Starting phenix.real_space_refine on Mon Dec 30 04:26:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8em4_28233/12_2024/8em4_28233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8em4_28233/12_2024/8em4_28233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8em4_28233/12_2024/8em4_28233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8em4_28233/12_2024/8em4_28233.map" model { file = "/net/cci-nas-00/data/ceres_data/8em4_28233/12_2024/8em4_28233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8em4_28233/12_2024/8em4_28233.cif" } 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. Time to flip 14 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59410 Number of models: 1 Model: "" Number of chains: 5 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: "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 Restraints were copied for chains: D Time building chain proxies: 32.22, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 12.35 Conformation dependent library (CDL) restraints added in 6.4 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... Secondary structure from input PDB file: 124 helices and 206 sheets defined 7.9% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.78 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.566A pdb=" N CYS A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 88 " --> pdb=" O TRP A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.853A pdb=" N GLN A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 4.084A pdb=" N CYS A 241 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 242 " --> pdb=" O TRP A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.267A pdb=" N CYS A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.349A pdb=" N SER A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 978 through 983 removed outlier: 3.819A pdb=" N GLY A 981 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1043 Processing helix chain 'A' and resid 1083 through 1086 removed outlier: 4.199A pdb=" N CYS A1086 " --> pdb=" O GLN A1083 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1083 through 1086' Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1205 through 1207 No H-bonds generated for 'chain 'A' and resid 1205 through 1207' Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1217 through 1222 removed outlier: 4.265A pdb=" N GLY A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.609A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1358 Processing helix chain 'A' and resid 1359 through 1361 No H-bonds generated for 'chain 'A' and resid 1359 through 1361' Processing helix chain 'A' and resid 1393 through 1397 Processing helix chain 'A' and resid 1694 through 1698 Processing helix chain 'A' and resid 1703 through 1708 removed outlier: 3.926A pdb=" N SER A1707 " --> pdb=" O PRO A1704 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2026 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 2119 through 2123 Processing helix chain 'A' and resid 2345 through 2354 removed outlier: 4.089A pdb=" N GLN A2349 " --> pdb=" O PRO A2346 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER A2350 " --> pdb=" O CYS A2347 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN A2351 " --> pdb=" O LEU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2654 through 2663 removed outlier: 3.826A pdb=" N GLN A2658 " --> pdb=" O PRO A2655 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE A2659 " --> pdb=" O CYS A2656 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN A2660 " --> pdb=" O ASP A2657 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2719 No H-bonds generated for 'chain 'A' and resid 2717 through 2719' Processing helix chain 'A' and resid 2729 through 2732 Processing helix chain 'A' and resid 2733 through 2738 Processing helix chain 'A' and resid 2758 through 2760 No H-bonds generated for 'chain 'A' and resid 2758 through 2760' Processing helix chain 'A' and resid 2769 through 2774 removed outlier: 4.567A pdb=" N ASP A2772 " --> pdb=" O ASP A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'A' and resid 3062 through 3065 Processing helix chain 'A' and resid 3066 through 3071 Processing helix chain 'A' and resid 3114 through 3118 Processing helix chain 'A' and resid 3156 through 3161 Processing helix chain 'A' and resid 3162 through 3165 removed outlier: 3.560A pdb=" N CYS A3165 " --> pdb=" O PRO A3162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3162 through 3165' Processing helix chain 'A' and resid 3460 through 3464 Processing helix chain 'A' and resid 3472 through 3478 removed outlier: 4.090A pdb=" N ASN A3475 " --> pdb=" O ALA A3472 " (cutoff:3.500A) Processing helix chain 'A' and resid 3531 through 3533 No H-bonds generated for 'chain 'A' and resid 3531 through 3533' Processing helix chain 'A' and resid 3569 through 3573 Processing helix chain 'A' and resid 3583 through 3586 Processing helix chain 'A' and resid 3587 through 3592 Processing helix chain 'A' and resid 3612 through 3614 No H-bonds generated for 'chain 'A' and resid 3612 through 3614' Processing helix chain 'A' and resid 3628 through 3635 Processing helix chain 'A' and resid 3653 through 3655 No H-bonds generated for 'chain 'A' and resid 3653 through 3655' Processing helix chain 'A' and resid 3664 through 3668 removed outlier: 4.253A pdb=" N ASP A3667 " --> pdb=" O ASP A3664 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3674 Processing helix chain 'A' and resid 3675 through 3679 Processing helix chain 'A' and resid 3698 through 3700 No H-bonds generated for 'chain 'A' and resid 3698 through 3700' Processing helix chain 'A' and resid 3710 through 3714 removed outlier: 3.889A pdb=" N GLN A3714 " --> pdb=" O SER A3711 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3719 Processing helix chain 'A' and resid 3777 through 3779 No H-bonds generated for 'chain 'A' and resid 3777 through 3779' Processing helix chain 'A' and resid 3789 through 3793 Processing helix chain 'A' and resid 3794 through 3798 Processing helix chain 'A' and resid 3816 through 3818 No H-bonds generated for 'chain 'A' and resid 3816 through 3818' Processing helix chain 'A' and resid 3858 through 3862 Processing helix chain 'A' and resid 4011 through 4015 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.566A pdb=" N CYS B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 88 " --> pdb=" O TRP B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.853A pdb=" N GLN B 101 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 removed outlier: 4.084A pdb=" N CYS B 241 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 242 " --> pdb=" O TRP B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 242' Processing helix chain 'B' and resid 281 through 285 removed outlier: 4.267A pdb=" N CYS B 285 " --> pdb=" O MET B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 285' Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.349A pdb=" N SER B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 978 through 983 removed outlier: 3.819A pdb=" N GLY B 981 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1083 through 1086 removed outlier: 4.199A pdb=" N CYS B1086 " --> pdb=" O GLN B1083 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1083 through 1086' Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1138 through 1142 Processing helix chain 'B' and resid 1164 through 1168 Processing helix chain 'B' and resid 1205 through 1207 No H-bonds generated for 'chain 'B' and resid 1205 through 1207' Processing helix chain 'B' and resid 1214 through 1216 No H-bonds generated for 'chain 'B' and resid 1214 through 1216' Processing helix chain 'B' and resid 1217 through 1222 removed outlier: 4.265A pdb=" N GLY B1222 " --> pdb=" O SER B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1250 No H-bonds