Starting phenix.real_space_refine on Wed Feb 14 08:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/02_2024/8em4_28233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/02_2024/8em4_28233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/02_2024/8em4_28233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/02_2024/8em4_28233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/02_2024/8em4_28233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/02_2024/8em4_28233_updated.pdb" } resolution = 2.83 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= 0.058 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 84 9.91 5 S 604 5.16 5 C 36772 2.51 5 N 10348 2.21 5 O 11602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3323": "OE1" <-> "OE2" Residue "A PHE 3393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3323": "OE1" <-> "OE2" Residue "B PHE 3393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4091": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 59410 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 29005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3818, 29005 Classifications: {'peptide': 3818} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PCIS': 4, 'PTRANS': 185, 'TRANS': 3628} Chain breaks: 5 Unresolved non-hydrogen bonds: 920 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 732 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 17, 'HIS:plan': 14, 'PHE:plan': 5, 'GLU:plan': 47, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 637 Chain: "B" Number of atoms: 29005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3818, 29005 Classifications: {'peptide': 3818} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PCIS': 4, 'PTRANS': 185, 'TRANS': 3628} Chain breaks: 5 Unresolved non-hydrogen bonds: 920 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 732 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 17, 'HIS:plan': 14, 'PHE:plan': 5, 'GLU:plan': 47, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 637 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 672 Unusual residues: {' CA': 42, 'NAG': 29, 'NGA': 16} Classifications: {'undetermined': 87} Link IDs: {None: 86} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 45 Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 672 Unusual residues: {' CA': 42, 'NAG': 29, 'NGA': 16} Classifications: {'undetermined': 87} Link IDs: {None: 86} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 45 Time building chain proxies: 23.12, per 1000 atoms: 0.39 Number of scatterers: 59410 At special positions: 0 Unit cell: (240.84, 223.56, 287.28, 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 84 19.99 S 604 16.00 O 11602 8.00 N 10348 7.00 C 36772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=240, 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=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 103 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.04 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=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.02 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.02 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.04 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.03 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.02 Simple disulfide: pdb=" SG CYS A1354 " - pdb=" SG CYS A1365 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A1416 " - pdb=" SG CYS A1429 " distance=2.04 Simple disulfide: pdb=" SG CYS A1705 " - pdb=" SG CYS A1714 " distance=2.03 Simple disulfide: pdb=" SG CYS A1710 " - pdb=" SG CYS A1726 " distance=2.04 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1741 " distance=2.03 Simple disulfide: pdb=" SG CYS A2023 " - pdb=" SG CYS A2034 " distance=2.03 Simple disulfide: pdb=" SG CYS A2030 " - pdb=" SG CYS A2044 " distance=2.03 Simple disulfide: pdb=" SG CYS A2046 " - pdb=" SG CYS A2059 " distance=2.02 Simple disulfide: pdb=" SG CYS A2347 " - pdb=" SG CYS A2358 " distance=2.03 Simple disulfide: pdb=" SG CYS A2354 " - pdb=" SG CYS A2369 " distance=2.03 Simple disulfide: pdb=" SG CYS A2371 " - pdb=" SG CYS A2383 " distance=2.03 Simple disulfide: pdb=" SG CYS A2518 " - pdb=" SG CYS A2652 " distance=2.03 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2667 " distance=2.03 Simple disulfide: pdb=" SG CYS A2663 " - pdb=" SG CYS A2676 " distance=2.03 Simple disulfide: pdb=" SG CYS A2678 " - pdb=" SG CYS A2693 " distance=2.03 Simple disulfide: pdb=" SG CYS A2701 " - pdb=" SG CYS A2713 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A3034 " - pdb=" SG CYS A3046 " distance=2.03 Simple disulfide: pdb=" SG CYS A3041 " - pdb=" SG CYS A3059 " distance=2.04 Simple disulfide: pdb=" SG CYS A3053 " - pdb=" SG CYS A3070 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.03 Simple disulfide: pdb=" SG CYS A3313 " - pdb=" SG CYS A3321 " distance=1.97 Simple disulfide: pdb=" SG CYS A3471 " - pdb=" SG CYS A3482 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A3637 " - pdb=" SG CYS A3649 " distance=2.02 Simple disulfide: pdb=" SG CYS A3644 " - pdb=" SG CYS A3662 " distance=2.03 Simple disulfide: pdb=" SG CYS A3656 " - pdb=" SG CYS A3673 " distance=2.03 Simple disulfide: pdb=" SG CYS A3680 " - pdb=" SG CYS A3694 " distance=2.03 Simple disulfide: pdb=" SG CYS A3688 " - pdb=" SG CYS A3707 " distance=2.03 Simple disulfide: pdb=" SG CYS A3701 " - pdb=" SG CYS A3716 " distance=2.03 Simple disulfide: pdb=" SG CYS A3721 " - pdb=" SG CYS A3734 " distance=2.03 Simple disulfide: pdb=" SG CYS A3729 " - pdb=" SG CYS A3747 " distance=2.04 Simple disulfide: pdb=" SG CYS A3741 " - pdb=" SG CYS A3756 " distance=2.01 Simple disulfide: pdb=" SG CYS A3761 " - pdb=" SG CYS A3773 " distance=2.03 Simple disulfide: pdb=" SG CYS A3768 " - pdb=" SG CYS A3786 " distance=2.03 Simple disulfide: pdb=" SG CYS A3780 " - pdb=" SG CYS A3795 " distance=2.03 Simple disulfide: pdb=" SG CYS A3800 " - pdb=" SG CYS A3812 " distance=2.02 Simple disulfide: pdb=" SG CYS A3807 " - pdb=" SG CYS A3825 " distance=2.04 Simple disulfide: pdb=" SG CYS A3819 " - pdb=" SG CYS A3834 " distance=2.02 Simple disulfide: pdb=" SG CYS A3844 " - pdb=" SG CYS A3856 " distance=2.03 Simple disulfide: pdb=" SG CYS A3851 " - pdb=" SG CYS A3869 " distance=2.03 Simple disulfide: pdb=" SG CYS A3863 " - pdb=" SG CYS A3880 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A4034 " - pdb=" SG CYS A4049 " distance=2.04 Simple disulfide: pdb=" SG CYS A4336 " - pdb=" SG CYS A4344 " distance=2.03 Simple disulfide: pdb=" SG CYS A4340 " - pdb=" SG CYS A4353 " distance=2.03 Simple disulfide: pdb=" SG CYS A4355 " - pdb=" SG CYS A4369 " distance=2.03 Simple disulfide: pdb=" SG CYS A4383 " - pdb=" SG CYS A4391 " distance=2.03 Simple disulfide: pdb=" SG CYS A4385 " - pdb=" SG CYS A4401 " distance=2.03 Simple disulfide: pdb=" SG CYS A4403 " - pdb=" SG CYS A4412 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 103 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 291 " distance=2.04 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=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 673 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 999 " - pdb=" SG CYS B1012 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1037 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1050 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1059 " distance=2.02 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1079 " distance=2.02 Simple disulfide: pdb=" SG CYS B1073 " - pdb=" SG CYS B1092 " distance=2.04 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B1110 " - pdb=" SG CYS B1122 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1157 " - pdb=" SG CYS B1175 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1184 " distance=2.03 Simple disulfide: pdb=" SG CYS B1188 " - pdb=" SG CYS B1201 " distance=2.03 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG CYS B1214 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B1251 " - pdb=" SG CYS B1267 " distance=2.02 Simple disulfide: pdb=" SG CYS B1354 " - pdb=" SG CYS B1365 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B1416 " - pdb=" SG CYS B1429 " distance=2.04 Simple disulfide: pdb=" SG CYS B1705 " - pdb=" SG CYS B1714 " distance=2.03 Simple disulfide: pdb=" SG CYS B1710 " - pdb=" SG CYS B1726 " distance=2.04 Simple disulfide: pdb=" SG CYS B1728 " - pdb=" SG CYS B1741 " distance=2.03 Simple disulfide: pdb=" SG CYS B2023 " - pdb=" SG CYS B2034 " distance=2.03 Simple disulfide: pdb=" SG CYS B2030 " - pdb=" SG CYS B2044 " distance=2.03 Simple disulfide: pdb=" SG CYS B2046 " - pdb=" SG CYS B2059 " distance=2.02 Simple disulfide: pdb=" SG CYS B2347 " - pdb=" SG CYS B2358 " distance=2.03 Simple disulfide: pdb=" SG CYS B2354 " - pdb=" SG CYS B2369 " distance=2.03 Simple disulfide: pdb=" SG CYS B2371 " - pdb=" SG CYS B2383 " distance=2.03 Simple disulfide: pdb=" SG CYS B2518 " - pdb=" SG CYS B2652 " distance=2.03 Simple disulfide: pdb=" SG CYS B2656 " - pdb=" SG CYS B2667 " distance=2.03 Simple disulfide: pdb=" SG CYS B2663 " - pdb=" SG CYS B2676 " distance=2.03 Simple disulfide: pdb=" SG CYS B2678 " - pdb=" SG CYS B2693 " distance=2.03 Simple disulfide: pdb=" SG CYS B2701 " - pdb=" SG CYS B2713 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B3034 " - pdb=" SG CYS B3046 " distance=2.03 Simple disulfide: pdb=" SG CYS B3041 " - pdb=" SG CYS B3059 " distance=2.04 Simple disulfide: pdb=" SG CYS B3053 " - pdb=" SG CYS B3070 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B3180 " - pdb=" SG CYS B3193 " distance=2.03 Simple disulfide: pdb=" SG CYS B3313 " - pdb=" SG CYS B3321 " distance=1.97 Simple disulfide: pdb=" SG CYS B3471 " - pdb=" SG CYS B3482 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B3637 " - pdb=" SG CYS B3649 " distance=2.02 Simple disulfide: pdb=" SG CYS B3644 " - pdb=" SG CYS B3662 " distance=2.03 Simple disulfide: pdb=" SG CYS B3656 " - pdb=" SG CYS B3673 " distance=2.03 Simple disulfide: pdb=" SG CYS B3680 " - pdb=" SG CYS B3694 " distance=2.03 Simple disulfide: pdb=" SG CYS B3688 " - pdb=" SG CYS B3707 " distance=2.03 Simple disulfide: pdb=" SG CYS B3701 " - pdb=" SG CYS B3716 " distance=2.03 Simple disulfide: pdb=" SG CYS B3721 " - pdb=" SG CYS B3734 " distance=2.03 Simple disulfide: pdb=" SG CYS B3729 " - pdb=" SG CYS B3747 " distance=2.04 Simple disulfide: pdb=" SG CYS B3741 " - pdb=" SG CYS B3756 " distance=2.01 Simple disulfide: pdb=" SG CYS B3761 " - pdb=" SG CYS B3773 " distance=2.03 Simple disulfide: pdb=" SG CYS B3768 " - pdb=" SG CYS B3786 " distance=2.03 Simple disulfide: pdb=" SG CYS B3780 " - pdb=" SG CYS B3795 " distance=2.03 Simple disulfide: pdb=" SG CYS B3800 " - pdb=" SG CYS B3812 " distance=2.02 Simple disulfide: pdb=" SG CYS B3807 " - pdb=" SG CYS B3825 " distance=2.04 Simple disulfide: pdb=" SG CYS B3819 " - pdb=" SG CYS B3834 " distance=2.02 Simple disulfide: pdb=" SG CYS B3844 " - pdb=" SG CYS B3856 " distance=2.03 Simple disulfide: pdb=" SG CYS B3851 " - pdb=" SG CYS B3869 " distance=2.03 Simple disulfide: pdb=" SG CYS B3863 " - pdb=" SG CYS B3880 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B4034 " - pdb=" SG CYS B4049 " distance=2.04 Simple disulfide: pdb=" SG CYS B4336 " - pdb=" SG CYS B4344 " distance=2.03 Simple disulfide: pdb=" SG CYS B4340 " - pdb=" SG CYS B4353 " distance=2.03 Simple disulfide: pdb=" SG CYS B4355 " - pdb=" SG CYS B4369 " distance=2.03 Simple disulfide: pdb=" SG CYS B4383 " - pdb=" SG CYS B4391 " distance=2.03 Simple disulfide: pdb=" SG CYS B4385 " - pdb=" SG CYS B4401 " distance=2.03 Simple disulfide: pdb=" SG CYS B4403 " - pdb=" SG CYS B4412 " distance=2.03 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=32, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A4702 " - " ASN A 340 " " NAG A4703 " - " ASN A 387 " " NAG A4704 " - " ASN A 462 " " NAG A4705 " - " ASN A 657 " " NAG A4706 " - " ASN A 865 " " NAG A4707 " - " ASN A1187 " " 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 A2548 " " NAG A4719 " - " ASN A3127 " " NAG A4720 " - " ASN A3213 " " NAG A4721 " - " ASN A3259 " " NAG A4722 " - " ASN A3317 " " NAG A4723 " - " ASN A3357 " " NAG A4724 " - " ASN A3448 " " NAG A4725 " - " ASN A3566 " " NAG A4726 " - " ASN A3682 " " NAG A4727 " - " ASN A3840 " " NAG A4728 " - " ASN A4070 " " NAG A4729 " - " ASN A4329 " " NAG A4787 " - " ASN A2488 " " NAG B4701 " - " ASN B4329 " " NAG B4706 " - " ASN B3127 " " NAG B4708 " - " ASN B1187 " " NAG B4709 " - " ASN B1676 " " NAG B4710 " - " ASN B2134 " " NAG B4711 " - " ASN B 657 " " NAG B4714 " - " ASN B1384 " " NAG B4717 " - " ASN B3840 " " NAG B4718 " - " ASN B1497 " " NAG B4719 " - " ASN B3259 " " NAG B4720 " - " ASN B1811 " " NAG B4722 " - " ASN B 865 " " NAG B4723 " - " ASN B1733 " " NAG B4727 " - " ASN B4070 " " NAG B4728 " - " ASN B3213 " " NAG B4730 " - " ASN B3357 " " NAG B4731 " - " ASN B3566 " " NAG B4733 " - " ASN B2396 " " NAG B4734 " - " ASN B 340 " " NAG B4735 " - " ASN B2225 " " NAG B4736 " - " ASN B3682 " " NAG B4739 " - " ASN B 387 " " NAG B4741 " - " ASN B3317 " " NAG B4742 " - " ASN B2488 " " NAG B4744 " - " ASN B1451 " " NAG B4748 " - " ASN B3448 " " NAG B4776 " - " ASN B 462 " " NAG B4778 " - " ASN B2548 " " NAG B4785 " - " ASN B1551 " " NAG C 1 " - " ASN A2178 " " NAG D 1 " - " ASN B2178 " Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.41 Conformation dependent library (CDL) restraints added in 8.7 seconds 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 198 sheets defined 5.8% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 