12038 1.32 - 1.45: 21312 1.45 - 1.59: 34868 1.59 - 1.72: 0 1.72 - 1.85: 872 Bond restraints: 69090 Sorted by residual: bond pdb=" C PRO B1000 " pdb=" O PRO B1000 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.18e-02 7.18e+03 1.48e+01 bond pdb=" C PRO A1000 " pdb=" O PRO A1000 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.18e-02 7.18e+03 1.48e+01 bond pdb=" C VAL A 996 " pdb=" O VAL A 996 " ideal model delta sigma weight residual 1.235 1.269 -0.034 9.90e-03 1.02e+04 1.17e+01 bond pdb=" C VAL B 996 " pdb=" O VAL B 996 " ideal model delta sigma weight residual 1.235 1.269 -0.034 9.90e-03 1.02e+04 1.17e+01 bond pdb=" N VAL A2694 " pdb=" CA VAL A2694 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 ... (remaining 69085 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.80: 2142 105.80 - 112.94: 34346 112.94 - 120.09: 27012 120.09 - 127.24: 29616 127.24 - 134.38: 1056 Bond angle restraints: 94172 Sorted by residual: angle pdb=" N ASN B2989 " pdb=" CA ASN B2989 " pdb=" C ASN B2989 " ideal model delta sigma weight residual 111.28 116.62 -5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" N ASN A2989 " pdb=" CA ASN A2989 " pdb=" C ASN A2989 " ideal model delta sigma weight residual 111.28 116.62 -5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" CA LYS A1270 " pdb=" C LYS A1270 " pdb=" O LYS A1270 " ideal model delta sigma weight residual 121.56 116.23 5.33 1.09e+00 8.42e-01 2.39e+01 angle pdb=" CA LYS B1270 " pdb=" C LYS B1270 " pdb=" O LYS B1270 " ideal model delta sigma weight residual 121.56 116.23 5.33 1.09e+00 8.42e-01 2.39e+01 angle pdb=" CA PRO A 64 " pdb=" C PRO A 64 " pdb=" O PRO A 64 " ideal model delta sigma weight residual 121.23 116.05 5.18 1.07e+00 8.73e-01 2.34e+01 ... (remaining 94167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 40090 17.95 - 35.90: 2594 35.90 - 53.86: 460 53.86 - 71.81: 126 71.81 - 89.76: 44 Dihedral angle restraints: 43314 sinusoidal: 18086 harmonic: 25228 Sorted by residual: dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS B 316 " pdb=" SG CYS B 316 " pdb=" SG CYS B 329 " pdb=" CB CYS B 329 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS B2663 " pdb=" SG CYS B2663 " pdb=" SG CYS B2676 " pdb=" CB CYS B2676 " ideal model delta sinusoidal sigma weight residual -86.00 -163.86 77.86 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 43311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 9418 0.114 - 0.228: 1008 0.228 - 0.342: 42 0.342 - 0.455: 4 0.455 - 0.569: 4 Chirality restraints: 10476 Sorted by residual: chirality pdb=" C1 NAG A4708 " pdb=" ND2 ASN A1384 " pdb=" C2 NAG A4708 " pdb=" O5 NAG A4708 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" C1 NAG B4708 " pdb=" ND2 ASN B1384 " pdb=" C2 NAG B4708 " pdb=" O5 NAG B4708 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" C1 NAG A4723 " pdb=" ND2 ASN A2989 " pdb=" C2 NAG A4723 " pdb=" O5 NAG A4723 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 10473 not shown) Planarity restraints: 12518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NGA B4747 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NGA B4747 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NGA B4747 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NGA B4747 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NGA B4747 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NGA A4747 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NGA A4747 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NGA A4747 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NGA A4747 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NGA A4747 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4732 " 0.338 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A4732 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A4732 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A4732 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG A4732 " 0.091 2.00e-02 2.50e+03 ... (remaining 12515 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1786 2.66 - 3.22: 65346 3.22 - 3.78: 102763 3.78 - 4.34: 149876 4.34 - 4.90: 240544 Nonbonded interactions: 560315 Sorted by model distance: nonbonded pdb=" OD1 ASP B3657 " pdb="CA CA B4782 " model vdw 2.097 2.510 nonbonded pdb=" OD1 ASP A3657 " pdb="CA CA A4782 " model vdw 2.097 2.510 nonbonded pdb=" OD2 ASP B1097 " pdb="CA CA B4763 " model vdw 2.117 2.510 nonbonded pdb=" OD2 ASP A1097 " pdb="CA CA A4763 " model vdw 2.117 2.510 nonbonded pdb=" OD2 ASP A3667 " pdb="CA CA A4782 " model vdw 2.136 2.510 ... (remaining 560310 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.480 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: 0.060 Extract box with map and model: 27.860 Check model and map are aligned: 0.740 Set scattering table: 0.500 Process input model: 222.200 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 274.