generated for 'chain 'B' and resid 1248 through 1250' Processing helix chain 'B' and resid 1260 through 1264 removed outlier: 3.609A pdb=" N HIS B1264 " --> pdb=" O SER B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1353 through 1358 Processing helix chain 'B' and resid 1359 through 1361 No H-bonds generated for 'chain 'B' and resid 1359 through 1361' Processing helix chain 'B' and resid 1393 through 1397 Processing helix chain 'B' and resid 1694 through 1698 Processing helix chain 'B' and resid 1703 through 1708 removed outlier: 3.926A pdb=" N SER B1707 " --> pdb=" O PRO B1704 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2026 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 2119 through 2123 Processing helix chain 'B' and resid 2345 through 2354 removed outlier: 4.089A pdb=" N GLN B2349 " --> pdb=" O PRO B2346 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER B2350 " --> pdb=" O CYS B2347 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN B2351 " --> pdb=" O LEU B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2654 through 2663 removed outlier: 3.826A pdb=" N GLN B2658 " --> pdb=" O PRO B2655 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE B2659 " --> pdb=" O CYS B2656 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B2660 " --> pdb=" O ASP B2657 " (cutoff:3.500A) Processing helix chain 'B' and resid 2717 through 2719 No H-bonds generated for 'chain 'B' and resid 2717 through 2719' Processing helix chain 'B' and resid 2729 through 2732 Processing helix chain 'B' and resid 2733 through 2738 Processing helix chain 'B' and resid 2758 through 2760 No H-bonds generated for 'chain 'B' and resid 2758 through 2760' Processing helix chain 'B' and resid 2769 through 2774 removed outlier: 4.567A pdb=" N ASP B2772 " --> pdb=" O ASP B2769 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing helix chain 'B' and resid 3062 through 3065 Processing helix chain 'B' and resid 3066 through 3071 Processing helix chain 'B' and resid 3114 through 3118 Processing helix chain 'B' and resid 3156 through 3161 Processing helix chain 'B' and resid 3162 through 3165 removed outlier: 3.560A pdb=" N CYS B3165 " --> pdb=" O PRO B3162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3162 through 3165' Processing helix chain 'B' and resid 3460 through 3464 Processing helix chain 'B' and resid 3472 through 3478 removed outlier: 4.090A pdb=" N ASN B3475 " --> pdb=" O ALA B3472 " (cutoff:3.500A) Processing helix chain 'B' and resid 3531 through 3533 No H-bonds generated for 'chain 'B' and resid 3531 through 3533' Processing helix chain 'B' and resid 3569 through 3573 Processing helix chain 'B' and resid 3583 through 3586 Processing helix chain 'B' and resid 3587 through 3592 Processing helix chain 'B' and resid 3612 through 3614 No H-bonds generated for 'chain 'B' and resid 3612 through 3614' Processing helix chain 'B' and resid 3628 through 3635 Processing helix chain 'B' and resid 3653 through 3655 No H-bonds generated for 'chain 'B' and resid 3653 through 3655' Processing helix chain 'B' and resid 3664 through 3668 removed outlier: 4.253A pdb=" N ASP B3667 " --> pdb=" O ASP B3664 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3674 Processing helix chain 'B' and resid 3675 through 3679 Processing helix chain 'B' and resid 3698 through 3700 No H-bonds generated for 'chain 'B' and resid 3698 through 3700' Processing helix chain 'B' and resid 3710 through 3714 removed outlier: 3.889A pdb=" N GLN B3714 " --> pdb=" O SER B3711 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3719 Processing helix chain 'B' and resid 3777 through 3779 No H-bonds generated for 'chain 'B' and resid 3777 through 3779' Processing helix chain 'B' and resid 3789 through 3793 Processing helix chain 'B' and resid 3794 through 3798 Processing helix chain 'B' and resid 3816 through 3818 No H-bonds generated for 'chain 'B' and resid 3816 through 3818' Processing helix chain 'B' and resid 3858 through 3862 Processing helix chain 'B' and resid 4011 through 4015 Processing sheet with id=AA1, 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=AA2, first strand: chain 'A' and resid 71 through 74 Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 364 Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA9, first strand: chain 'A' and resid 413 through 418 removed outlier: 6.923A pdb=" N LEU A 403 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.690A pdb=" N VAL A 447 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 474 removed outlier: 4.141A pdb=" N ASN A 470 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 490 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 511 through 517 removed outlier: 3.691A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 537 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 558 through 564 removed outlier: 3.808A pdb=" N GLY A 560 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 580 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.868A pdb=" N GLY A 605 " --> pdb=" O THR A 616 " (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=AB6, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AB7, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB8, 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=AB9, first strand: chain 'A' and resid 742 through 748 removed outlier: 4.196A pdb=" N GLY A 744 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE A 764 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 785 through 791 removed outlier: 4.101A pdb=" N CYS A 787 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 807 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 827 through 833 removed outlier: 3.942A pdb=" N SER A 829 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 850 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 871 through 877 removed outlier: 3.696A pdb=" N GLY A 873 " --> pdb=" O VAL A 886 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 915 through 921 removed outlier: 3.781A pdb=" N GLY A 917 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 935 " --> pdb=" O VAL A 949 " (cutoff:3.500A) Processing sheet with id=AC5, 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=AC6, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id=AC7, 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=AC8, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id=AC9, 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=AD1, first strand: chain 'A' and resid 1155 through 1156 Processing sheet with id=AD2, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AD3, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id=AD4, 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=AD5, first strand: chain 'A' and resid 1380 through 1382 Processing sheet with id=AD6, first strand: chain 'A' and resid 1404 through 1408 Processing sheet with id=AD7, first strand: chain 'A' and resid 1420 through 1422 Processing sheet with id=AD8, first strand: chain 'A' and resid 1456 through 1461 removed outlier: 3.961A pdb=" N LEU A1437 " --> pdb=" O ILE A1452 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A1689 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1469 through 1475 removed outlier: 4.010A pdb=" N ALA A1471 " --> pdb=" O SER A1484 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A1491 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1512 through 1518 removed outlier: 3.996A pdb=" N MET A1514 " --> pdb=" O THR A1527 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A1534 " --> pdb=" O LEU A1547 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1555 through 1561 removed outlier: 3.740A pdb=" N GLY A1557 " --> pdb=" O SER A1572 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A1580 " --> pdb=" O ILE A1593 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1601 