27.41 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 83 through 87 removed outlier: 3.566A pdb=" N CYS A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.084A pdb=" N CYS A 241 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.655A pdb=" N ILE A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 313' Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' 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 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 979 through 982 Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1096 through 1099 No H-bonds generated for 'chain 'A' and resid 1096 through 1099' Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1204 through 1206 No H-bonds generated for 'chain 'A' and resid 1204 through 1206' Processing helix chain 'A' and resid 1215 through 1221 removed outlier: 4.277A pdb=" N SER A1218 " --> pdb=" O LYS A1215 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP A1219 " --> pdb=" O ASP A1216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A1221 " --> pdb=" O SER A1218 " (cutoff:3.500A) 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 1261 through 1263 No H-bonds generated for 'chain 'A' and resid 1261 through 1263' Processing helix chain 'A' and resid 1352 through 1360 removed outlier: 3.803A pdb=" N PHE A1357 " --> pdb=" O CYS A1354 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN A1358 " --> pdb=" O LEU A1355 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A1359 " --> pdb=" O HIS A1356 " (cutoff:3.500A) 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 1704 through 1707 removed outlier: 3.926A pdb=" N SER A1707 " --> pdb=" O PRO A1704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1704 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 2120 through 2122 No H-bonds generated for 'chain 'A' and resid 2120 through 2122' 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 2659 through 2662 Processing helix chain 'A' and resid 2716 through 2718 No H-bonds generated for 'chain 'A' and resid 2716 through 2718' Processing helix chain 'A' and resid 2729 through 2732 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 2770 through 2773 Processing helix chain 'A' and resid 3049 through 3051 No H-bonds generated for 'chain 'A' and resid 3049 through 3051' Processing helix chain 'A' and resid 3063 through 3065 No H-bonds generated for 'chain 'A' and resid 3063 through 3065' 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 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 3473 through 3477 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 3572 No H-bonds generated for 'chain 'A' and resid 3570 through 3572' Processing helix chain 'A' and resid 3584 through 3586 No H-bonds generated for 'chain 'A' and resid 3584 through 3586' 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 3629 through 3634 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 3665 through 3667 No H-bonds generated for 'chain 'A' and resid 3665 through 3667' 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 3699 No H-bonds generated for 'chain 'A' and resid 3697 through 3699' Processing helix chain 'A' and resid 3711 through 3713 No H-bonds generated for 'chain 'A' and resid 3711 through 3713' Processing helix chain 'A' and resid 3716 through 3718 No H-bonds generated for 'chain 'A' and resid 3716 through 3718' Processing helix chain 'A' and resid 3776 through 3778 No H-bonds generated for 'chain 'A' and resid 3776 through 3778' Processing helix chain 'A' and resid 3790 through 3792 No H-bonds generated for 'chain 'A' and resid 3790 through 3792' Processing helix chain 'A' and resid 3795 through 3797 No H-bonds generated for 'chain 'A' and resid 3795 through 3797' 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 3859 through 3861 No H-bonds generated for 'chain 'A' and resid 3859 through 3861' 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 83 through 87 removed outlier: 3.566A pdb=" N CYS B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 237 through 241 removed outlier: 4.084A pdb=" N CYS B 241 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.655A pdb=" N ILE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 652 through 654 No H-bonds generated for 'chain 'B' and resid 652 through 654' 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 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 979 through 982 Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1082 through 1085 Processing helix chain 'B' and resid 1096 through 1099 No H-bonds generated for 'chain 'B' and resid 1096 through 1099' Processing helix chain 'B' and resid 1125 through 1127 No H-bonds generated for 'chain 'B' and resid 1125 through 1127' Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1204 through 1206 No H-bonds generated for 'chain 'B' and resid 1204 through 1206' Processing helix chain 'B' and resid 1215 through 1221 removed outlier: 4.277A pdb=" N SER B1218 " --> pdb=" O LYS B1215 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP B1219 " --> pdb=" O ASP B1216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B1221 " --> pdb=" O SER B1218 " (cutoff:3.500A) 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 1261 through 1263 No H-bonds generated for 'chain 'B' and resid 1261 through 1263' Processing helix chain 'B' and resid 1352 through 1360 removed outlier: 3.803A pdb=" N PHE B1357 " --> pdb=" O CYS B1354 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B1358 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY B1359 " --> pdb=" O HIS B1356 " (cutoff:3.500A) 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 1704 through 1707 removed outlier: 3.926A pdb=" N SER B1707 " --> pdb=" O PRO B1704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1704 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 2120 through 2122 No H-bonds generated for 'chain 'B' and resid 2120 through 2122' 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 2659 through 2662 Processing helix chain 'B' and resid 2716 through 2718 No H-bonds generated for 'chain 'B' and resid 2716 through 2718' Processing helix chain 'B' and resid 2729 through 2732 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 2770 through 2773 Processing helix chain 'B' and resid 3049 through 3051 No H-bonds generated for 'chain 'B' and resid 3049 through 3051' Processing helix chain 'B' and resid 3063 through 3065 No H-bonds generated for 'chain 'B' and resid 3063 through 3065' 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 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 3473 through 3477 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 3572 No H-bonds generated for 'chain 'B' and resid 3570 through 3572' Processing helix chain 'B' and resid 3584 through 3586 No H-bonds generated for 'chain 'B' and resid 3584 through 3586' 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 3629 through 3634 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 3665 through 3667 No H-bonds generated for 'chain 'B' and resid 3665 through 3667' 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 3699 No H-bonds generated for 'chain 'B' and resid 3697 through 3699' Processing helix chain 'B' and resid 3711 through 3713 No H-bonds generated for 'chain 'B' and resid 3711 through 3713' Processing helix chain 'B' and resid 3716 through 3718 No H-bonds generated for 'chain 'B' and resid 3716 through 3718' Processing helix chain 'B' and resid 3776 through 3778 No H-bonds generated for 'chain 'B' and resid 3776 through 3778' Processing helix chain 'B' and resid 3790 through 3792 No H-bonds generated for 'chain 'B' and resid 3790 through 3792' Processing helix chain 'B' and resid 3795 through 3797 No H-bonds generated for 'chain 'B' and resid 3795 through 3797' 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 3859 through 3861 No H-bonds generated for 'chain 'B' and resid 3859 through 3861' 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 33 through 35 removed outlier: 3.643A pdb=" N TYR A 39 " --> pdb=" O CYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 71 through 74 Processing sheet with id= C, first strand: chain 'A' and resid 226 through 229 removed outlier: 3.772A pdb=" N GLN A 233 " --> pdb=" O CYS A 229 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 269 through 272 removed outlier: 3.673A pdb=" N CYS A 272 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 277 " --> pdb=" O CYS A 272 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 336 through 338 Processing sheet with id= F, first strand: chain 'A' and resid 360 through 364 Processing sheet with id= G, first strand: chain 'A' and resid 376 through 379 Processing sheet with id= H, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.323A pdb=" N VAL A 405 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE A 415 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP A 407 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE A 413 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 428 through 431 removed outlier: 3.711A pdb=" N LEU A 461 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER A 449 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU A 459 " --> pdb=" O SER A 449 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 471 through 474 removed outlier: 3.648A pdb=" N ILE A 504 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 492 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 502 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 494 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG A 500 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 511 through 517 removed outlier: 6.543A pdb=" N SER A 526 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A 514 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 524 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 516 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A 522 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A 539 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP A 549 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE A 541 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ARG A 547 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 558 through 564 removed outlier: 6.705A pdb=" N VAL A 573 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 561 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR A 571 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 563 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 569 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 582 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR A 592 " --> pdb=" O THR A 582 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 603 through 609 removed outlier: 6.540A pdb=" N THR A 616 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 606 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 614 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU A 608 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS A 625 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL A 636 " --> pdb=" O LYS A 625 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 672 through 675 Processing sheet with id= O, first strand: chain 'A' and resid 694 through 696 Processing sheet with id= P, first strand: chain 'A' and resid 718 through 721 removed outlier: 3.774A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 742 through 748 removed outlier: 6.728A pdb=" N SER A 757 " --> pdb=" O VAL A 743 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 745 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 755 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE A 747 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 753 " --> pdb=" O PHE A 747 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 778 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN A 766 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL A 776 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LYS A 768 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 774 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 785 through 791 removed outlier: 6.432A pdb=" N THR A 800 " --> pdb=" O GLU A 786 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 788 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR A 798 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A 790 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN A 796 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 809 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLN A 819 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS A 811 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG A 817 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 827 through 833 removed outlier: 6.670A pdb=" N SER A 842 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A 830 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE A 840 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 832 " --> pdb=" O TYR A 838 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 838 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG A 852 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TRP A 854 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 860 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 903 through 905 removed outlier: 3.696A pdb=" N GLY A 873 " --> pdb=" O VAL A 886 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 915 through 921 removed outlier: 6.590A pdb=" N THR