Starting phenix.real_space_refine on Fri Dec 8 19:19:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/12_2023/8em4_28233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/12_2023/8em4_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_28233/12_2023/8em4_28233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/12_2023/8em4_28233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/12_2023/8em4_28233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em4_28233/12_2023/8em4_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 23.80, per 1000 atoms: 0.40 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: 17.46 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: 27.34 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: 63.63 Time building geometry restraints manager: 19.40 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 27.100 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 164.580 Find NCS groups from input model: 4.530 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.120 ------------------------------------------------------------------------------- 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 : 5.151 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: 1.5511 time to fit residues: 474.1201 Evaluate side-chains 140 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 5.223 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 6.8625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 60752 Z= 0.195 Angle : 0.599 9.277 82706 Z= 0.319 Chirality : 0.047 0.352 9144 Planarity : 0.004 0.052 10880 Dihedral : 6.502 59.502 10234 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.65 % Allowed : 4.97 % Favored : 94.39 % 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: -0.22 (0.10), residues: 7612 helix: -3.65 (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 0.015 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 0.010 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 184 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 5.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 174 average time/residue: 1.5110 time to fit residues: 343.7910 Evaluate side-chains 148 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 5.274 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.6313 time to fit residues: 8.9893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 384 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 575 optimal weight: 0.6980 chunk 471 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 693 optimal weight: 4.9990 chunk 748 optimal weight: 50.0000 chunk 617 optimal weight: 0.7980 chunk 687 optimal weight: 40.0000 chunk 236 optimal weight: 5.9990 chunk 556 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 978 HIS A1367 GLN A1576 HIS A2195 HIS A2263 HIS A3460 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS B1367 GLN B1576 HIS B2195 HIS B2263 HIS B3460 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 60752 Z= 0.298 Angle : 0.597 10.674 82706 Z= 0.313 Chirality : 0.047 0.369 9144 Planarity : 0.004 0.045 10880 Dihedral : 6.161 56.545 10234 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.78 % Allowed : 5.92 % Favored : 93.30 % Cbeta Deviations : 0.03 % 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: -0.22 (0.10), residues: 7612 helix: -3.51 (0.28), residues: 172 sheet: 0.04 (0.10), residues: 2420 loop : -0.04 (0.09), residues: 5020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2293 HIS 0.006 0.001 HIS B2195 PHE 0.016 0.001 PHE B2330 TYR 0.024 0.001 TYR B2210 ARG 0.006 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 184 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 5.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 176 average time/residue: 1.3395 time to fit residues: 319.8481 Evaluate side-chains 150 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 5.255 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.6375 time to fit residues: 9.0750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 684 optimal weight: 10.0000 chunk 521 optimal weight: 1.9990 chunk 359 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 465 optimal weight: 0.3980 chunk 695 optimal weight: 9.9990 chunk 736 optimal weight: 20.0000 chunk 363 optimal weight: 4.9990 chunk 659 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS A1798 ASN A3324 ASN A3331 HIS A3854 HIS B 431 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 HIS B1798 ASN B3324 ASN B3331 HIS B3854 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 60752 Z= 0.365 Angle : 0.601 8.383 82706 Z= 0.315 Chirality : 0.048 0.337 9144 Planarity : 0.004 0.049 10880 Dihedral : 6.020 58.990 10234 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.20 % Allowed : 6.79 % Favored : 92.01 % 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: -0.36 (0.10), residues: 7612 helix: -3.42 (0.27), residues: 172 sheet: -0.19 (0.10), residues: 2468 loop : -0.06 (0.09), residues: 4972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2293 HIS 0.011 0.001 HIS A2195 PHE 0.019 0.001 PHE B2330 TYR 0.027 0.002 TYR A2210 ARG 0.005 0.000 ARG B1834 *********************** 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 210 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 136 time to evaluate : 5.226 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: 74 outliers final: 28 residues processed: 196 average time/residue: 1.3840 time to fit residues: 366.3128 Evaluate side-chains 156 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 5.237 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 6 average time/residue: 0.8671 time to fit residues: 14.7048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 613 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 10 optimal weight: 40.0000 chunk 548 optimal weight: 2.9990 chunk 303 optimal