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 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 : 0.007 0.062 69090 Z= 0.459 Angle : 1.282 11.917 94172 Z= 0.749 Chirality : 0.071 0.569 10476 Planarity : 0.014 0.304 12438 Dihedral : 12.127 89.758 26160 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.43 % Allowed : 5.10 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.09), residues: 8748 helix: -4.03 (0.16), residues: 242 sheet: 0.37 (0.10), residues: 2458 loop : -0.86 (0.08), residues: 6048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.008 TRP A 85 HIS 0.043 0.006 HIS A1075 PHE 0.070 0.008 PHE A2787 TYR 0.074 0.009 TYR A2482 ARG 0.072 0.005 ARG B3350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 5.819 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 2630 MET cc_start: 0.5938 (mmm) cc_final: 0.5736 (mmm) REVERT: B 2630 MET cc_start: 0.5936 (mmm) cc_final: 0.5735 (mmm) outliers start: 30 outliers final: 10 residues processed: 303 average time/residue: 1.4477 time to fit residues: 595.4095 Evaluate side-chains 158 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3072 THR Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 3072 THR Chi-restraints excluded: chain B residue 3076 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 738 optimal weight: 8.9990 chunk 662 optimal weight: 0.7980 chunk 367 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 446 optimal weight: 7.9990 chunk 353 optimal weight: 30.0000 chunk 685 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 416 optimal weight: 0.6980 chunk 509 optimal weight: 0.9980 chunk 793 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 431 HIS A 826 ASN A1363 HIS A1673 HIS ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2263 HIS A4185 GLN A4206 GLN B 129 HIS B 431 HIS B 826 ASN B1363 HIS B1673 HIS ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2263 HIS B4185 GLN B4206 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 69090 Z= 0.266 Angle : 0.666 10.521 94172 Z= 0.354 Chirality : 0.048 0.402 10476 Planarity : 0.004 0.075 12438 Dihedral : 6.960 59.770 12086 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.30 % Allowed : 7.56 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 8748 helix: -3.46 (0.22), residues: 230 sheet: 0.26 (0.10), residues: 2536 loop : -0.20 (0.09), residues: 5982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B2527 HIS 0.005 0.001 HIS B1645 PHE 0.023 0.002 PHE B2884 TYR 0.016 0.002 TYR A3136 ARG 0.006 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 157 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 17 residues processed: 229 average time/residue: 1.3037 time to fit residues: 419.5691 Evaluate side-chains 159 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 5.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 2707 THR Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 441 optimal weight: 9.9990 chunk 246 optimal weight: 0.4980 chunk 660 optimal weight: 3.9990 chunk 540 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 795 optimal weight: 6.9990 chunk 858 optimal weight: 1.9990 chunk 708 optimal weight: 10.0000 chunk 788 optimal weight: 0.9980 chunk 271 optimal weight: 20.0000 chunk 637 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 69090 Z= 0.166 Angle : 0.575 9.694 94172 Z= 0.304 Chirality : 0.046 0.320 10476 Planarity : 0.004 0.051 12438 Dihedral : 6.397 56.061 12080 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.48 % Allowed : 7.92 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.09), residues: 8748 helix: -3.14 (0.24), residues: 254 sheet: 0.29 (0.10), residues: 2510 loop : -0.05 (0.09), residues: 5984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 930 HIS 0.003 0.001 HIS A1647 PHE 0.019 0.001 PHE B2884 TYR 0.017 0.001 TYR A3136 ARG 0.012 0.000 ARG B 931 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 155 time to evaluate : 5.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3857 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8537 (mt) REVERT: B 3857 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8534 (mt) outliers start: 102 outliers final: 28 residues processed: 240 average time/residue: 1.2277 time to fit residues: 419.1011 Evaluate side-chains 175 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3857 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3857 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 785 optimal weight: 9.9990 chunk 597 optimal weight: 0.0370 chunk 412 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 379 optimal weight: 9.9990 chunk 533 optimal weight: 5.9990 chunk 797 optimal weight: 20.0000 chunk 844 optimal weight: 2.9990 chunk 416 optimal weight: 0.8980 chunk 756 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 833 HIS ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 69090 Z= 0.227 Angle : 0.566 9.707 94172 Z= 0.295 Chirality : 0.046 0.286 10476 Planarity : 0.004 0.048 12438 Dihedral : 6.231 55.981 12080 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.26 % Allowed : 8.91 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 8748 helix: -2.82 (0.28), residues: 218 sheet: 0.19 (0.10), residues: 2474 loop : -0.01 (0.09), residues: 6056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 930 HIS 0.003 0.001 HIS B 602 PHE 0.017 0.001 PHE B2884 TYR 0.015 0.001 TYR A3136 ARG 0.004 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 142 