A 928 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A 918 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE A 926 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 920 " --> pdb=" O ASN A 924 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 950 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 937 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL A 948 " --> pdb=" O ARG A 937 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 986 through 990 removed outlier: 3.529A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id= X, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 3.598A pdb=" N LYS A1036 " --> pdb=" O CYS A1032 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 1070 through 1073 removed outlier: 4.031A pdb=" N GLN A1078 " --> pdb=" O CYS A1073 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 3.888A pdb=" N MET A1121 " --> pdb=" O CYS A1117 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id= AB, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id= AC, first strand: chain 'A' and resid 1364 through 1368 removed outlier: 3.507A pdb=" N ARG A1364 " --> pdb=" O VAL A1375 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A1368 " --> pdb=" O GLY A1371 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 1380 through 1382 Processing sheet with id= AE, first strand: chain 'A' and resid 1404 through 1408 Processing sheet with id= AF, first strand: chain 'A' and resid 1420 through 1422 Processing sheet with id= AG, first strand: chain 'A' and resid 1689 through 1693 removed outlier: 4.124A pdb=" N GLY A1689 " --> pdb=" O ALA A1442 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A1437 " --> pdb=" O ILE A1452 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 1469 through 1475 removed outlier: 6.674A pdb=" N SER A1484 " --> pdb=" O VAL A1470 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A1472 " --> pdb=" O PHE A1482 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A1482 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A1474 " --> pdb=" O ARG A1480 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A1480 " --> pdb=" O PHE A1474 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A1505 " --> pdb=" O THR A1491 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A1493 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL A1503 " --> pdb=" O SER A1493 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 1512 through 1518 removed outlier: 6.775A pdb=" N THR A1527 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A1515 " --> pdb=" O TYR A1525 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A1525 " --> pdb=" O ILE A1515 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A1517 " --> pdb=" O ASN A1523 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A1523 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A1536 " --> pdb=" O VAL A1546 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL A1546 " --> pdb=" O VAL A1536 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS A1538 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG A1544 " --> pdb=" O LYS A1538 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 1555 through 1561 removed outlier: 6.518A pdb=" N SER A1572 " --> pdb=" O ARG A1556 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A1558 " --> pdb=" O PHE A1570 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A1570 " --> pdb=" O LEU A1558 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU A1560 " --> pdb=" O VAL A1568 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A1568 " --> pdb=" O LEU A1560 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG A1582 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL A1592 " --> pdb=" O ARG A1582 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N SER A1584 " --> pdb=" O ARG A1590 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A1590 " --> pdb=" O SER A1584 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 1601 through 1607 removed outlier: 6.810A pdb=" N MET A1616 " --> pdb=" O CYS A1602 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1604 " --> pdb=" O TYR A1614 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR A1614 " --> pdb=" O LEU A1604 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A1606 " --> pdb=" O LEU A1612 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A1612 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A1625 " --> pdb=" O GLN A1635 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN A1635 " --> pdb=" O PHE A1625 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP A1627 " --> pdb=" O ARG A1633 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG A1633 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 1646 through 1652 removed outlier: 6.617A pdb=" N THR A1659 " --> pdb=" O HIS A1647 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A1649 " --> pdb=" O PHE A1657 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE A1657 " --> pdb=" O LEU A1649 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A1651 " --> pdb=" O SER A1655 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A1681 " --> pdb=" O VAL A1666 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A1668 " --> pdb=" O VAL A1679 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A1679 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN A1670 " --> pdb=" O GLN A1677 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLN A1677 " --> pdb=" O ASN A1670 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A' and resid 1713 through 1716 Processing sheet with id= AN, first strand: chain 'A' and resid 1732 through 1734 Processing sheet with id= AO, first strand: chain 'A' and resid 1757 through 1761 Processing sheet with id= AP, first strand: chain 'A' and resid 1785 through 1787 removed outlier: 3.504A pdb=" N ALA A1816 " --> pdb=" O ILE A1802 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG A1804 " --> pdb=" O ALA A1814 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA A1814 " --> pdb=" O ARG A1804 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LYS A1806 " --> pdb=" O ARG A1812 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG A1812 " --> pdb=" O LYS A1806 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'A' and resid 1824 through 1830 removed outlier: 6.471A pdb=" N THR A1839 " --> pdb=" O LEU A1825 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A1827 " --> pdb=" O TYR A1837 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR A1837 " --> pdb=" O LEU A1827 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A1829 " --> pdb=" O ASN A1835 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN A1835 " --> pdb=" O LEU A1829 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A1848 " --> pdb=" O THR A1860 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR A1860 " --> pdb=" O VAL A1848 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A1850 " --> pdb=" O GLY A1858 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY A1858 " --> pdb=" O THR A1850 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 1874 through 1880 removed outlier: 6.588A pdb=" N SER A1889 " --> pdb=" O VAL A1875 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A1877 " --> pdb=" O TYR A1887 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A1887 " --> pdb=" O ILE A1877 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A1879 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS A1885 " --> pdb=" O VAL A1879 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER A1903 " --> pdb=" O ILE A1913 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE A1913 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN A1905 " --> pdb=" O LEU A1911 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A1911 " --> pdb=" O ASN A1905 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'A' and resid 1925 through 1928 removed outlier: 6.372A pdb=" N ARG A1946 " --> pdb=" O ILE A1956 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE A1956 " --> pdb=" O ARG A1946 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'A' and resid 1964 through 1970 removed outlier: 6.534A pdb=" N SER A1977 " --> pdb=" O TRP A1965 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A1967 " --> pdb=" O TYR A1975 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A1975 " --> pdb=" O LEU A1967 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A1969 " --> pdb=" O PHE A1973 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE A1973 " --> pdb=" O VAL A1969 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A1999 " --> pdb=" O ILE A1984 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG A1986 " --> pdb=" O VAL A1997 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A1997 " --> pdb=" O ARG A1986 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ASP A1988 " --> pdb=" O LYS A1995 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS A1995 " --> pdb=" O ASP A1988 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 2033 through 2036 Processing sheet with id= AV, first strand: chain 'A' and resid 2050 through 2052 Processing sheet with id= AW, first strand: chain 'A' and resid 2327 through 2331 Processing sheet with id= AX, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.892A pdb=" N CYS A2113 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A2101 " --> pdb=" O TYR A2111 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A2111 " --> pdb=" O ALA A2101 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL A2103 " --> pdb=" O PHE A2109 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A2109 " --> pdb=" O VAL A2103 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A2127 " --> pdb=" O ASN A2137 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN A2137 " --> pdb=" O ARG A2127 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'A' and resid 2151 through 2154 removed outlier: 6.675A pdb=" N VAL A2174 " --> pdb=" O VAL A2184 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A2184 " --> pdb=" O VAL A2174 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG A2176 " --> pdb=" O ARG A2182 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG A2182 " --> pdb=" O ARG A2176 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 6.180A pdb=" N ALA A2208 " --> pdb=" O ARG A2194 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A2196 " --> pdb=" O PHE A2206 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A2206 " --> pdb=" O ILE A2196 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL A2198 " --> pdb=" O TYR A2204 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR A2204 " --> pdb=" O VAL A2198 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A2230 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A2218 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL A2228 " --> pdb=" O ARG A2218 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'A' and resid 2240 through 2243 removed outlier: 3.698A pdb=" N TYR A2248 " --> pdb=" O ASP A2243 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG A2261 " --> pdb=" O VAL A2271 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL A2271 " --> pdb=" O ARG A2261 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N HIS A2263 " --> pdb=" O SER A2269 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER A2269 " --> pdb=" O HIS A2263 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 6.722A pdb=" N VAL A2294 " --> pdb=" O TYR A2282 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A2284 " --> pdb=" O ILE A2292 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A2292 " --> pdb=" O ILE A2284 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A2286 " --> pdb=" O SER A2290 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER A2290 " --> pdb=" O VAL A2286 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A2318 " --> pdb=" O VAL A2301 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A2303 " --> pdb=" O VAL A2316 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL A2316 " --> pdb=" O GLN A2303 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'A' and resid 2357 through 2359 Processing sheet with id= BD, first strand: chain 'A' and resid 2641 through 2644 Processing sheet with id= BE, first strand: chain 'A' and resid 2426 through 2428 Processing sheet with id= BF, first strand: chain 'A' and resid 2472 through 2475 removed outlier: 6.391A pdb=" N SER A2493 " --> pdb=" O VAL A2503 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL A2503 " --> pdb=" O SER A2493 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA A2495 " --> pdb=" O ARG A2501 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG A2501 " --> pdb=" O ALA A2495 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'A' and resid 2513 through 2516 removed outlier: 6.137A pdb=" N ARG A2535 " --> pdb=" O PRO A2545 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR A2537 " --> pdb=" O ARG A2543 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG A2543 " --> pdb=" O THR A2537 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'A' and resid 2554 through 2560 removed outlier: 6.714A pdb=" N ALA A2569 " --> pdb=" O ASN A2555 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A2557 " --> pdb=" O TYR A2567 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR A2567 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A2559 " --> pdb=" O LEU A2565 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A2565 " --> pdb=" O LEU A2559 