weight: 20.0000 chunk 628 optimal weight: 0.2980 chunk 509 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 376 optimal weight: 0.0980 chunk 661 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** B2637 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 60752 Z= 0.171 Angle : 0.537 10.719 82706 Z= 0.280 Chirality : 0.045 0.328 9144 Planarity : 0.004 0.048 10880 Dihedral : 5.662 56.124 10234 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.89 % Allowed : 7.51 % Favored : 91.60 % 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: -0.32 (0.10), residues: 7612 helix: -3.34 (0.27), residues: 172 sheet: -0.13 (0.10), residues: 2418 loop : -0.05 (0.09), residues: 5022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2293 HIS 0.009 0.001 HIS B 435 PHE 0.012 0.001 PHE B2330 TYR 0.019 0.001 TYR B 39 ARG 0.003 0.000 ARG A2120 *********************** 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 183 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 128 time to evaluate : 5.407 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: 55 outliers final: 28 residues processed: 175 average time/residue: 1.3686 time to fit residues: 321.7211 Evaluate side-chains 152 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 5.969 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 1.0255 time to fit residues: 12.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 247 optimal weight: 2.9990 chunk 663 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 432 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 737 optimal weight: 5.9990 chunk 612 optimal weight: 10.0000 chunk 341 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 387 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** A2637 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1803 HIS B3683 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2960 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= 0.278 Angle : 0.557 11.025 82706 Z= 0.289 Chirality : 0.046 0.321 9144 Planarity : 0.004 0.047 10880 Dihedral : 5.623 54.801 10234 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.00 % Allowed : 7.83 % Favored : 91.17 % 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: -0.39 (0.10), residues: 7612 helix: -3.29 (0.27), residues: 184 sheet: -0.25 (0.10), residues: 2436 loop : -0.05 (0.09), residues: 4992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B3288 HIS 0.007 0.001 HIS A2195 PHE 0.016 0.001 PHE B2330 TYR 0.022 0.001 TYR B2210 ARG 0.003 0.000 ARG A2120 *********************** 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 188 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 126 time to evaluate : 5.237 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: 62 outliers final: 38 residues processed: 180 average time/residue: 1.3754 time to fit residues: 332.0615 Evaluate side-chains 162 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 5.259 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 34 residues processed: 4 average time/residue: 1.0450 time to fit residues: 12.9680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 710 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 420 optimal weight: 30.0000 chunk 538 optimal weight: 0.9990 chunk 417 optimal weight: 20.0000 chunk 620 optimal weight: 3.9990 chunk 411 optimal weight: 0.6980 chunk 734 optimal weight: 30.0000 chunk 459 optimal weight: 10.0000 chunk 447 optimal weight: 0.9980 chunk 339 optimal weight: 0.0170 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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** A1803 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 60752 Z= 0.185 Angle : 0.532 11.694 82706 Z= 0.275 Chirality : 0.045 0.323 9144 Planarity : 0.003 0.047 10880 Dihedral : 5.480 53.950 10234 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.86 % Allowed : 8.09 % Favored : 91.05 % 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: -0.37 (0.10), residues: 7612 helix: -3.24 (0.26), residues: 196 sheet: -0.20 (0.10), residues: 2452 loop : -0.05 (0.09), residues: 4964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2293 HIS 0.005 0.001 HIS A3683 PHE 0.013 0.001 PHE B2330 TYR 0.017 0.001 TYR A2210 ARG 0.003 0.000 ARG B2120 *********************** 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 181 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 5.201 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: 53 outliers final: 38 residues processed: 173 average time/residue: 1.3500 time to fit residues: 314.3617 Evaluate side-chains 164 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 5.277 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 1.3352 time to fit residues: 12.3429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 454 optimal weight: 8.9990 chunk 293 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 142 optimal weight: 0.7980 chunk 466 optimal weight: 7.9990 chunk 500 optimal weight: 7.9990 chunk 363 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 577 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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** A 994 GLN A4063 ASN ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 GLN B4063 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3269 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= 0.260 Angle : 0.562 13.131 82706 Z= 0.285 Chirality : 0.046 0.314 9144 Planarity : 0.004 0.047 10880 Dihedral : 5.480 56.993 10234 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.76 % Allowed : 8.38 % 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: -0.41 (0.10), residues: 7612 helix: -3.16 (0.26), residues: 196 sheet: -0.28 (0.10), residues: 2418 loop : -0.06 (0.09), residues: 4998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3288 HIS 0.006 0.001 HIS A2195 PHE 0.015 0.001 PHE A2330 TYR 