through 1607 removed outlier: 3.956A pdb=" N GLY A1603 " --> pdb=" O MET A1616 " (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=AE4, 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: 6.759A pdb=" N VAL A1666 " --> pdb=" O VAL A1680 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1713 through 1716 Processing sheet with id=AE6, first strand: chain 'A' and resid 1732 through 1734 Processing sheet with id=AE7, first strand: chain 'A' and resid 1757 through 1761 removed outlier: 4.010A pdb=" N GLY A2007 " --> pdb=" O VAL A1752 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1785 through 1787 removed outlier: 6.785A pdb=" N ILE A1802 " --> pdb=" O PHE A1815 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 1826 through 1830 removed outlier: 3.731A pdb=" N GLY A1826 " --> pdb=" O THR A1839 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A1846 " --> pdb=" O LEU A1861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1874 through 1880 removed outlier: 3.663A pdb=" N GLY A1876 " --> pdb=" O SER A1889 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1901 " --> pdb=" O LEU A1914 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1922 through 1928 removed outlier: 5.327A pdb=" N VAL A1924 " --> pdb=" O ALA A1937 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A1937 " --> pdb=" O VAL A1924 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A1944 " --> pdb=" O LEU A1957 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 1964 through 1970 removed outlier: 3.515A pdb=" N GLY A1966 " --> pdb=" O SER A1977 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A1984 " --> pdb=" O PHE A1998 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 2033 through 2036 Processing sheet with id=AF5, first strand: chain 'A' and resid 2050 through 2052 Processing sheet with id=AF6, first strand: chain 'A' and resid 2091 through 2092 removed outlier: 6.990A pdb=" N PHE A2065 " --> pdb=" O ILE A2329 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A2329 " --> pdb=" O PHE A2065 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A2067 " --> pdb=" O VAL A2327 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A2327 " --> pdb=" O VAL A2067 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A2069 " --> pdb=" O ARG A2325 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 4.189A pdb=" N HIS A2100 " --> pdb=" O CYS A2113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A2125 " --> pdb=" O ILE A2138 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 2147 through 2154 removed outlier: 5.719A pdb=" N ILE A2148 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A2165 " --> pdb=" O ILE A2148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A2150 " --> pdb=" O THR A2163 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A2163 " --> pdb=" O GLY A2150 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A2170 " --> pdb=" O LYS A2187 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A2187 " --> pdb=" O THR A2170 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A2172 " --> pdb=" O LEU A2185 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR A2181 " --> pdb=" O ARG A2176 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 6.765A pdb=" N ILE A2216 " --> pdb=" O LEU A2229 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 4.228A pdb=" N GLY A2239 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A2252 " --> pdb=" O GLY A2239 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A2248 " --> pdb=" O ASP A2243 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A2259 " --> pdb=" O VAL A2272 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 3.936A pdb=" N GLY A2283 " --> pdb=" O VAL A2294 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A2301 " --> pdb=" O ILE A2317 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 2357 through 2359 Processing sheet with id=AG4, first strand: chain 'A' and resid 2375 through 2376 Processing sheet with id=AG5, first strand: chain 'A' and resid 2416 through 2417 removed outlier: 4.900A pdb=" N GLY A2640 " --> pdb=" O SER A2394 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 2421 through 2422 Processing sheet with id=AG7, first strand: chain 'A' and resid 2421 through 2422 removed outlier: 6.663A pdb=" N ILE A2447 " --> pdb=" O SER A2464 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER A2464 " --> pdb=" O ILE A2447 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR A2449 " --> pdb=" O LEU A2462 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU A2462 " --> pdb=" O TYR A2449 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASN A2451 " --> pdb=" O THR A2460 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N THR A2460 " --> pdb=" O ASN A2451 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 2469 through 2475 removed outlier: 4.389A pdb=" N GLY A2471 " --> pdb=" O SER A2484 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A2491 " --> pdb=" O ILE A2504 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 2510 through 2516 removed outlier: 4.007A pdb=" N ALA A2512 " --> pdb=" O THR A2525 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A2533 " --> pdb=" O ILE A2546 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 2554 through 2560 removed outlier: 3.564A pdb=" N GLY A2556 " --> pdb=" O ALA A2569 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A2576 " --> pdb=" O VAL A2589 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 2596 through 2602 removed outlier: 6.505A pdb=" N THR A2609 " --> pdb=" O PHE A2597 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A2599 " --> pdb=" O TYR A2607 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR A2607 " --> pdb=" O LEU A2599 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL A2601 " --> pdb=" O TYR A2605 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A2605 " --> pdb=" O VAL A2601 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A2615 " --> pdb=" O ASP A2610 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 2666 through 2668 Processing sheet with id=AH4, first strand: chain 'A' and resid 2684 through 2687 Processing sheet with id=AH5, first strand: chain 'A' and resid 2705 through 2708 Processing sheet with id=AH6, 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=AH7, first strand: chain 'A' and resid 3038 through 3040 Processing sheet with id=AH8, 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=AH9, first strand: chain 'A' and resid 3127 through 3130 Processing sheet with id=AI1, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id=AI2, first strand: chain 'A' and resid 3168 through 3172 Processing sheet with id=AI3, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AI4, first strand: chain 'A' and resid 3221 through 3226 removed outlier: 6.575A pdb=" N ILE A3211 " --> pdb=" O ILE A3224 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 3231 through 3237 removed outlier: 4.107A pdb=" N ALA A3233 " --> pdb=" O ILE A3246 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A3253 " --> pdb=" O ILE A3266 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 4.092A pdb=" N SER A3276 " --> pdb=" O LEU A3289 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A3296 " --> pdb=" O LEU A3309 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 3.724A pdb=" N GLY A3327 " --> pdb=" O ALA A3340 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A3348 " --> pdb=" O ILE A3361 " (cutoff:3.500A) Processing sheet with id=AI8, 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: 6.627A pdb=" N ILE A3391 " --> pdb=" O VAL A3404 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'A' and resid 3412 through 3418 removed outlier: 3.933A pdb=" N ALA A3414 " --> pdb=" O THR A3425 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A3432 " --> pdb=" O LEU A3446 