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG A2578 " --> pdb=" O VAL A2588 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL A2588 " --> pdb=" O ARG A2578 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR A2580 " --> pdb=" O ARG A2586 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG A2586 " --> pdb=" O THR A2580 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 3.503A pdb=" N LYS A2615 " --> pdb=" O ASP A2610 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A2598 " --> pdb=" O THR A2609 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'A' and resid 2666 through 2668 Processing sheet with id= BK, first strand: chain 'A' and resid 2684 through 2687 Processing sheet with id= BL, first strand: chain 'A' and resid 2705 through 2708 Processing sheet with id= BM, first strand: chain 'A' and resid 2746 through 2749 removed outlier: 3.870A pdb=" N ARG A2753 " --> pdb=" O CYS A2749 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'A' and resid 3038 through 3041 removed outlier: 3.793A pdb=" N GLN A3045 " --> pdb=" O CYS A3041 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'A' and resid 3081 through 3084 removed outlier: 3.562A pdb=" N HIS A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'A' and resid 3127 through 3130 Processing sheet with id= BQ, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id= BR, first strand: chain 'A' and resid 3168 through 3172 Processing sheet with id= BS, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id= BT, first strand: chain 'A' and resid 3456 through 3459 removed outlier: 3.515A pdb=" N LEU A3225 " --> pdb=" O ILE A3211 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN A3213 " --> pdb=" O LEU A3223 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A3223 " --> pdb=" O ASN A3213 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'A' and resid 3231 through 3237 removed outlier: 6.700A pdb=" N ILE A3246 " --> pdb=" O VAL A3232 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A3234 " --> pdb=" O TYR A3244 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR A3244 " --> pdb=" O LEU A3234 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A3236 " --> pdb=" O ARG A3242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A3242 " --> pdb=" O PHE A3236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A3267 " --> pdb=" O ILE A3253 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A3255 " --> pdb=" O THR A3265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR A3265 " --> pdb=" O ARG A3255 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE A3257 " --> pdb=" O GLN A3263 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN A3263 " --> pdb=" O PHE A3257 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 6.809A pdb=" N LEU A3289 " --> pdb=" O GLU A3275 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A3277 " --> pdb=" O TYR A3287 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR A3287 " --> pdb=" O LEU A3277 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A3279 " --> pdb=" O LYS A3285 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A3285 " --> pdb=" O VAL A3279 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A3310 " --> pdb=" O LEU A3296 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A3298 " --> pdb=" O MET A3308 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET A3308 " --> pdb=" O VAL A3298 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP A3300 " --> pdb=" O ARG A3306 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG A3306 " --> pdb=" O ASP A3300 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 6.483A pdb=" N ALA A3340 " --> pdb=" O ARG A3326 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A3328 " --> pdb=" O TYR A3338 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A3338 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU A3330 " --> pdb=" O TYR A3336 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A3336 " --> pdb=" O LEU A3330 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG A3350 " --> pdb=" O VAL A3360 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL A3360 " --> pdb=" O ARG A3350 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'A' and resid 3371 through 3375 removed outlier: 3.671A pdb=" N ALA A3371 " --> pdb=" O ALA A3384 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A3391 " --> pdb=" O TYR A3405 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE A3393 " --> pdb=" O THR A3403 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR A3403 " --> pdb=" O PHE A3393 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP A3395 " --> pdb=" O ARG A3401 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG A3401 " --> pdb=" O ASP A3395 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'A' and resid 3412 through 3418 removed outlier: 6.659A pdb=" N THR A3425 " --> pdb=" O PHE A3413 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A3415 " --> pdb=" O PHE A3423 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A3423 " --> pdb=" O LEU A3415 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A3417 " --> pdb=" O THR A3421 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR A3421 " --> pdb=" O ILE A3417 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A3447 " --> pdb=" O VAL A3432 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A3434 " --> pdb=" O VAL A3445 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL A3445 " --> pdb=" O LYS A3434 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'A' and resid 3481 through 3484 Processing sheet with id= CA, first strand: chain 'A' and resid 3499 through 3504 Processing sheet with id= CB, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id= CC, first strand: chain 'A' and resid 3560 through 3562 removed outlier: 3.643A pdb=" N ASN A3566 " --> pdb=" O CYS A3562 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'A' and resid 3600 through 3602 Processing sheet with id= CE, first strand: chain 'A' and resid 3641 through 3643 Processing sheet with id= CF, first strand: chain 'A' and resid 3685 through 3687 Processing sheet with id= CG, first strand: chain 'A' and resid 3726 through 3729 removed outlier: 3.620A pdb=" N HIS A3733 " --> pdb=" O CYS A3729 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'A' and resid 3765 through 3768 Processing sheet with id= CI, first strand: chain 'A' and resid 3804 through 3806 Processing sheet with id= CJ, first strand: chain 'A' and resid 3849 through 3851 Processing sheet with id= CK, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id= CL, first strand: chain 'A' and resid 4022 through 4026 Processing sheet with id= CM, first strand: chain 'A' and resid 4038 through 4043 removed outlier: 3.563A pdb=" N MET A4041 " --> pdb=" O ARG A4048 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'A' and resid 4321 through 4323 removed outlier: 6.542A pdb=" N LYS A4068 " --> pdb=" O GLU A4078 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU A4078 " --> pdb=" O LYS A4068 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A4070 " --> pdb=" O PHE A4076 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE A4076 " --> pdb=" O ASN A4070 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'A' and resid 4089 through 4092 Processing sheet with id= CP, first strand: chain 'A' and resid 4148 through 4152 removed outlier: 3.554A pdb=" N ASP A4162 " --> pdb=" O ARG A4167 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A4167 " --> pdb=" O ASP A4162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A4182 " --> pdb=" O ILE A4168 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A4170 " --> pdb=" O TRP A4180 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP A4180 " --> pdb=" O VAL A4170 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR A4172 " --> pdb=" O ARG A4178 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG A4178 " --> pdb=" O THR A4172 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 6.621A pdb=" N THR A4204 " --> pdb=" O ALA A4190 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A4192 " --> pdb=" O PHE A4202 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A4202 " --> pdb=" O ILE A4192 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL A4194 " --> pdb=" O LEU A4200 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A4200 " --> pdb=" O VAL A4194 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER A4214 " --> pdb=" O VAL A4224 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A4224 " --> pdb=" O SER A4214 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP A4216 " --> pdb=" O ARG A4222 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A4222 " --> pdb=" O TRP A4216 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'A' and resid 4233 through 4239 removed outlier: 6.692A pdb=" N SER A4249 " --> pdb=" O ASN A4234 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A4236 " --> pdb=" O TYR A4247 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A4247 " --> pdb=" O LEU A4236 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A4238 " --> pdb=" O ARG A4245 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A4245 " --> pdb=" O ILE A4238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A4258 " --> pdb=" O LEU A4268 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU A4268 " --> pdb=" O SER A4258 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS A4260 " --> pdb=" O ARG A4266 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ARG A4266 " --> pdb=" O LYS A4260 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 6.520A pdb=" N VAL A4289 " --> pdb=" O PHE A4277 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A4279 " --> pdb=" O TYR A4287 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A4287 " --> pdb=" O LEU A4279 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE A4281 " --> pdb=" O GLN A4285 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN A4285 " --> pdb=" O ILE A4281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A4311 " --> pdb=" O VAL A4296 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG A4298 " --> pdb=" O LYS A4309 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS A4309 " --> pdb=" O ARG A4298 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id= CU, first strand: chain 'A' and resid 4390 through 4393 Processing sheet with id= CV, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.643A pdb=" N TYR B 39 " --> pdb=" O CYS B 35 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'B' and resid 71 through 74 Processing sheet with id= CX, first strand: chain 'B' and resid 226 through 229 removed outlier: 3.772A pdb=" N GLN B 233 " --> pdb=" O CYS B 229 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'B' and resid 269 through 272 removed outlier: 3.673A pdb=" N CYS B 272 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG B 277 " --> pdb=" O CYS B 272 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'B' and resid 336 through 338 Processing sheet with id= DA, first strand: chain 'B' and resid 360 through 364 Processing sheet with id= DB, first strand: chain 'B' and resid 376 through 379 Processing sheet with id= DC, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.323A pdb=" N VAL B 405 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE B 415 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP B 407 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE B 413 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'B' and resid 428 through 431 removed outlier: 3.711A pdb=" N LEU B 461 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER B 449 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU B 459 " --> pdb=" O SER B 449 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'B' and resid 471 through 474 removed outlier: 3.648A pdb=" N ILE B 504 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 492 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR B 502 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN B 494 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG B 500 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'B' and resid 511 through 517 removed outlier: 6.543A pdb=" N SER B 526 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 514 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE B 524 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 516 " --> pdb=" O TYR B 522 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 522 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG B 539 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP B 549 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE B 541 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ARG B 547 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'B' and resid 558 through 564 removed outlier: 6.705A pdb=" N VAL B 573 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 561 " --> pdb=" O TYR B 571 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR B 571 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 563 " --> pdb=" O ARG B 569 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG B 569 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 582 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR B 592 " --> pdb=" O THR B 582 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'B' and resid 603 through 609 removed outlier: 6.540A pdb=" N THR B 616 " --> pdb=" O PHE B 604 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 606 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE B 614 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU B 608 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS B 625 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL B 636 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'B' and resid 672 through 675 Processing sheet with id= DJ, first strand: chain 'B' and resid 694 through 696 Processing sheet with id= DK, first strand: chain 'B' and resid 718 through 721 removed outlier: 3.774A pdb=" N HIS B 958 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'B' and resid 742 through 748 removed outlier: 6.728A pdb=" N SER B 757 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 745 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE B 755 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE B 747 " --> pdb=" O THR B 753 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR B 753 " --> pdb=" O PHE B 747 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 778 " --> pdb=" O ILE B 764 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN B 766 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL B 776 " --> pdb=" O GLN B 766 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LYS B 768 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS B 774 " --> pdb=" O LYS B 768 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'B' and resid 785 through 791 removed outlier: 6.432A pdb=" N THR B 800 " --> pdb=" O GLU B 786 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 788 " --> pdb=" O TYR B 798 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR B 798 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE B 790 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B 796 " --> pdb=" O PHE B 790 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 809 " --> pdb=" O GLN B 819 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLN B 819 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS B 811 " --> pdb=" O ARG B 817 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG B 817 " --> pdb=" O LYS B 811 " (cutoff:3.500A) Processing sheet with id= DN, first strand: chain 'B' and resid 827 through 833 removed outlier: 6.670A pdb=" N SER B 842 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE B 830 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE B 840 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL B 832 " --> pdb=" O TYR B 838 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR B 838 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG B 852 " --> pdb=" O PRO B 862 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TRP B 854 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 860 " --> pdb=" O TRP B 854 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'B' and resid 903 through 905 removed outlier: 3.696A pdb=" N GLY B 873 " --> pdb=" O VAL B 886 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'B' and resid 915 through 921 removed outlier: 6.590A pdb=" N THR B 928 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 918 " --> pdb=" O PHE B 926 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE B 926 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL B 920 " --> pdb=" O ASN B 924 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 950 " --> pdb=" O ILE B 935 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 937 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B 948 " --> pdb=" O ARG B 937 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'B' and resid 986 through 990 removed outlier: 3.529A pdb=" N GLN B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id= DS, first strand: chain 'B' and resid 1030 through 1032 removed outlier: 3.598A pdb=" N LYS B1036 " --> pdb=" O CYS B1032 " (cutoff:3.500A) Processing sheet with id= DT, first strand: chain 'B' and resid 1070 through 1073 removed outlier: 4.031A pdb=" N GLN B1078 " --> pdb=" O CYS B1073 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 'B' and resid 1114 through 1117 removed outlier: 3.888A pdb=" N MET B1121 " --> pdb=" O CYS B1117 " (cutoff:3.500A) Processing sheet with id= DV, first strand: chain 'B' and resid 1192 through 1194 Processing sheet with id= DW, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id= DX, first strand: chain 'B' and resid 1364 through 1368 removed outlier: 3.507A pdb=" N ARG B1364 " --> pdb=" O VAL B1375 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B1368 " --> pdb=" O GLY B1371 " (cutoff:3.500A) Processing sheet with id= DY, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id= DZ, first strand: chain 'B' and resid 1404 through 1408 Processing sheet with id= EA, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id= EB, first strand: chain 'B' and resid 1689 through 1693 removed outlier: 4.124A pdb=" N GLY B1689 " --> pdb=" O ALA B1442 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B1437 " --> pdb=" O ILE B1452 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain 'B' and resid 1469 through 1475 removed outlier: 6.674A pdb=" N SER B1484 " --> pdb=" O VAL B1470 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B1472 " --> pdb=" O PHE B1482 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE B1482 " --> pdb=" O LEU B1472 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE B1474 " --> pdb=" O ARG B1480 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG B1480 " --> pdb=" O PHE B1474 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B1505 " --> pdb=" O THR B1491 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER B1493 " --> pdb=" O VAL B1503 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL B1503 " --> pdb=" O SER B1493 " (cutoff:3.500A) Processing sheet with id= ED, first strand: chain 'B' and resid 1512 through 1518 removed outlier: 6.775A pdb=" N THR B1527 " --> pdb=" O GLU B1513 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B1515 " --> pdb=" O TYR B1525 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B1525 " --> pdb=" O ILE B1515 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B1517 " --> pdb=" O ASN B1523 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN B1523 " --> pdb=" O VAL B1517 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B1536 " --> pdb=" O VAL B1546 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL B1546 " --> pdb=" O VAL B1536 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS B1538 " --> pdb=" O ARG B1544 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG B1544 " --> pdb=" O LYS B1538 " (cutoff:3.500A) Processing sheet with id= EE, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 6.518A pdb=" N SER B1572 " --> pdb=" O ARG B1556 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU B1558 " --> pdb=" O PHE B1570 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE B1570 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU B1560 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B1568 " --> pdb=" O LEU B1560 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B1582 " --> pdb=" O VAL B1592 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL B1592 " --> pdb=" O ARG B1582 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N SER B1584 " --> pdb=" O ARG B1590 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG B1590 " --> pdb=" O SER B1584 " (cutoff:3.500A) Processing sheet with id= EF, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 6.810A pdb=" N MET B1616 " --> pdb=" O CYS B1602 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B1604 " --> pdb=" O TYR B1614 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR B1614 " --> pdb=" O LEU B1604 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE B1606 " --> pdb=" O LEU B1612 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1612 " --> pdb=" O ILE B1606 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B1625 " --> pdb=" O GLN B1635 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN B1635 " --> pdb=" O PHE B1625 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP B1627 " --> pdb=" O ARG B1633 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG B1633 " --> pdb=" O ASP B1627 " (cutoff:3.500A) Processing sheet with id= EG, first strand: chain 'B' and resid 1646 through 1652 removed outlier: 6.617A pdb=" N THR B1659 " --> pdb=" O HIS B1647 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B1649 " --> pdb=" O PHE B1657 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE B1657 " --> pdb=" O LEU B1649 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU B1651 " --> pdb=" O SER B1655 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B1681 " --> pdb=" O VAL B1666 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN B1668 " --> pdb=" O VAL B1679 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B1679 " --> pdb=" O GLN B1668 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN B1670 " --> pdb=" O GLN B1677 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLN B1677 " --> pdb=" O ASN B1670 " (cutoff:3.500A) Processing sheet with id= EH, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id= EI, first strand: chain 'B' and resid 1732 through 1734 Processing sheet with id= EJ, first strand: chain 'B' and resid 1757 through 1761 Processing sheet with id= EK, first strand: chain 'B' and resid 1785 through 1787 removed outlier: 3.504A pdb=" N ALA B1816 " --> pdb=" O ILE B1802 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG B1804 " --> pdb=" O ALA B1814 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA B1814 " --> pdb=" O ARG B1804 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LYS B1806 " --> pdb=" O ARG B1812 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG B1812 " --> pdb=" O LYS B1806 " (cutoff:3.500A) Processing sheet with id= EL, first strand: chain 'B' and resid 1824 through 1830 removed outlier: 6.471A pdb=" N THR B1839 " --> pdb=" O LEU B1825 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B1827 " --> pdb=" O TYR B1837 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B1837 " --> pdb=" O LEU B1827 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU B1829 " --> pdb=" O ASN B1835 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B1835 " --> pdb=" O LEU B1829 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B1848 " --> pdb=" O THR B1860 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR B1860 " --> pdb=" O VAL B1848 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B1850 " --> pdb=" O GLY B1858 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY B1858 " --> pdb=" O THR B1850 " (cutoff:3.500A) Processing sheet with id= EM, first strand: chain 'B' and resid 1874 through 1880 removed outlier: 6.588A pdb=" N SER B1889 " --> pdb=" O VAL B1875 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B1877 " --> pdb=" O TYR B1887 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR B1887 " --> pdb=" O ILE B1877 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B1879 " --> pdb=" O LYS B1885 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS B1885 " --> pdb=" O VAL B1879 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER B1903 " --> pdb=" O ILE B1913 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B1913 " --> pdb=" O SER B1903 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN B1905 " --> pdb=" O LEU B1911 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B1911 " --> pdb=" O ASN B1905 " (cutoff:3.500A) Processing sheet with id= EN, first strand: chain 'B' and resid 1925 through 1928 removed outlier: 6.372A pdb=" N ARG B1946 " --> pdb=" O ILE B1956 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE B1956 " --> pdb=" O ARG B1946 " (cutoff:3.500A) Processing sheet with id= EO, first strand: chain 'B' and resid 1964 through 1970 removed outlier: 6.534A pdb=" N SER B1977 " --> pdb=" O TRP B1965 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B1967 " --> pdb=" O TYR B1975 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR B1975 " --> pdb=" O LEU B1967 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B1969 " --> pdb=" O PHE B1973 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B1973 " --> pdb=" O VAL B1969 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B1999 " --> pdb=" O ILE B1984 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG B1986 " --> pdb=" O VAL B1997 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B1997 " --> pdb=" O ARG B1986 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ASP B1988 " --> pdb=" O LYS B1995 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS B1995 " --> pdb=" O ASP B1988 " (cutoff:3.500A) Processing sheet with id= EP, first strand: chain 'B' and resid 2033 through 2036 Processing sheet with id= EQ, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id= ER, first strand: chain 'B' and resid 2327 through 2331 Processing sheet with id= ES, first strand: chain 'B' and resid 2098 through 2104 removed outlier: 6.892A pdb=" N CYS B2113 " --> pdb=" O LEU B2099 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B2101 " --> pdb=" O TYR B2111 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B2111 " --> pdb=" O ALA B2101 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B2103 " --> pdb=" O PHE B2109 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE B2109 " --> pdb=" O VAL B2103 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B2127 " --> pdb=" O ASN B2137 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN B2137 " --> pdb=" O ARG B2127 " (cutoff:3.500A) Processing sheet with id= ET, first strand: chain 'B' and resid 2151 