0.021 0.001 TYR B2210 ARG 0.002 0.000 ARG B2120 *********************** 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 173 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 126 time to evaluate : 6.152 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: 47 outliers final: 36 residues processed: 168 average time/residue: 1.4088 time to fit residues: 320.6480 Evaluate side-chains 160 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 5.237 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 1.3721 time to fit residues: 14.1978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 668 optimal weight: 8.9990 chunk 703 optimal weight: 9.9990 chunk 641 optimal weight: 8.9990 chunk 684 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 chunk 537 optimal weight: 0.6980 chunk 210 optimal weight: 0.5980 chunk 618 optimal weight: 0.6980 chunk 647 optimal weight: 0.9990 chunk 682 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** A3324 ASN ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3324 ASN B4206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 60752 Z= 0.177 Angle : 0.547 13.465 82706 Z= 0.276 Chirality : 0.045 0.318 9144 Planarity : 0.004 0.045 10880 Dihedral : 5.355 59.111 10234 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.73 % Allowed : 8.61 % Favored : 90.67 % 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: -0.37 (0.10), residues: 7612 helix: -3.22 (0.26), residues: 196 sheet: -0.26 (0.10), residues: 2466 loop : -0.02 (0.09), residues: 4950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2293 HIS 0.004 0.001 HIS A4387 PHE 0.012 0.001 PHE B2330 TYR 0.017 0.001 TYR A2210 ARG 0.003 0.000 ARG A2120 *********************** 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 170 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 5.363 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: 45 outliers final: 25 residues processed: 165 average time/residue: 1.3934 time to fit residues: 307.5906 Evaluate side-chains 149 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 5.214 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 1.3272 time to fit residues: 8.6958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 449 optimal weight: 0.7980 chunk 723 optimal weight: 9.9990 chunk 441 optimal weight: 8.9990 chunk 343 optimal weight: 30.0000 chunk 503 optimal weight: 3.9990 chunk 759 optimal weight: 20.0000 chunk 698 optimal weight: 30.0000 chunk 604 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 466 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 A2356 HIS A3683 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2195 HIS B2356 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 60752 Z= 0.427 Angle : 0.624 13.386 82706 Z= 0.316 Chirality : 0.047 0.297 9144 Planarity : 0.004 0.048 10880 Dihedral : 5.644 55.783 10234 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.47 % Allowed : 8.83 % Favored : 90.70 % 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: -0.50 (0.10), residues: 7612 helix: -3.05 (0.27), residues: 206 sheet: -0.42 (0.10), residues: 2410 loop : -0.08 (0.09), residues: 4996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B3288 HIS 0.009 0.001 HIS B1921 PHE 0.021 0.001 PHE B2330 TYR 0.026 0.001 TYR A2210 ARG 0.004 0.000 ARG A1753 ********************** 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 159 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 5.243 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: 29 outliers final: 26 residues processed: 158 average time/residue: 1.4354 time to fit residues: 301.9185 Evaluate side-chains 152 residues out of total 6704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 5.293 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 7.0885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.821 > 50: distance: 54 - 160: 36.297 distance: 57 - 157: 33.338 distance: 72 - 149: 31.887 distance: 75 - 146: 21.032 distance: 92 - 132: 28.644 distance: 95 - 129: 31.975 distance: 112 - 117: 21.905 distance: 117 - 118: 10.505 distance: 117 - 123: 8.294 distance: 118 - 119: 30.122 distance: 118 - 121: 9.832 distance: 119 - 124: 14.039 distance: 121 - 122: 19.315 distance: 122 - 123: 3.517 distance: 124 - 125: 26.442 distance: 125 - 128: 9.157 distance: 126 - 129: 35.289 distance: 129 - 130: 6.119 distance: 130 - 131: 13.645 distance: 130 - 133: 9.868 distance: 131 - 132: 8.512 distance: 131 - 138: 15.793 distance: 133 - 134: 15.853 distance: 134 - 135: 11.518 distance: 135 - 136: 17.356 distance: 136 - 137: 12.194 distance: 138 - 139: 21.068 distance: 138 - 233: 20.044 distance: 139 - 140: 20.517 distance: 139 - 142: 16.843 distance: 140 - 141: 10.699 distance: 140 - 146: 14.833 distance: 141 - 230: 26.376 distance: 142 - 143: 5.167 distance: 142 - 144: 15.587 distance: 143 - 145: 15.045 distance: 146 - 147: 6.652 distance: 147 - 148: 8.404 distance: 147 - 150: 12.448 distance: 148 - 149: 25.157 distance: 148 - 151: 4.341 distance: 151 - 152: 4.214 distance: 152 - 153: 6.853 distance: 152 - 155: 13.210 distance: 153 - 154: 16.305 distance: 153 - 157: 17.171 distance: 155 - 156: 29.233 distance: 157 - 158: 33.162 distance: 158 - 159: 14.232 distance: 158 - 161: 15.843 distance: 159 - 160: 22.506 distance: 159 - 162: 17.471 distance: 163 - 164: 10.591 distance: 164 - 165: 49.812 distance: 164 - 170: 11.896 distance: 166 - 167: 25.420 distance: 167 - 168: 15.086 distance: 167 - 169: 24.172 distance: 171 - 172: 16.750 distance: 171 - 174: 27.763 distance: 172 - 173: 21.939 distance: 172 - 178: 13.932 distance: 174 - 175: 16.582 distance: 175 - 176: 11.621 distance: 176 - 177: 9.216 distance: 179 - 180: 19.311 distance: 179 - 182: 9.499 distance: 180 - 181: 14.134 distance: 180 - 186: 28.432 distance: 182 - 183: 22.069 distance: 183 - 184: 11.062 distance: 183 - 185: 27.395