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 3481 through 3484 Processing sheet with id=AJ2, first strand: chain 'A' and resid 3499 through 3504 Processing sheet with id=AJ3, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id=AJ4, 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=AJ5, first strand: chain 'A' and resid 3600 through 3602 Processing sheet with id=AJ6, first strand: chain 'A' and resid 3641 through 3643 Processing sheet with id=AJ7, first strand: chain 'A' and resid 3685 through 3687 Processing sheet with id=AJ8, 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=AJ9, first strand: chain 'A' and resid 3765 through 3768 Processing sheet with id=AK1, first strand: chain 'A' and resid 3804 through 3806 Processing sheet with id=AK2, first strand: chain 'A' and resid 3849 through 3851 Processing sheet with id=AK3, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id=AK4, first strand: chain 'A' and resid 4022 through 4026 Processing sheet with id=AK5, 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=AK6, first strand: chain 'A' and resid 4075 through 4080 removed outlier: 3.778A pdb=" N TYR A4079 " --> pdb=" O ILE A4066 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A4066 " --> pdb=" O TYR A4079 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'A' and resid 4086 through 4092 removed outlier: 4.025A pdb=" N ALA A4088 " --> pdb=" O THR A4106 " (cutoff:3.500A) Processing sheet with id=AK8, 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: 6.801A pdb=" N ILE A4168 " --> pdb=" O LEU A4181 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 3.876A pdb=" N ALA A4191 " --> pdb=" O THR A4204 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE A4212 " --> pdb=" O LEU A4225 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'A' and resid 4233 through 4239 removed outlier: 3.678A pdb=" N GLY A4235 " --> pdb=" O SER A4249 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A4256 " --> pdb=" O ILE A4269 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 4.121A pdb=" N SER A4278 " --> pdb=" O VAL A4289 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A4296 " --> pdb=" O LEU A4310 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id=AL4, first strand: chain 'A' and resid 4390 through 4393 Processing sheet with id=AL5, 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=AL6, first strand: chain 'B' and resid 71 through 74 Processing sheet with id=AL7, 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=AL8, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AL9, first strand: chain 'B' and resid 320 through 321 Processing sheet with id=AM1, first strand: chain 'B' and resid 336 through 338 Processing sheet with id=AM2, first strand: chain 'B' and resid 360 through 364 Processing sheet with id=AM3, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AM4, first strand: chain 'B' and resid 413 through 418 removed outlier: 6.923A pdb=" N LEU B 403 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'B' and resid 428 through 431 removed outlier: 6.690A pdb=" N VAL B 447 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'B' and resid 468 through 474 removed outlier: 4.141A pdb=" N ASN B 470 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 490 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'B' and resid 511 through 517 removed outlier: 3.691A pdb=" N GLY B 513 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 537 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'B' and resid 558 through 564 removed outlier: 3.808A pdb=" N GLY B 560 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 580 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.868A pdb=" N GLY B 605 " --> pdb=" O THR B 616 " (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=AN1, first strand: chain 'B' and resid 672 through 675 Processing sheet with id=AN2, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AN3, 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=AN4, first strand: chain 'B' and resid 742 through 748 removed outlier: 4.196A pdb=" N GLY B 744 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE B 764 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'B' and resid 785 through 791 removed outlier: 4.101A pdb=" N CYS B 787 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 807 " --> pdb=" O ILE B 820 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'B' and resid 827 through 833 removed outlier: 3.942A pdb=" N SER B 829 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 850 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'B' and resid 871 through 877 removed outlier: 3.696A pdb=" N GLY B 873 " --> pdb=" O VAL B 886 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'B' and resid 915 through 921 removed outlier: 3.781A pdb=" N GLY B 917 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 935 " --> pdb=" O VAL B 949 " (cutoff:3.500A) Processing sheet with id=AN9, 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=AO1, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id=AO2, 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=AO3, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AO4, 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=AO5, first strand: chain 'B' and resid 1155 through 1156 Processing sheet with id=AO6, first strand: chain 'B' and resid 1192 through 1194 Processing sheet with id=AO7, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AO8, 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=AO9, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id=AP1, first strand: chain 'B' and resid 1404 through 1408 Processing sheet with id=AP2, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id=AP3, first strand: chain 'B' and resid 1456 through 1461 removed outlier: 3.961A pdb=" N LEU B1437 " --> pdb=" O ILE B1452 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B1689 " --> pdb=" O ALA B1442 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'B' and resid 1469 through 1475 removed outlier: 4.010A pdb=" N ALA B1471 " --> pdb=" O SER B1484 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B1491 " --> pdb=" O VAL B1504 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'B' and resid 1512 through 1518 removed outlier: 3.996A pdb=" N MET B1514 " --> pdb=" O THR B1527 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE B1534 " --> pdb=" O LEU B1547 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 3.740A pdb=" N GLY B1557 " --> pdb=" O SER B1572 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B1580 " --> pdb=" O ILE B1593 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 3.956A pdb=" N GLY B1603 " --> pdb=" O MET B1616 " (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=AP8, 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: 6.759A pdb=" N VAL B1666 " --> pdb=" O VAL B1680 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id=AQ1, first strand: chain 'B' and resid 1732 through 1734 Processing sheet with id=AQ2, first strand: chain 'B' and resid 1757 through 1761 removed outlier: 4.010A pdb=" N GLY B2007 " --> pdb=" O VAL B1752 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'B' and resid 1785 through 1787 removed outlier: 6.785A pdb=" N ILE B1802 " --> pdb=" O PHE B1815 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'B' and resid 1826 through 1830 removed outlier: 3.731A pdb=" N GLY B1826 " --> pdb=" O THR B1839 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B1846 " --> pdb=" O LEU B1861 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'B' and resid 1874 through 1880 removed outlier: 3.663A pdb=" N GLY B1876 " --> pdb=" O SER B1889 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B1901 " --> pdb=" O LEU B1914 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'B' and resid 1922 through 1928 