through 2154 removed outlier: 6.675A pdb=" N VAL B2174 " --> pdb=" O VAL B2184 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL B2184 " --> pdb=" O VAL B2174 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG B2176 " --> pdb=" O ARG B2182 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B2182 " --> pdb=" O ARG B2176 " (cutoff:3.500A) Processing sheet with id= EU, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 6.180A pdb=" N ALA B2208 " --> pdb=" O ARG B2194 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B2196 " --> pdb=" O PHE B2206 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B2206 " --> pdb=" O ILE B2196 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL B2198 " --> pdb=" O TYR B2204 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR B2204 " --> pdb=" O VAL B2198 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B2230 " --> pdb=" O ILE B2216 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B2218 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B2228 " --> pdb=" O ARG B2218 " (cutoff:3.500A) Processing sheet with id= EV, first strand: chain 'B' and resid 2240 through 2243 removed outlier: 3.698A pdb=" N TYR B2248 " --> pdb=" O ASP B2243 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG B2261 " --> pdb=" O VAL B2271 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL B2271 " --> pdb=" O ARG B2261 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N HIS B2263 " --> pdb=" O SER B2269 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER B2269 " --> pdb=" O HIS B2263 " (cutoff:3.500A) Processing sheet with id= EW, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 6.722A pdb=" N VAL B2294 " --> pdb=" O TYR B2282 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B2284 " --> pdb=" O ILE B2292 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B2292 " --> pdb=" O ILE B2284 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B2286 " --> pdb=" O SER B2290 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B2290 " --> pdb=" O VAL B2286 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B2318 " --> pdb=" O VAL B2301 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN B2303 " --> pdb=" O VAL B2316 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL B2316 " --> pdb=" O GLN B2303 " (cutoff:3.500A) Processing sheet with id= EX, first strand: chain 'B' and resid 2357 through 2359 Processing sheet with id= EY, first strand: chain 'B' and resid 2641 through 2644 Processing sheet with id= EZ, first strand: chain 'B' and resid 2426 through 2428 Processing sheet with id= FA, first strand: chain 'B' and resid 2472 through 2475 removed outlier: 6.391A pdb=" N SER B2493 " --> pdb=" O VAL B2503 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B2503 " --> pdb=" O SER B2493 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA B2495 " --> pdb=" O ARG B2501 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG B2501 " --> pdb=" O ALA B2495 " (cutoff:3.500A) Processing sheet with id= FB, first strand: chain 'B' and resid 2513 through 2516 removed outlier: 6.137A pdb=" N ARG B2535 " --> pdb=" O PRO B2545 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR B2537 " --> pdb=" O ARG B2543 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG B2543 " --> pdb=" O THR B2537 " (cutoff:3.500A) Processing sheet with id= FC, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 6.714A pdb=" N ALA B2569 " --> pdb=" O ASN B2555 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B2557 " --> pdb=" O TYR B2567 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR B2567 " --> pdb=" O LEU B2557 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B2559 " --> pdb=" O LEU B2565 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B2565 " --> pdb=" O LEU B2559 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG B2578 " --> pdb=" O VAL B2588 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL B2588 " --> pdb=" O ARG B2578 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR B2580 " --> pdb=" O ARG B2586 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG B2586 " --> pdb=" O THR B2580 " (cutoff:3.500A) Processing sheet with id= FD, first strand: chain 'B' and resid 2615 through 2620 removed outlier: 3.503A pdb=" N LYS B2615 " --> pdb=" O ASP B2610 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B2598 " --> pdb=" O THR B2609 " (cutoff:3.500A) Processing sheet with id= FE, first strand: chain 'B' and resid 2666 through 2668 Processing sheet with id= FF, first strand: chain 'B' and resid 2684 through 2687 Processing sheet with id= FG, first strand: chain 'B' and resid 2705 through 2708 Processing sheet with id= FH, first strand: chain 'B' and resid 2746 through 2749 removed outlier: 3.870A pdb=" N ARG B2753 " --> pdb=" O CYS B2749 " (cutoff:3.500A) Processing sheet with id= FI, first strand: chain 'B' and resid 3038 through 3041 removed outlier: 3.793A pdb=" N GLN B3045 " --> pdb=" O CYS B3041 " (cutoff:3.500A) Processing sheet with id= FJ, first strand: chain 'B' and resid 3081 through 3084 removed outlier: 3.562A pdb=" N HIS B3088 " --> pdb=" O CYS B3084 " (cutoff:3.500A) Processing sheet with id= FK, first strand: chain 'B' and resid 3127 through 3130 Processing sheet with id= FL, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id= FM, first strand: chain 'B' and resid 3168 through 3172 Processing sheet with id= FN, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id= FO, first strand: chain 'B' and resid 3456 through 3459 removed outlier: 3.515A pdb=" N LEU B3225 " --> pdb=" O ILE B3211 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN B3213 " --> pdb=" O LEU B3223 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B3223 " --> pdb=" O ASN B3213 " (cutoff:3.500A) Processing sheet with id= FP, first strand: chain 'B' and resid 3231 through 3237 removed outlier: 6.700A pdb=" N ILE B3246 " --> pdb=" O VAL B3232 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B3234 " --> pdb=" O TYR B3244 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR B3244 " --> pdb=" O LEU B3234 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE B3236 " --> pdb=" O ARG B3242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B3242 " --> pdb=" O PHE B3236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B3267 " --> pdb=" O ILE B3253 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B3255 " --> pdb=" O THR B3265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR B3265 " --> pdb=" O ARG B3255 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE B3257 " --> pdb=" O GLN B3263 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN B3263 " --> pdb=" O PHE B3257 " (cutoff:3.500A) Processing sheet with id= FQ, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 6.809A pdb=" N LEU B3289 " --> pdb=" O GLU B3275 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B3277 " --> pdb=" O TYR B3287 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B3287 " --> pdb=" O LEU B3277 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B3279 " --> pdb=" O LYS B3285 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B3285 " --> pdb=" O VAL B3279 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B3310 " --> pdb=" O LEU B3296 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B3298 " --> pdb=" O MET B3308 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET B3308 " --> pdb=" O VAL B3298 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP B3300 " --> pdb=" O ARG B3306 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG B3306 " --> pdb=" O ASP B3300 " (cutoff:3.500A) Processing sheet with id= FR, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 6.483A pdb=" N ALA B3340 " --> pdb=" O ARG B3326 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE B3328 " --> pdb=" O TYR B3338 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B3338 " --> pdb=" O ILE B3328 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B3330 " --> pdb=" O TYR B3336 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B3336 " --> pdb=" O LEU B3330 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG B3350 " --> pdb=" O VAL B3360 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL B3360 " --> pdb=" O ARG B3350 " (cutoff:3.500A) Processing sheet with id= FS, first strand: chain 'B' and resid 3371 through 3375 removed outlier: 3.671A pdb=" N ALA B3371 " --> pdb=" O ALA B3384 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B3391 " --> pdb=" O TYR B3405 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B3393 " --> pdb=" O THR B3403 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR B3403 " --> pdb=" O PHE B3393 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP B3395 " --> pdb=" O ARG B3401 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B3401 " --> pdb=" O ASP B3395 " (cutoff:3.500A) Processing sheet with id= FT, first strand: chain 'B' and resid 3412 through 3418 removed outlier: 6.659A pdb=" N THR B3425 " --> pdb=" O PHE B3413 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B3415 " --> pdb=" O PHE B3423 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE B3423 " --> pdb=" O LEU B3415 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B3417 " --> pdb=" O THR B3421 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR B3421 " --> pdb=" O ILE B3417 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B3447 " --> pdb=" O VAL B3432 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS B3434 " --> pdb=" O VAL B3445 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL B3445 " --> pdb=" O LYS B3434 " (cutoff:3.500A) Processing sheet with id= FU, first strand: chain 'B' and resid 3481 through 3484 Processing sheet with id= FV, first strand: chain 'B' and resid 3499 through 3504 Processing sheet with id= FW, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id= FX, first strand: chain 'B' and resid 3560 through 3562 removed outlier: 3.643A pdb=" N ASN B3566 " --> pdb=" O CYS B3562 " (cutoff:3.500A) Processing sheet with id= FY, first strand: chain 'B' and resid 3600 through 3602 Processing sheet with id= FZ, first strand: chain 'B' and resid 3641 through 3643 Processing sheet with id= GA, first strand: chain 'B' and resid 3685 through 3687 Processing sheet with id= GB, first strand: chain 'B' and resid 3726 through 3729 removed outlier: 3.620A pdb=" N HIS B3733 " --> pdb=" O CYS B3729 " (cutoff:3.500A) Processing sheet with id= GC, first strand: chain 'B' and resid 3765 through 3768 Processing sheet with id= GD, first strand: chain 'B' and resid 3804 through 3806 Processing sheet with id= GE, first strand: chain 'B' and resid 3849 through 3851 Processing sheet with id= GF, first strand: chain 'B' and resid 3997 through 3999 Processing sheet with id= GG, first strand: chain 'B' and resid 4022 through 4026 Processing sheet with id= GH, first strand: chain 'B' and resid 4038 through 4043 removed outlier: 3.563A pdb=" N MET B4041 " --> pdb=" O ARG B4048 " (cutoff:3.500A) Processing sheet with id= GI, first strand: chain 'B' and resid 4321 through 4323 removed outlier: 6.542A pdb=" N LYS B4068 " --> pdb=" O GLU B4078 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU B4078 " --> pdb=" O LYS B4068 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B4070 " --> pdb=" O PHE B4076 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE B4076 " --> pdb=" O ASN B4070 " (cutoff:3.500A) Processing sheet with id= GJ, first strand: chain 'B' and resid 4089 through 4092 Processing sheet with id= GK, first strand: chain 'B' and resid 4148 through 4152 removed outlier: 3.554A pdb=" N ASP B4162 " --> pdb=" O ARG B4167 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B4167 " --> pdb=" O ASP B4162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B4182 " --> pdb=" O ILE B4168 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B4170 " --> pdb=" O TRP B4180 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP B4180 " --> pdb=" O VAL B4170 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B4172 " --> pdb=" O ARG B4178 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG B4178 " --> pdb=" O THR B4172 " (cutoff:3.500A) Processing sheet with id= GL, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 6.621A pdb=" N THR B4204 " --> pdb=" O ALA B4190 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B4192 " --> pdb=" O PHE B4202 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B4202 " --> pdb=" O ILE B4192 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B4194 " --> pdb=" O LEU B4200 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU B4200 " --> pdb=" O VAL B4194 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B4214 " --> pdb=" O VAL B4224 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B4224 " --> pdb=" O SER B4214 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP B4216 " --> pdb=" O ARG B4222 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG B4222 " --> pdb=" O TRP B4216 " (cutoff:3.500A) Processing sheet with id= GM, first strand: chain 'B' and resid 4233 through 4239 removed outlier: 6.692A pdb=" N SER B4249 " --> pdb=" O ASN B4234 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B4236 " --> pdb=" O TYR B4247 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR B4247 " --> pdb=" O LEU B4236 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B4238 " --> pdb=" O ARG B4245 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG B4245 " --> pdb=" O ILE B4238 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER B4258 " --> pdb=" O LEU B4268 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B4268 " --> pdb=" O SER B4258 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS B4260 " --> pdb=" O ARG B4266 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ARG B4266 " --> pdb=" O LYS B4260 " (cutoff:3.500A) Processing sheet with id= GN, first strand: chain 'B' and resid 4276 through 4282 removed outlier: 6.520A pdb=" N VAL B4289 " --> pdb=" O PHE B4277 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B4279 " --> pdb=" O TYR B4287 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR B4287 " --> pdb=" O LEU B4279 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE B4281 " --> pdb=" O GLN B4285 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN B4285 " --> pdb=" O ILE B4281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B4311 " --> pdb=" O VAL B4296 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B4298 " --> pdb=" O LYS B4309 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS B4309 " --> pdb=" O ARG B4298 " (cutoff:3.500A) Processing sheet with id= GO, first strand: chain 'B' and resid 4343 through 4347 Processing sheet with id= GP, first strand: chain 'B' and resid 4390 through 4393 1326 hydrogen bonds defined for protein. 