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3857 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8608 (mt) REVERT: B 3857 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (mt) outliers start: 87 outliers final: 29 residues processed: 217 average time/residue: 1.2449 time to fit residues: 385.2583 Evaluate side-chains 169 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2707 THR Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3857 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3857 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 703 optimal weight: 50.0000 chunk 479 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 629 optimal weight: 3.9990 chunk 348 optimal weight: 0.6980 chunk 720 optimal weight: 10.0000 chunk 583 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 431 optimal weight: 7.9990 chunk 758 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 overall best weight: 3.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4145 GLN B4145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 69090 Z= 0.315 Angle : 0.583 10.082 94172 Z= 0.304 Chirality : 0.046 0.253 10476 Planarity : 0.004 0.046 12438 Dihedral : 6.178 56.317 12080 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.51 % Allowed : 9.56 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8748 helix: -2.63 (0.28), residues: 230 sheet: -0.11 (0.10), residues: 2638 loop : -0.06 (0.09), residues: 5880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 930 HIS 0.005 0.001 HIS A2195 PHE 0.014 0.002 PHE B2884 TYR 0.016 0.001 TYR B 765 ARG 0.005 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 139 time to evaluate : 5.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3857 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 3857 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8571 (mt) outliers start: 104 outliers final: 36 residues processed: 224 average time/residue: 1.2224 time to fit residues: 392.1726 Evaluate side-chains 172 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1793 ILE Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2690 ASN Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3683 HIS Chi-restraints excluded: chain A residue 3857 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1793 ILE Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3857 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 284 optimal weight: 0.5980 chunk 760 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 496 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 845 optimal weight: 0.9990 chunk 701 optimal weight: 20.0000 chunk 391 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 443 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2446 GLN ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 69090 Z= 0.194 Angle : 0.542 9.999 94172 Z= 0.281 Chirality : 0.045 0.314 10476 Planarity : 0.004 0.043 12438 Dihedral : 5.987 57.196 12080 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.30 % Allowed : 10.18 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8748 helix: -2.53 (0.29), residues: 218 sheet: -0.20 (0.10), residues: 2618 loop : -0.02 (0.09), residues: 5912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 930 HIS 0.003 0.001 HIS A3733 PHE 0.014 0.001 PHE B2884 TYR 0.015 0.001 TYR B 765 ARG 0.003 0.000 ARG B2182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 136 time to evaluate : 5.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 957 MET cc_start: 0.7602 (mmm) cc_final: 0.7352 (mmp) REVERT: A 3857 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 957 MET cc_start: 0.7594 (mmm) cc_final: 0.7349 (mmp) REVERT: B 3857 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8556 (mt) outliers start: 90 outliers final: 40 residues processed: 214 average time/residue: 1.2326 time to fit residues: 378.8117 Evaluate side-chains 174 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1566 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2690 ASN Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3734 CYS Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3857 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 2951 SER Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3734 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3857 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 815 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 481 optimal weight: 2.9990 chunk 617 optimal weight: 6.9990 chunk 478 optimal weight: 2.9990 chunk 711 optimal weight: 20.0000 chunk 472 optimal weight: 9.9990 chunk 842 optimal weight: 2.9990 chunk 527 optimal weight: 4.9990 chunk 513 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A 819 GLN ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3801 HIS B 368 HIS B 435 HIS B 819 GLN ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 69090 Z= 0.321 Angle : 0.587 10.564 94172 Z= 0.303 Chirality : 0.046 0.311 10476 Planarity : 0.004 0.045 12438 Dihedral : 6.073 59.707 12080 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.51 % Allowed : 10.27 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.09), residues: 8748 helix: -2.54 (0.29), residues: 230 sheet: -0.37 (0.10), residues: 2652 loop : -0.12 (0.09), residues: 5866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 930 HIS 0.005 0.001 HIS B2195 PHE 0.015 0.001 PHE A4277 TYR 0.016 0.001 TYR B 765 ARG 0.004 0.000 ARG B2182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 132 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3857 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8551 (mt) REVERT: A 3862 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7602 (pp) REVERT: B 3857 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8552 (mt) REVERT: B 3862 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7599 (pp) outliers start: 104 outliers final: 41 residues processed: 216 average time/residue: 1.2518 time to fit residues: 385.2607 Evaluate side-chains 173 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 5.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1566 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1755 ASN Chi-restraints excluded: chain A residue 1793 ILE Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2690 ASN Chi-restraints excluded: chain A residue 2951 SER Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3683 HIS Chi-restraints excluded: chain A residue 3857 ILE Chi-restraints excluded: chain A residue 3862 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1755 ASN Chi-restraints excluded: chain B residue 1793 ILE Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1893 THR Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2951 SER Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3857 ILE Chi-restraints excluded: chain B residue 3862 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 521 optimal weight: 7.9990 chunk 336 optimal weight: 0.8980 chunk 503 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 535 optimal weight: 0.6980 chunk 573 optimal weight: 0.9980 chunk 416 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 662 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 69090 Z= 0.143 Angle : 0.538 11.537 94172 Z= 0.275 Chirality : 0.045 0.481 10476 Planarity : 0.004 0.045 12438 Dihedral : 5.754 55.815 12078 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.03 % Allowed : 11.01 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.09), residues: 8748 helix: -2.44 (0.30), residues: 218 sheet: -0.29 (0.10), residues: 2568 loop : -0.08 (0.09), residues: 5962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 930 HIS 0.004 0.000 HIS A2403 PHE 0.018 0.001 PHE A1474 TYR 0.016 0.001 TYR B 765 ARG 0.002 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 130 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3857 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8454 (mt) REVERT: A 3862 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7607 (pp) REVERT: B 3857 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 3862 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7605 (pp) outliers start: 71 outliers final: 39 residues processed: 191 average time/residue: 1.3290 time to fit residues: 356.0335 Evaluate side-chains 173 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 5.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1566 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2319 ASP Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2690 ASN Chi-restraints excluded: chain A residue 2951 SER Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3857 ILE Chi-restraints excluded: chain A residue 3862 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2319 ASP Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 2951 SER Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3857 ILE Chi-restraints excluded: chain B residue 3862 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 766 optimal weight: 8.9990 chunk 807 optimal weight: 1.9990 chunk 736 optimal weight: 6.9990 chunk 785 optimal weight: 3.9990 chunk 806 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 616 optimal weight: 8.9990 chunk 240 optimal weight: 8.9990 chunk 709 optimal weight: 6.9990 chunk 742 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A1295 ASN ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2084 HIS A2403 HIS A3599 ASN ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2084 HIS B2403 HIS B3599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 69090 Z= 0.417 Angle : 0.628 12.979 94172 Z= 0.322 Chirality : 0.047 0.468 10476 Planarity : 0.004 0.044 12438 Dihedral : 6.079 56.829 12078 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.13 % Allowed : 10.92 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.09), residues: 8748 helix: -2.36 (0.31), residues: 218 sheet: -0.53 (0.10), residues: 2604 loop : -0.19 (0.09), residues: 5926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 930 HIS 0.007 0.001 HIS A2195 PHE 0.017 0.002 PHE B4277 TYR 0.016 0.002 TYR B 765 ARG 0.005 0.001 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 128 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3674 MET cc_start: 0.6490 (mmm) cc_final: 0.6176 (mmp) REVERT: A 3862 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7715 (pp) REVERT: A 4041 MET cc_start: 0.7260 (ppp) cc_final: 