removed outlier: 5.327A pdb=" N VAL B1924 " --> pdb=" O ALA B1937 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B1937 " --> pdb=" O VAL B1924 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B1944 " --> pdb=" O LEU B1957 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'B' and resid 1964 through 1970 removed outlier: 3.515A pdb=" N GLY B1966 " --> pdb=" O SER B1977 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B1984 " --> pdb=" O PHE B1998 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'B' and resid 2033 through 2036 Processing sheet with id=AQ9, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id=AR1, first strand: chain 'B' and resid 2091 through 2092 removed outlier: 6.990A pdb=" N PHE B2065 " --> pdb=" O ILE B2329 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE B2329 " --> pdb=" O PHE B2065 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B2067 " --> pdb=" O VAL B2327 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B2327 " --> pdb=" O VAL B2067 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B2069 " --> pdb=" O ARG B2325 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'B' and resid 2098 through 2104 removed outlier: 4.189A pdb=" N HIS B2100 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B2125 " --> pdb=" O ILE B2138 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'B' and resid 2147 through 2154 removed outlier: 5.719A pdb=" N ILE B2148 " --> pdb=" O ALA B2165 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B2165 " --> pdb=" O ILE B2148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B2150 " --> pdb=" O THR B2163 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B2163 " --> pdb=" O GLY B2150 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR B2170 " --> pdb=" O LYS B2187 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS B2187 " --> pdb=" O THR B2170 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B2172 " --> pdb=" O LEU B2185 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B2181 " --> pdb=" O ARG B2176 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 6.765A pdb=" N ILE B2216 " --> pdb=" O LEU B2229 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 4.228A pdb=" N GLY B2239 " --> pdb=" O VAL B2252 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B2252 " --> pdb=" O GLY B2239 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B2248 " --> pdb=" O ASP B2243 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B2259 " --> pdb=" O VAL B2272 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 3.936A pdb=" N GLY B2283 " --> pdb=" O VAL B2294 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B2301 " --> pdb=" O ILE B2317 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'B' and resid 2357 through 2359 Processing sheet with id=AR8, first strand: chain 'B' and resid 2375 through 2376 Processing sheet with id=AR9, first strand: chain 'B' and resid 2416 through 2417 removed outlier: 4.900A pdb=" N GLY B2640 " --> pdb=" O SER B2394 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'B' and resid 2421 through 2422 Processing sheet with id=AS2, first strand: chain 'B' and resid 2421 through 2422 removed outlier: 6.663A pdb=" N ILE B2447 " --> pdb=" O SER B2464 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER B2464 " --> pdb=" O ILE B2447 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B2449 " --> pdb=" O LEU B2462 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU B2462 " --> pdb=" O TYR B2449 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASN B2451 " --> pdb=" O THR B2460 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N THR B2460 " --> pdb=" O ASN B2451 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'B' and resid 2469 through 2475 removed outlier: 4.389A pdb=" N GLY B2471 " --> pdb=" O SER B2484 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B2491 " --> pdb=" O ILE B2504 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'B' and resid 2510 through 2516 removed outlier: 4.007A pdb=" N ALA B2512 " --> pdb=" O THR B2525 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B2533 " --> pdb=" O ILE B2546 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 3.564A pdb=" N GLY B2556 " --> pdb=" O ALA B2569 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B2576 " --> pdb=" O VAL B2589 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'B' and resid 2596 through 2602 removed outlier: 6.505A pdb=" N THR B2609 " --> pdb=" O PHE B2597 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU B2599 " --> pdb=" O TYR B2607 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B2607 " --> pdb=" O LEU B2599 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL B2601 " --> pdb=" O TYR B2605 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR B2605 " --> pdb=" O VAL B2601 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B2615 " --> pdb=" O ASP B2610 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'B' and resid 2666 through 2668 Processing sheet with id=AS8, first strand: chain 'B' and resid 2684 through 2687 Processing sheet with id=AS9, first strand: chain 'B' and resid 2705 through 2708 Processing sheet with id=AT1, 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=AT2, first strand: chain 'B' and resid 3038 through 3040 Processing sheet with id=AT3, 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=AT4, first strand: chain 'B' and resid 3127 through 3130 Processing sheet with id=AT5, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id=AT6, first strand: chain 'B' and resid 3168 through 3172 Processing sheet with id=AT7, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id=AT8, first strand: chain 'B' and resid 3221 through 3226 removed outlier: 6.575A pdb=" N ILE B3211 " --> pdb=" O ILE B3224 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'B' and resid 3231 through 3237 removed outlier: 4.107A pdb=" N ALA B3233 " --> pdb=" O ILE B3246 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B3253 " --> pdb=" O ILE B3266 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 4.092A pdb=" N SER B3276 " --> pdb=" O LEU B3289 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B3296 " --> pdb=" O LEU B3309 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 3.724A pdb=" N GLY B3327 " --> pdb=" O ALA B3340 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B3348 " --> pdb=" O ILE B3361 " (cutoff:3.500A) Processing sheet with id=AU3, 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: 6.627A pdb=" N ILE B3391 " --> pdb=" O VAL B3404 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'B' and resid 3412 through 3418 removed outlier: 3.933A pdb=" N ALA B3414 " --> pdb=" O THR B3425 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B3432 " --> pdb=" O LEU B3446 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'B' and resid 3481 through 3484 Processing sheet with id=AU6, first strand: chain 'B' and resid 3499 through 3504 Processing sheet with id=AU7, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id=AU8, 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=AU9, first strand: chain 'B' and resid 3600 through 3602 Processing sheet with id=AV1, first strand: chain 'B' and resid 3641 through 3643 Processing sheet with id=AV2, first strand: chain 'B' and resid 3685 through 3687 Processing sheet with id=AV3, 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=AV4, first strand: chain 'B' and resid 3765 through 3768 Processing sheet with id=AV5, first strand: chain 'B' and resid 3804 through 3806 Processing sheet with id=AV6, first strand: chain 'B' and resid 3849 through 3851 Processing sheet with id=AV7, first strand: chain 'B' and resid 3997 through 3999 Processing sheet with id=AV8, first strand: chain 'B' and resid 4022 through 4026 Processing sheet with id=AV9, 