3300 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: 67.37 Time building geometry restraints manager: 19.38 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: 10122 1.32 - 1.45: 17440 1.45 - 1.58: 32474 1.58 - 1.71: 0 1.71 - 1.84: 716 Bond restraints: 60752 Sorted by residual: bond pdb=" N HIS A3451 " pdb=" CA HIS A3451 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.17e-02 7.31e+03 1.42e+01 bond pdb=" N HIS B3451 " pdb=" CA HIS B3451 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.17e-02 7.31e+03 1.42e+01 bond pdb=" C PRO A3453 " pdb=" O PRO A3453 " ideal model delta sigma weight residual 1.238 1.192 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" C PRO B3453 " pdb=" O PRO B3453 " ideal model delta sigma weight residual 1.238 1.192 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" C THR A3684 " pdb=" O THR A3684 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.39e-02 5.18e+03 1.24e+01 ... (remaining 60747 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.93: 1648 105.93 - 113.16: 31954 113.16 - 120.40: 23158 120.40 - 127.63: 25034 127.63 - 134.87: 912 Bond angle restraints: 82706 Sorted by residual: angle pdb=" O ASN A3691 " pdb=" C ASN A3691 " pdb=" N TYR A3692 " ideal model delta sigma weight residual 123.10 128.76 -5.66 1.15e+00 7.56e-01 2.42e+01 angle pdb=" O ASN B3691 " pdb=" C ASN B3691 " pdb=" N TYR B3692 " ideal model delta sigma weight residual 123.10 128.76 -5.66 1.15e+00 7.56e-01 2.42e+01 angle pdb=" CA VAL B3447 " pdb=" C VAL B3447 " pdb=" O VAL B3447 " ideal model delta sigma weight residual 121.45 116.59 4.86 1.00e+00 1.00e+00 2.37e+01 angle pdb=" CA VAL A3447 " pdb=" C VAL A3447 " pdb=" O VAL A3447 " ideal model delta sigma weight residual 121.45 116.59 4.86 1.00e+00 1.00e+00 2.37e+01 angle pdb=" CA PHE A3320 " pdb=" C PHE A3320 " pdb=" O PHE A3320 " ideal model delta sigma weight residual 121.46 115.77 5.69 1.17e+00 7.31e-01 2.36e+01 ... (remaining 82701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 35108 17.05 - 34.11: 2122 34.11 - 51.16: 394 51.16 - 68.21: 132 68.21 - 85.27: 42 Dihedral angle restraints: 37798 sinusoidal: 15828 harmonic: 21970 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 256 " pdb=" CB CYS A 256 " ideal model delta sinusoidal sigma weight residual -86.00 -157.98 71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 256 " pdb=" CB CYS B 256 " ideal model delta sinusoidal sigma weight residual -86.00 -157.98 71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 229 " pdb=" SG CYS A 229 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 -151.04 65.04 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 37795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 8842 0.124 - 0.248: 278 0.248 - 0.371: 18 0.371 - 0.495: 4 0.495 - 0.619: 2 Chirality restraints: 9144 Sorted by residual: chirality pdb=" C1 NAG A4787 " pdb=" ND2 ASN A2488 " pdb=" C2 NAG A4787 " pdb=" O5 NAG A4787 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" C1 NAG B4742 " pdb=" ND2 ASN B2488 " pdb=" C2 NAG B4742 " pdb=" O5 NAG B4742 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.01e+00 ... (remaining 9141 not shown) Planarity restraints: 10940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NGA B4770 " -0.101 2.00e-02 2.50e+03 8.51e-02 9.05e+01 pdb=" C7 NGA B4770 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NGA B4770 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NGA B4770 " 0.140 2.00e-02 2.50e+03 pdb=" O7 NGA B4770 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NGA A4732 " -0.101 2.00e-02 2.50e+03 8.51e-02 9.05e+01 pdb=" C7 NGA A4732 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NGA A4732 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NGA A4732 " 0.140 2.00e-02 2.50e+03 pdb=" O7 NGA A4732 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 571 " -0.089 2.00e-02 2.50e+03 5.64e-02 6.37e+01 pdb=" CG TYR A 571 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 571 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR A 571 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 571 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 571 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 571 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 571 " -0.096 2.00e-02 2.50e+03 ... (remaining 10937 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1776 2.69 - 3.24: 57548 3.24 - 3.79: 89627 3.79 - 4.35: 125938 4.35 - 4.90: 209565 Nonbonded interactions: 484454 Sorted by model distance: nonbonded pdb=" OD2 ASP B3785 " pdb="CA CA B4759 " model vdw 2.135 2.510 nonbonded pdb=" OD2 ASP A3785 " pdb="CA CA A4765 " model vdw 2.135 2.510 nonbonded pdb=" OD1 ASN A3097 " pdb="CA CA A4758 " model vdw 2.150 2.510 nonbonded pdb=" OD1 ASN B3097 " pdb="CA CA B4765 " model vdw 2.150 2.510 nonbonded pdb=" OD1 ASP A3781 " pdb="CA CA A4765 " model vdw 2.159 2.510 ... (remaining 484449 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' and (resid 28 through 4413 or resid 4706 or resid 4708 through 4711 o \ r resid 4714 or resid 4717 through 4720 or resid 4722 through 4723 or resid 4727 \ through 4728 or resid 4738 or resid 4740 or resid 4746 through 4747 or resid 47 \ 49 through 4769 or resid 4771 through 4775 or resid 4777 or resid 4779 or resid \ 4781 or resid 4786)) selection = (chain 'B' and (resid 28 through 4413 or resid 4706 or resid 4708 through 4711 o \ r resid 4714 or resid 4717 through 4720 or resid 4722 through 4723 or resid 4727 \ through 4728 or resid 4738 or resid 4740 or resid 4746 through 4747 or resid 47 \ 49 through 4769 or resid 4771 through 4775 or resid 4777 or resid 4779 or resid \ 4781 or resid 4786)) } 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: 6.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 26.990 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 169.230 Find NCS groups from input model: 4.450 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 60752 Z= 0.362 Angle : 0.992 8.174 82706 Z= 0.579 Chirality : 0.058 0.619 9144 Planarity : 0.007 0.085 10880 Dihedral : 11.787 85.268 22982 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.13 % Allowed : 2.56 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.47 (0.09), residues: 7612 helix: -3.88 (0.22), residues: 196 sheet: 0.42 (0.10), residues: 2434 loop : -0.52 (0.09), residues: 4982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A2524 HIS 0.009 0.001 HIS A3683 PHE 0.054 0.002 PHE B3423 TYR 0.096 0.003 TYR A 571 ARG 0.014 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 230 time to evaluate : 5.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 238 average time/residue: 1.5564 time to fit residues: 472.7278 Evaluate side-chains 140 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 3101 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 3101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 643 optimal weight: 20.0000 chunk 577 optimal weight: 0.3980 chunk 320 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 389 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 597 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 chunk 363 optimal weight: 0.3980 chunk 444 optimal weight: 10.0000 chunk 691 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 HIS A 895 HIS A1151 HIS A1712 HIS ** A3460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 HIS B 895 HIS B1151 HIS B1712 HIS ** B3460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 60752 Z= 0.194 Angle : 0.600 8.780 82706 Z= 0.320 Chirality : 0.047 0.349 9144 Planarity : 0.004 0.057 10880 Dihedral : 6.548 59.588 10240 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.58 % Allowed : 5.05 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 7612 helix: -3.64 (0.24), residues: 196 sheet: 0.27 (0.10), residues: 2482 loop : -0.15 (0.09), residues: 4934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 45 HIS 0.006 0.001 HIS A3683 PHE 0.015 0.001 PHE A3297 TYR 0.018 0.001 TYR A4030 ARG 0.009 0.000 ARG B2506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1010 MET cc_start: 0.6868 (mpt) cc_final: 0.6621 (mpt) REVERT: A 1462 LEU cc_start: 0.8128 (mt) cc_final: 0.7601 (mt) REVERT: B 1010 MET cc_start: 0.6874 (mpt) cc_final: 0.6628 (mpt) REVERT: B 1462 LEU cc_start: 0.8124 (mt) cc_final: 0.7602 (mt) outliers start: 36 outliers final: 12 residues processed: 172 average time/residue: 1.5092 time to fit residues: 335.3544 Evaluate side-chains 148 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3878 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 384 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 575 optimal weight: 0.6980 chunk 471 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 693 optimal weight: 0.6980 chunk 748 optimal weight: 50.0000 chunk 617 optimal weight: 6.9990 chunk 687 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 556 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2195 HIS A2263 HIS A3460 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2195 HIS B2263 HIS B3460 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 60752 Z= 0.210 Angle : 0.572 9.361 82706 Z= 0.300 Chirality : 0.047 0.327 9144 Planarity : 0.004 0.044 10880 Dihedral : 6.059 57.643 10236 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.65 % Allowed : 5.99 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.15 (0.10), residues: 7612 helix: -3.50 (0.28), residues: 172 sheet: 0.13 (0.10), residues: 2424 loop : -0.01 (0.09), residues: 5016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3288 HIS 0.006 0.001 HIS B3683 PHE 0.015 0.001 PHE A 541 TYR 0.019 0.001 TYR A2210 ARG 0.007 0.000 ARG B2506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1010 MET cc_start: 0.6985 (mpt) cc_final: 0.6680 (mpt) REVERT: A 3467 MET cc_start: 0.3809 (ptm) cc_final: 0.2425 (mpt) REVERT: B 1010 MET cc_start: 0.6984 (mpt) cc_final: 0.6678 (mpt) REVERT: B 3467 MET cc_start: 0.3810 (ptm) cc_final: 0.2428 (mpt) outliers start: 40 outliers final: 14 residues processed: 168 average time/residue: 1.3389 time to fit residues: 298.7365 Evaluate side-chains 146 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 7.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3878 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 684 optimal weight: 20.0000 chunk 521 optimal weight: 0.1980 chunk 359 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 465 optimal weight: 0.2980 chunk 695 optimal weight: 7.9990 chunk 736 optimal weight: 8.9990 chunk 363 optimal weight: 6.9990 chunk 659 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 GLN A1576 HIS A1798 ASN ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1367 GLN B1576 HIS B1798 ASN B3854 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 60752 Z= 0.289 Angle : 0.566 7.695 82706 Z= 0.298 Chirality : 0.047 0.336 9144 Planarity : 0.004 0.046 10880 Dihedral : 5.909 59.854 10236 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.07 % Allowed : 6.44 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.24 (0.10), residues: 7612 helix: -3.36 (0.28), residues: 172 sheet: -0.07 (0.10), residues: 2462 loop : 0.00 (0.09), residues: 4978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3288 HIS 0.006 0.001 HIS B2195 PHE 0.017 0.001 PHE B2330 TYR 0.024 0.001 TYR A2210 ARG 0.007 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 136 time to evaluate : 5.053 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 outliers start: 66 outliers final: 26 residues processed: 188 average time/residue: 1.2798 time to fit residues: 322.8206 Evaluate side-chains 154 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 4.