0.7048 (ppp) REVERT: B 3862 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7710 (pp) REVERT: B 4041 MET cc_start: 0.7262 (ppp) cc_final: 0.7049 (ppp) outliers start: 78 outliers final: 46 residues processed: 194 average time/residue: 1.3394 time to fit residues: 364.4955 Evaluate side-chains 176 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1566 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1755 ASN Chi-restraints excluded: chain A residue 1793 ILE Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2319 ASP Chi-restraints excluded: chain A residue 2690 ASN Chi-restraints excluded: chain A residue 2951 SER Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3637 CYS Chi-restraints excluded: chain A residue 3734 CYS Chi-restraints excluded: chain A residue 3862 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1755 ASN Chi-restraints excluded: chain B residue 1793 ILE Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2319 ASP Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3637 CYS Chi-restraints excluded: chain B residue 3734 CYS Chi-restraints excluded: chain B residue 3862 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 782 optimal weight: 20.0000 chunk 515 optimal weight: 5.9990 chunk 830 optimal weight: 1.9990 chunk 506 optimal weight: 0.0770 chunk 393 optimal weight: 3.9990 chunk 577 optimal weight: 9.9990 chunk 870 optimal weight: 3.9990 chunk 801 optimal weight: 0.8980 chunk 693 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 535 optimal weight: 0.3980 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2403 HIS ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 69090 Z= 0.172 Angle : 0.549 12.789 94172 Z= 0.280 Chirality : 0.046 0.672 10476 Planarity : 0.004 0.046 12438 Dihedral : 5.802 55.602 12078 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.83 % Allowed : 11.30 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.09), residues: 8748 helix: -2.30 (0.32), residues: 206 sheet: -0.47 (0.10), residues: 2544 loop : -0.11 (0.09), residues: 5998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 930 HIS 0.004 0.001 HIS A2403 PHE 0.013 0.001 PHE B2884 TYR 0.017 0.001 TYR B 765 ARG 0.003 0.000 ARG A3017 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 5.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3674 MET cc_start: 0.6493 (mmm) cc_final: 0.6208 (mmp) REVERT: A 3862 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7703 (pp) REVERT: B 3674 MET cc_start: 0.6420 (mmm) cc_final: 0.6040 (mmp) REVERT: B 3862 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7672 (pp) outliers start: 57 outliers final: 42 residues processed: 180 average time/residue: 1.3690 time to fit residues: 347.4643 Evaluate side-chains 172 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 5.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1566 ASP Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 2319 ASP Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2951 SER Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3637 CYS Chi-restraints excluded: chain A residue 3734 CYS Chi-restraints excluded: chain A residue 3862 ILE Chi-restraints excluded: chain A residue 4036 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain B residue 1175 CYS Chi-restraints excluded: chain B residue 1214 CYS Chi-restraints excluded: chain B residue 1518 ASP Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1710 CYS Chi-restraints excluded: chain B residue 1984 ILE Chi-restraints excluded: chain B residue 2319 ASP Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3467 MET Chi-restraints excluded: chain B residue 3637 CYS Chi-restraints excluded: chain B residue 3734 CYS Chi-restraints excluded: chain B residue 3862 ILE Chi-restraints excluded: chain B residue 4036 ASP Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 425 optimal weight: 3.9990 chunk 550 optimal weight: 6.9990 chunk 738 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 639 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 192 optimal weight: 10.0000 chunk 694 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS A3387 HIS ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS B3387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.059754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.040267 restraints weight = 392603.761| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.59 r_work: 0.2938 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 69090 Z= 0.318 Angle : 0.585 13.055 94172 Z= 0.298 Chirality : 0.045 0.511 10476 Planarity : 0.004 0.044 12438 Dihedral : 5.909 55.416 12078 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.81 % Allowed : 11.37 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.09), residues: 8748 helix: -2.31 (0.31), residues: 218 sheet: -0.55 (0.10), residues: 2548 loop : -0.18 (0.09), residues: 5982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 930 HIS 0.005 0.001 HIS A2195 PHE 0.013 0.001 PHE A 604 TYR 0.016 0.001 TYR B 765 ARG 0.004 0.000 ARG A 678 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13061.72 seconds wall clock time: 232 minutes 9.15 seconds (13929.15 seconds total)