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=AW1, first strand: chain 'B' and resid 4075 through 4080 removed outlier: 3.778A pdb=" N TYR B4079 " --> pdb=" O ILE B4066 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B4066 " --> pdb=" O TYR B4079 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'B' and resid 4086 through 4092 removed outlier: 4.025A pdb=" N ALA B4088 " --> pdb=" O THR B4106 " (cutoff:3.500A) Processing sheet with id=AW3, 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: 6.801A pdb=" N ILE B4168 " --> pdb=" O LEU B4181 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 3.876A pdb=" N ALA B4191 " --> pdb=" O THR B4204 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B4212 " --> pdb=" O LEU B4225 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'B' and resid 4233 through 4239 removed outlier: 3.678A pdb=" N GLY B4235 " --> pdb=" O SER B4249 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B4256 " --> pdb=" O ILE B4269 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'B' and resid 4276 through 4282 removed outlier: 4.121A pdb=" N SER B4278 " --> pdb=" O VAL B4289 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B4296 " --> pdb=" O LEU B4310 " (cutoff:3.500A) Processing sheet with id=AW7, first strand: chain 'B' and resid 4343 through 4347 Processing sheet with id=AW8, first strand: chain 'B' and resid 4390 through 4393 1794 hydrogen bonds defined for protein. 4164 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: 85.16 Time building geometry restraints manager: 14.72 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: 0.00 - 1.63: 75368 1.63 - 3.27: 5982 3.27 - 4.90: 1148 4.90 - 6.54: 176 6.54 - 8.17: 32 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: 1766 2.69 - 3.24: 57066 3.24 - 3.79: 89019 3.79 - 4.35: 125112 4.35 - 4.90: 209635 Nonbonded interactions: 482598 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 482593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 11.250 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: 0.080 Extract box with map and model: 2.070 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 186.780 Find NCS groups from input model: 3.920 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.620 ------------------------------------------------------------------------------- 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= 0.363 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 to be fit. rotamer outliers: 8 poor density : 230 time to evaluate : 5.191 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: 1.4935 time to fit residues: 455.8867 Evaluate side-chains 140 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 5.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 3101 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 3101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 643 optimal weight: 50.0000 chunk 577 optimal weight: 0.3980 chunk 320 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 389 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 597 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 363 optimal weight: 0.7980 chunk 444 optimal weight: 4.9990 chunk 691 optimal weight: 50.0000 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 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 HIS A 895 HIS A1151 HIS A1367 GLN A1712 HIS A2263 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 HIS B 895 HIS B1151 HIS B1367 GLN B1712 HIS B2263 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.1461 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 : 0.645 9.754 82706 Z= 0.344 Chirality : 0.049 0.362 9144 Planarity : 0.004 0.047 10880 Dihedral : 6.538 59.660 10240 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.58 % Allowed : 4.95 % Favored : 94.47 % 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: -0.33 (0.10), residues: 7612 helix: -3.65 (0.25), residues: 184 sheet: 0.18 (0.10), residues: 2446 loop : -0.24 (0.09), residues: 4982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2251 HIS 0.006 0.001 HIS A2195 PHE 0.015 0.001 PHE A2390 TYR 0.020 0.002 TYR B2210 ARG 0.010 0.000 ARG A2506 *********************** 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 180 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 5.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 170 average time/residue: 1.4803 time to fit residues: 328.1040 Evaluate side-chains 141 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 5.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1465 ASP Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 384 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 575 optimal weight: 0.5980 chunk 471 optimal weight: 20.0000 chunk 190 optimal weight: 0.7980 chunk 693 optimal weight: 30.0000 chunk 748 optimal weight: 50.0000 chunk 617 optimal weight: 0.0000 chunk 687 optimal weight: 0.1980 chunk 236 optimal weight: 2.9990 chunk 556 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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** A3460 HIS A3854 HIS ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3457 HIS B3460 HIS B3854 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 60752 Z= 0.140 Angle : 0.581 13.348 82706 Z= 0.307 Chirality : 0.048 0.587 9144 Planarity : 0.004 0.045 10880 Dihedral : 5.995 55.766 10236 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.76 % Allowed : 5.60 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 7612 helix: -3.44 (0.27), residues: 184 sheet: 0.19 (0.10), residues: 2414 loop : -0.11 (0.09), residues: 5014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 439 HIS 0.006 0.001 HIS A3683 PHE 0.014 0.001 PHE B1115 TYR 0.014 0.001 TYR A4030 ARG 0.007 0.000 ARG B2506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15224 Ramachandran restraints generated. 7612 Oldfield, 0 Emsley, 7612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 5.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2070 MET cc_start: 0.8382 (ptp) cc_final: 0.8149 (mpp) REVERT: A 3467 MET cc_start: 0.3648 (ptm) cc_final: 0.2358 (mpt) REVERT: B 2070 MET cc_start: 0.8381 (ptp) cc_final: 0.8154 (mpp) REVERT: B 3467 MET cc_start: 0.3649 (ptm) cc_final: 0.2359 (mpt) outliers start: 47 outliers final: 16 residues processed: 171 average time/residue: 1.5176 time to fit residues: 342.1846 Evaluate side-chains 145 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 534 GLN Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3826 LEU Chi-restraints excluded: chain B residue 3878 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 684 optimal weight: 0.3980 chunk 521 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 330 optimal weight: 5.9990 chunk 465 optimal weight: 4.9990 chunk 695 optimal weight: 20.0000 chunk 736 optimal weight: 10.0000 chunk 363 optimal weight: 4.9990 chunk 659 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 A 985 HIS A 994 GLN A1576 HIS A1798 ASN A2195 HIS B 826 ASN B 833 HIS B 985 HIS B 994 GLN B1576 HIS B1798 ASN B2195 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2264 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= 0.309 Angle : 0.599 9.850 82706 Z= 0.314 Chirality : 0.047 0.338 9144 Planarity : 0.004 0.046 10880 Dihedral : 5.854 59.198 10236 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.05 % Allowed : 6.18 % Favored : 92.77 % 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: -0.28 (0.10), residues: 7612 helix: -3.25 (0.28), residues: 184 sheet: -0.04 (0.10), residues: 2440 loop : -0.05 (0.09), residues: 4988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B3288 HIS 0.006 0.001 HIS A2195 PHE 0.016 0.001 PHE B2330 TYR 0.022 0.001 TYR B2210 ARG 0.004 0.000 ARG A1413 *********************** 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 198 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 28 residues processed: 182 average time/residue: 1.4080 time to fit residues: 339.4165 Evaluate side-chains 155 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 5.