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 1465 ASP Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3878 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 613 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 10 optimal weight: 0.0170 chunk 548 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 628 optimal weight: 0.9980 chunk 509 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 376 optimal weight: 50.0000 chunk 661 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS A3331 HIS A3854 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 HIS B3331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 60752 Z= 0.237 Angle : 0.543 9.537 82706 Z= 0.284 Chirality : 0.046 0.328 9144 Planarity : 0.004 0.047 10880 Dihedral : 5.713 57.718 10236 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.05 % Allowed : 7.15 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 7612 helix: -3.29 (0.28), residues: 172 sheet: -0.16 (0.10), residues: 2452 loop : -0.00 (0.09), residues: 4988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2293 HIS 0.006 0.001 HIS A2195 PHE 0.015 0.001 PHE A2330 TYR 0.020 0.001 TYR A2210 ARG 0.003 0.000 ARG B2120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 130 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 26 residues processed: 183 average time/residue: 1.3371 time to fit residues: 325.9722 Evaluate side-chains 148 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 4.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 247 optimal weight: 10.0000 chunk 663 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 432 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 chunk 737 optimal weight: 6.9990 chunk 612 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 387 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2356 HIS A2637 GLN A3324 ASN A3683 HIS A3811 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2356 HIS B2637 GLN B3324 ASN B3683 HIS B3811 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 60752 Z= 0.582 Angle : 0.678 10.504 82706 Z= 0.351 Chirality : 0.051 0.302 9144 Planarity : 0.004 0.051 10880 Dihedral : 6.166 56.513 10236 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.15 % Allowed : 7.65 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.53 (0.10), residues: 7612 helix: -3.25 (0.27), residues: 172 sheet: -0.46 (0.10), residues: 2492 loop : -0.09 (0.09), residues: 4948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2608 HIS 0.015 0.001 HIS A2195 PHE 0.023 0.002 PHE A2330 TYR 0.032 0.002 TYR B2210 ARG 0.006 0.001 ARG B2006 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 124 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3395 ASP cc_start: 0.5417 (OUTLIER) cc_final: 0.5051 (p0) REVERT: A 4403 CYS cc_start: 0.4606 (OUTLIER) cc_final: 0.4021 (m) REVERT: B 3395 ASP cc_start: 0.5365 (OUTLIER) cc_final: 0.5048 (p0) REVERT: B 4403 CYS cc_start: 0.4610 (OUTLIER) cc_final: 0.4028 (m) outliers start: 71 outliers final: 30 residues processed: 183 average time/residue: 1.3729 time to fit residues: 335.1980 Evaluate side-chains 156 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 5.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3395 ASP Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 710 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 420 optimal weight: 10.0000 chunk 538 optimal weight: 2.9990 chunk 417 optimal weight: 50.0000 chunk 620 optimal weight: 0.8980 chunk 411 optimal weight: 20.0000 chunk 734 optimal weight: 30.0000 chunk 459 optimal weight: 9.9990 chunk 447 optimal weight: 10.0000 chunk 339 optimal weight: 40.0000 overall best weight: 6.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 HIS A1567 ASN A1740 ASN A2084 HIS A2195 HIS ** A3387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3428 ASN A4063 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 HIS B1232 HIS B1567 ASN B1740 ASN B2084 HIS B2195 HIS B4063 ASN ** B4206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.097 60752 Z= 0.770 Angle : 0.759 12.154 82706 Z= 0.392 Chirality : 0.054 0.293 9144 Planarity : 0.005 0.061 10880 Dihedral : 6.670 55.393 10236 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.33 % Allowed : 7.59 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.89 (0.10), residues: 7612 helix: -3.23 (0.26), residues: 182 sheet: -0.72 (0.10), residues: 2432 loop : -0.35 (0.09), residues: 4998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2293 HIS 0.014 0.002 HIS A2195 PHE 0.028 0.002 PHE A2330 TYR 0.028 0.002 TYR A2210 ARG 0.009 0.001 ARG B2743 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 128 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6236 (m) REVERT: A 1010 MET cc_start: 0.7120 (mpt) cc_final: 0.6881 (mpt) REVERT: A 1119 ASN cc_start: 0.3661 (OUTLIER) cc_final: 0.3395 (p0) REVERT: A 3395 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5796 (p0) REVERT: A 4403 CYS cc_start: 0.4235 (OUTLIER) cc_final: 0.3383 (m) REVERT: B 234 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6244 (m) REVERT: B 1010 MET cc_start: 0.7122 (mpt) cc_final: 0.6881 (mpt) REVERT: B 1119 ASN cc_start: 0.3671 (OUTLIER) cc_final: 0.3402 (p0) REVERT: B 3395 ASP cc_start: 0.6107 (OUTLIER) cc_final: 0.5796 (p0) REVERT: B 4403 CYS cc_start: 0.4248 (OUTLIER) cc_final: 0.3399 (m) outliers start: 82 outliers final: 46 residues processed: 200 average time/residue: 1.1957 time to fit residues: 326.3944 Evaluate side-chains 180 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 126 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 958 HIS Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1440 VAL Chi-restraints excluded: chain A residue 1568 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2492 ASN Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2610 ASP Chi-restraints excluded: chain A residue 2731 ASP Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1440 VAL Chi-restraints excluded: chain B residue 1568 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2492 ASN Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2610 ASP Chi-restraints excluded: chain B residue 2731 ASP Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3395 ASP Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 454 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 438 optimal weight: 6.9990 chunk 221 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 466 optimal weight: 5.9990 chunk 500 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 577 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1803 HIS A3428 ASN ** A3782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1803 HIS B4206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 60752 Z= 0.213 Angle : 0.579 12.578 82706 Z= 0.297 Chirality : 0.046 0.310 9144 Planarity : 0.004 0.056 10880 Dihedral : 6.086 54.951 10236 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.89 % Allowed : 8.10 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.66 (0.10), residues: 7612 helix: -3.16 (0.27), residues: 182 sheet: -0.46 (0.10), residues: 2378 loop : -0.24 (0.09), residues: 5052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2293 HIS 0.004 0.001 HIS A4387 PHE 0.013 0.001 PHE A2065 TYR 0.018 0.001 TYR A4030 ARG 0.004 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 126 time to evaluate : 5.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6461 (m) REVERT: A 1010 MET cc_start: 0.6998 (mpt) cc_final: 0.6658 (mpt) REVERT: A 2067 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9055 (t) REVERT: A 2522 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7615 (ptp) REVERT: A 4134 ARG cc_start: 0.3774 (OUTLIER) cc_final: 0.3018 (pmt-80) REVERT: A 4403 CYS cc_start: 0.4836 (OUTLIER) cc_final: 0.3872 (m) REVERT: B 234 CYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6468 (m) REVERT: B 1010 MET cc_start: 0.7004 (mpt) cc_final: 0.6663 (mpt) REVERT: B 2067 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9058 (t) REVERT: B 2522 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7612 (ptp) REVERT: B 4134 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.3029 (pmt-80) REVERT: B 4403 CYS cc_start: 0.4837 (OUTLIER) cc_final: 0.3873 (m) outliers start: 55 outliers final: 28 residues processed: 175 average time/residue: 1.3775 time to fit residues: 321.5336 Evaluate side-chains 164 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2610 ASP Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4134 ARG Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2610 ASP Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4134 ARG Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 668 optimal weight: 30.0000 chunk 703 optimal weight: 0.0040 chunk 641 optimal weight: 0.9990 chunk 684 optimal weight: 6.9990 chunk 411 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 537 optimal weight: 0.3980 chunk 210 optimal weight: 0.8980 chunk 618 optimal weight: 0.7980 chunk 647 optimal weight: 1.9990 chunk 682 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 60752 Z= 0.144 Angle : 0.561 14.249 82706 Z= 0.283 Chirality : 0.045 0.313 9144 Planarity : 0.004 0.049 10880 Dihedral : 5.668 56.409 10236 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.65 % Allowed : 8.38 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.55 (0.10), residues: 7612 helix: -3.13 (0.27), residues: 194 sheet: -0.40 (0.10), residues: 2406 loop : -0.15 (0.09), residues: 5012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2524 HIS 0.004 0.001 HIS A 985 PHE 0.015 0.001 PHE B 692 TYR 0.016 0.001 TYR A4030 ARG 0.003 0.000 ARG B2120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 5.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6465 (m) REVERT: A 1010 MET cc_start: 0.6922 (mpt) cc_final: 0.6645 (mpt) REVERT: A 4403 CYS cc_start: 0.4902 (OUTLIER) cc_final: 0.3982 (m) REVERT: B 234 CYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6469 (m) REVERT: B 1010 MET cc_start: 0.6916 (mpt) cc_final: 0.6623 (mpt) REVERT: B 2610 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7575 (p0) REVERT: B 4403 CYS cc_start: 0.4903 (OUTLIER) cc_final: 0.3983 (m) outliers start: 40 outliers final: 27 residues processed: 159 average time/residue: 1.4111 time to fit residues: 296.8684 Evaluate side-chains 158 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2610 ASP Chi-restraints excluded: chain A residue 2731 ASP Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2610 ASP Chi-restraints excluded: chain B residue 2731 ASP Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 449 optimal weight: 5.9990 chunk 723 optimal weight: 9.9990 chunk 441 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 503 optimal weight: 7.9990 chunk 759 optimal weight: 1.9990 chunk 698 optimal weight: 10.0000 chunk 604 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 466 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3428 ASN ** A3811 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 GLN B1496 GLN ** B3811 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 60752 Z= 0.632 Angle : 0.717 19.804 82706 Z= 0.363 Chirality : 0.051 0.305 9144 Planarity : 0.004 0.052 10880 Dihedral : 6.222 59.676 10236 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.74 % Allowed : 8.44 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.76 (0.10), residues: 7612 helix: -2.99 (0.28), residues: 194 sheet: -0.68 (0.10), residues: 2398 loop : -0.23 (0.09), residues: 5020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1965 HIS 0.009 0.001 HIS A2195 PHE 0.023 0.002 PHE A2065 TYR 0.028 0.002 TYR B2210 ARG 0.006 0.001 ARG B1563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6699 (OUTLIER) cc_final: 0.6223 (m) REVERT: A 4134 ARG cc_start: 0.3956 (OUTLIER) cc_final: 0.3120 (pmt-80) REVERT: A 4403 CYS cc_start: 0.4435 (OUTLIER) cc_final: 0.3227 (m) REVERT: B 234 CYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6229 (m) REVERT: B 4134 ARG cc_start: 0.3964 (OUTLIER) cc_final: 0.3081 (pmt-80) REVERT: B 4403 CYS cc_start: 0.4440 (OUTLIER) cc_final: 0.3235 (m) outliers start: 46 outliers final: 29 residues processed: 168 average time/residue: 1.4361 time to fit residues: 318.1847 Evaluate side-chains 161 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 4.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2492 ASN Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2731 ASP Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4134 ARG Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2389 ASP Chi-restraints excluded: chain B residue 2492 ASN Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2731 ASP Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4134 ARG Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 480 optimal weight: 9.9990 chunk 643 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 557 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 605 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 621 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3428 ASN A3811 HIS ** A4206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 ASN B3811 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.083880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.052532 restraints weight = 315481.653| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.67 r_work: 0.2850 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 60752 Z= 0.243 Angle : 0.591 18.013 82706 Z= 0.298 Chirality : 0.046 0.309 9144 Planarity : 0.004 0.052 10880 Dihedral : 5.865 59.530 10236 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.60 % Allowed : 8.54 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.63 (0.10), residues: 7612 helix: -2.99 (0.28), residues: 194 sheet: -0.51 (0.11), residues: 2362 loop : -0.19 (0.09), residues: 5056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1483 HIS 0.004 0.001 HIS A2195 PHE 0.012 0.001 PHE B2162 TYR 0.014 0.001 TYR B2210 ARG 0.003 0.000 ARG B2096 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12085.63 seconds wall clock time: 213 minutes 56.32 seconds (12836.32 seconds total)