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 534 GLN Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3231 VAL Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3231 VAL Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3826 LEU Chi-restraints excluded: chain B residue 3878 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 613 optimal weight: 6.9990 chunk 418 optimal weight: 30.0000 chunk 10 optimal weight: 40.0000 chunk 548 optimal weight: 3.9990 chunk 303 optimal weight: 20.0000 chunk 628 optimal weight: 5.9990 chunk 509 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 376 optimal weight: 0.9980 chunk 661 optimal weight: 10.0000 chunk 185 optimal weight: 0.0770 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A1803 HIS A2541 ASN B1803 HIS B2541 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 60752 Z= 0.298 Angle : 0.584 10.037 82706 Z= 0.306 Chirality : 0.047 0.321 9144 Planarity : 0.004 0.047 10880 Dihedral : 5.732 59.133 10236 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.92 % Allowed : 6.73 % Favored : 92.35 % 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: -0.35 (0.10), residues: 7612 helix: -3.17 (0.28), residues: 184 sheet: -0.14 (0.11), residues: 2374 loop : -0.09 (0.09), residues: 5054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2293 HIS 0.007 0.001 HIS A 435 PHE 0.015 0.001 PHE A2330 TYR 0.019 0.001 TYR A2210 ARG 0.014 0.000 ARG A1364 *********************** 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 184 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 5.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4201 MET cc_start: 0.5891 (mtm) cc_final: 0.5678 (mtp) REVERT: B 4201 MET cc_start: 0.5891 (mtm) cc_final: 0.5677 (mtp) outliers start: 57 outliers final: 30 residues processed: 176 average time/residue: 1.4108 time to fit residues: 330.4002 Evaluate side-chains 153 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3231 VAL Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3231 VAL Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3826 LEU Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 247 optimal weight: 7.9990 chunk 663 optimal weight: 6.9990 chunk 145 optimal weight: 0.0170 chunk 432 optimal weight: 0.0050 chunk 181 optimal weight: 0.9980 chunk 737 optimal weight: 9.9990 chunk 612 optimal weight: 9.9990 chunk 341 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 387 optimal weight: 3.9990 overall best weight: 1.4036 ------------------------------------------------------------------------------- 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 ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 60752 Z= 0.199 Angle : 0.561 11.133 82706 Z= 0.293 Chirality : 0.046 0.327 9144 Planarity : 0.004 0.048 10880 Dihedral : 5.551 59.166 10236 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.79 % Allowed : 7.41 % Favored : 91.80 % 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: -2.90 (0.30), residues: 184 sheet: -0.13 (0.11), residues: 2354 loop : -0.07 (0.09), residues: 5074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2293 HIS 0.007 0.001 HIS A4387 PHE 0.012 0.001 PHE B2330 TYR 0.015 0.001 TYR B2210 ARG 0.005 0.000 ARG B1364 *********************** 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 174 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 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: A 234 CYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6354 (m) REVERT: A 4201 MET cc_start: 0.5828 (mtm) cc_final: 0.5454 (mtp) REVERT: A 4403 CYS cc_start: 0.4292 (OUTLIER) cc_final: 0.3494 (m) REVERT: B 234 CYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6363 (m) REVERT: B 4201 MET cc_start: 0.5827 (mtm) cc_final: 0.5452 (mtp) REVERT: B 4403 CYS cc_start: 0.4286 (OUTLIER) cc_final: 0.3492 (m) outliers start: 49 outliers final: 28 residues processed: 168 average time/residue: 1.3628 time to fit residues: 304.9196 Evaluate side-chains 155 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1443 SER Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3231 VAL Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1443 SER Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3231 VAL Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 710 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 420 optimal weight: 30.0000 chunk 538 optimal weight: 0.9990 chunk 417 optimal weight: 9.9990 chunk 620 optimal weight: 3.9990 chunk 411 optimal weight: 6.9990 chunk 734 optimal weight: 9.9990 chunk 459 optimal weight: 5.9990 chunk 447 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2356 HIS A2637 GLN A3324 ASN ** A3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3683 HIS A4063 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2356 HIS B2637 GLN B3324 ASN ** B3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3683 HIS B4063 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 60752 Z= 0.584 Angle : 0.712 11.735 82706 Z= 0.367 Chirality : 0.052 0.296 9144 Planarity : 0.005 0.052 10880 Dihedral : 6.111 59.425 10236 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.13 % Allowed : 7.41 % Favored : 91.46 % 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: -0.58 (0.10), residues: 7612 helix: -2.86 (0.29), residues: 196 sheet: -0.42 (0.11), residues: 2376 loop : -0.18 (0.09), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1965 HIS 0.017 0.001 HIS A2195 PHE 0.022 0.002 PHE B2330 TYR 0.029 0.002 TYR B2210 ARG 0.019 0.001 ARG A2444 *********************** 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 193 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 123 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6408 (m) REVERT: A 2212 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: A 4201 MET cc_start: 0.5745 (mtm) cc_final: 0.5345 (mtp) REVERT: A 4403 CYS cc_start: 0.4653 (OUTLIER) cc_final: 0.4216 (m) REVERT: B 234 CYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6411 (m) REVERT: B 2212 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: B 4201 MET cc_start: 0.5745 (mtm) cc_final: 0.5345 (mtp) REVERT: B 4403 CYS cc_start: 0.4647 (OUTLIER) cc_final: 0.4212 (m) outliers start: 70 outliers final: 36 residues processed: 181 average time/residue: 1.3085 time to fit residues: 318.8179 Evaluate side-chains 165 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1568 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2610 ASP Chi-restraints excluded: chain A residue 3231 VAL Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1568 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2212 GLN Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2610 ASP Chi-restraints excluded: chain B residue 3231 VAL Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 454 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 chunk 221 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 466 optimal weight: 7.9990 chunk 500 optimal weight: 2.9990 chunk 363 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 577 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1436 ASN ** A3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3806 GLN ** B3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3806 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3318 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= 0.200 Angle : 0.584 12.984 82706 Z= 0.300 Chirality : 0.046 0.318 9144 Planarity : 0.004 0.049 10880 Dihedral : 5.723 58.544 10236 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.78 % Allowed : 7.91 % Favored : 91.31 % 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: -0.42 (0.10), residues: 7612 helix: -2.75 (0.30), residues: 196 sheet: -0.24 (0.11), residues: 2404 loop : -0.11 (0.09), residues: 5012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2293 HIS 0.005 0.001 HIS B4387 PHE 0.012 0.001 PHE A1615 TYR 0.014 0.001 TYR B2210 ARG 0.010 0.000 ARG A2444 *********************** 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 171 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6164 (m) REVERT: A 2212 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: A 4403 CYS cc_start: 0.4616 (OUTLIER) cc_final: 0.4137 (m) REVERT: B 234 CYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6167 (m) REVERT: B 2212 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: B 3457 HIS cc_start: 0.5295 (OUTLIER) cc_final: 0.5032 (m-70) REVERT: B 4403 CYS cc_start: 0.4611 (OUTLIER) cc_final: 0.4134 (m) outliers start: 48 outliers final: 32 residues processed: 165 average time/residue: 1.3771 time to fit residues: 304.4441 Evaluate side-chains 162 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 958 HIS Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2522 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3231 VAL Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2212 GLN Chi-restraints excluded: chain B residue 2328 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3231 VAL Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3457 HIS Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 668 optimal weight: 40.0000 chunk 703 optimal weight: 20.0000 chunk 641 optimal weight: 50.0000 chunk 684 optimal weight: 1.9990 chunk 411 optimal weight: 0.0570 chunk 298 optimal weight: 3.9990 chunk 537 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 618 optimal weight: 0.9990 chunk 647 optimal weight: 0.9980 chunk 682 optimal weight: 5.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 60752 Z= 0.151 Angle : 0.569 14.563 82706 Z= 0.290 Chirality : 0.045 0.319 9144 Planarity : 0.004 0.049 10880 Dihedral : 5.402 58.563 10236 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.76 % Allowed : 7.93 % Favored : 91.31 % 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: -0.35 (0.10), residues: 7612 helix: -2.72 (0.31), residues: 184 sheet: -0.22 (0.10), residues: 2432 loop : -0.05 (0.09), residues: 4996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 799 HIS 0.007 0.001 HIS B4387 PHE 0.012 0.001 PHE B 541 TYR 0.013 0.001 TYR B2210 ARG 0.010 0.000 ARG A2444 *********************** 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 to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6177 (m) REVERT: A 621 MET cc_start: 0.6558 (mmm) cc_final: 0.6223 (mmt) REVERT: A 4134 ARG cc_start: 0.3292 (OUTLIER) cc_final: 0.1455 (pmt-80) REVERT: A 4403 CYS cc_start: 0.4467 (OUTLIER) cc_final: 0.3946 (m) REVERT: B 234 CYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6184 (m) REVERT: B 621 MET cc_start: 0.6493 (mmm) cc_final: 0.6211 (mmt) REVERT: B 3457 HIS cc_start: 0.5381 (OUTLIER) cc_final: 0.5057 (m-70) REVERT: B 4134 ARG cc_start: 0.3295 (OUTLIER) cc_final: 0.1458 (pmt-80) REVERT: B 4403 CYS cc_start: 0.4458 (OUTLIER) cc_final: 0.3940 (m) outliers start: 47 outliers final: 30 residues processed: 162 average time/residue: 1.4363 time to fit residues: 306.8836 Evaluate side-chains 160 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3231 VAL Chi-restraints excluded: chain A residue 3337 VAL Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4134 ARG Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3231 VAL Chi-restraints excluded: chain B residue 3337 VAL Chi-restraints excluded: chain B residue 3457 HIS Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4134 ARG Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 449 optimal weight: 2.9990 chunk 723 optimal weight: 40.0000 chunk 441 optimal weight: 9.9990 chunk 343 optimal weight: 9.9990 chunk 503 optimal weight: 4.9990 chunk 759 optimal weight: 9.9990 chunk 698 optimal weight: 7.9990 chunk 604 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 466 optimal weight: 6.9990 chunk 370 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1232 HIS ** A3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1232 HIS ** B3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 60752 Z= 0.520 Angle : 0.685 13.914 82706 Z= 0.349 Chirality : 0.050 0.290 9144 Planarity : 0.004 0.051 10880 Dihedral : 5.863 57.360 10236 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.57 % Allowed : 8.14 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 7612 helix: -2.60 (0.31), residues: 196 sheet: -0.37 (0.11), residues: 2410 loop : -0.17 (0.09), residues: 5006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A2251 HIS 0.011 0.001 HIS B2195 PHE 0.020 0.002 PHE A2330 TYR 0.023 0.002 TYR B2210 ARG 0.009 0.001 ARG A2444 ********************** 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 161 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 5.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 CYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6156 (m) REVERT: A 4134 ARG cc_start: 0.3020 (OUTLIER) cc_final: 0.1106 (pmt-80) REVERT: A 4403 CYS cc_start: 0.4669 (OUTLIER) cc_final: 0.4146 (m) REVERT: B 234 CYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6162 (m) REVERT: B 621 MET cc_start: 0.6620 (mmm) cc_final: 0.6308 (mmt) REVERT: B 3457 HIS cc_start: 0.5402 (OUTLIER) cc_final: 0.5044 (m-70) REVERT: B 4134 ARG cc_start: 0.3022 (OUTLIER) cc_final: 0.1106 (pmt-80) REVERT: B 4403 CYS cc_start: 0.4668 (OUTLIER) cc_final: 0.4145 (m) outliers start: 35 outliers final: 22 residues processed: 155 average time/residue: 1.4661 time to fit residues: 299.2694 Evaluate side-chains 153 residues out of total 6704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 5.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 2067 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2328 THR Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 3878 HIS Chi-restraints excluded: chain A residue 4134 ARG Chi-restraints excluded: chain A residue 4385 CYS Chi-restraints excluded: chain A residue 4403 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1122 CYS Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 2067 VAL Chi-restraints excluded: chain B residue 2069 SER Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 3457 HIS Chi-restraints excluded: chain B residue 3878 HIS Chi-restraints excluded: chain B residue 4134 ARG Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4403 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 480 optimal weight: 8.9990 chunk 643 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 557 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 605 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 621 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 111 optimal weight: 40.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.083670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.052472 restraints weight = 314526.137| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.14 r_work: 0.2834 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 60752 Z= 0.329 Angle : 0.621 18.002 82706 Z= 0.316 Chirality : 0.047 0.305 9144 Planarity : 0.004 0.050 10880 Dihedral : 5.720 54.598 10236 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.66 % Allowed : 8.22 % Favored : 91.12 % 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: -0.52 (0.10), residues: 7612 helix: -2.52 (0.32), residues: 196 sheet: -0.41 (0.10), residues: 2436 loop : -0.13 (0.09), residues: 4980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2293 HIS 0.006 0.001 HIS B2195 PHE 0.016 0.001 PHE A2330 TYR 0.016 0.001 TYR B1622 ARG 0.009 0.000 ARG B2444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10995.13 seconds wall clock time: 194 minutes 26.69 seconds (11666.69 seconds total)