Starting phenix.real_space_refine on Sat Sep 28 10:00:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/09_2024/8em7_28241.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/09_2024/8em7_28241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/09_2024/8em7_28241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/09_2024/8em7_28241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/09_2024/8em7_28241.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em7_28241/09_2024/8em7_28241.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 88 9.91 5 S 764 5.16 5 C 41716 2.51 5 N 11682 2.21 5 O 13302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67552 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 32850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4378, 32850 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 406} Link IDs: {'PCIS': 5, 'PTRANS': 213, 'TRANS': 4159} Chain breaks: 1 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1631 Unresolved non-hydrogen dihedrals: 1031 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 33, 'ASP:plan': 61, 'TYR:plan': 2, 'ASN:plan1': 32, 'HIS:plan': 12, 'PHE:plan': 1, 'GLU:plan': 55, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 901 Chain: "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: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 898 Unusual residues: {' CA': 44, 'NAG': 39, 'NGA': 22} Classifications: {'undetermined': 105} Link IDs: {None: 104} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 61 Restraints were copied for chains: D, B Time building chain proxies: 161.05, per 1000 atoms: 2.38 Number of scatterers: 67552 At special positions: 0 Unit cell: (158.53, 219.95, 241.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 88 19.99 S 764 16.00 O 13302 8.00 N 11682 7.00 C 41716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=161, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 40 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 80 " distance=2.04 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 93 " distance=2.02 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 103 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 120 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 179 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 208 " distance=2.04 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 217 " distance=2.02 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 306 " distance=2.04 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " distance=2.02 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.04 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 703 " distance=2.04 Simple disulfide: pdb=" SG CYS A 973 " - pdb=" SG CYS A 987 " distance=2.04 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.04 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.02 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.02 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.03 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.04 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.04 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.05 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1135 " distance=2.04 Simple disulfide: pdb=" SG CYS A1129 " - pdb=" SG CYS A1144 " distance=2.04 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS A1162 " distance=2.02 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.04 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.04 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.04 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A1272 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1297 " distance=2.03 Simple disulfide: pdb=" SG CYS A1291 " - pdb=" SG CYS A1306 " distance=2.03 Simple disulfide: pdb=" SG CYS A1313 " - pdb=" SG CYS A1326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1339 " distance=2.05 Simple disulfide: pdb=" SG CYS A1333 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1354 " - pdb=" SG CYS A1365 " distance=2.04 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1374 " distance=2.02 Simple disulfide: pdb=" SG CYS A1376 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1401 " - pdb=" SG CYS A1414 " distance=2.03 Simple disulfide: pdb=" SG CYS A1416 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1705 " - pdb=" SG CYS A1714 " distance=2.04 Simple disulfide: pdb=" SG CYS A1710 " - pdb=" SG CYS A1726 " distance=2.02 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1741 " distance=2.03 Simple disulfide: pdb=" SG CYS A2023 " - pdb=" SG CYS A2034 " distance=2.04 Simple disulfide: pdb=" SG CYS A2030 " - pdb=" SG CYS A2044 " distance=2.03 Simple disulfide: pdb=" SG CYS A2046 " - pdb=" SG CYS A2059 " distance=2.03 Simple disulfide: pdb=" SG CYS A2347 " - pdb=" SG CYS A2358 " distance=2.04 Simple disulfide: pdb=" SG CYS A2354 " - pdb=" SG CYS A2369 " distance=2.04 Simple disulfide: pdb=" SG CYS A2371 " - pdb=" SG CYS A2383 " distance=2.03 Simple disulfide: pdb=" SG CYS A2518 " - pdb=" SG CYS A2652 " distance=2.04 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2667 " distance=2.04 Simple disulfide: pdb=" SG CYS A2663 " - pdb=" SG CYS A2676 " distance=2.03 Simple disulfide: pdb=" SG CYS A2678 " - pdb=" SG CYS A2693 " distance=2.05 Simple disulfide: pdb=" SG CYS A2701 " - pdb=" SG CYS A2713 " distance=2.04 Simple disulfide: pdb=" SG CYS A2708 " - pdb=" SG CYS A2726 " distance=2.03 Simple disulfide: pdb=" SG CYS A2720 " - pdb=" SG CYS A2737 " distance=2.04 Simple disulfide: pdb=" SG CYS A2742 " - pdb=" SG CYS A2754 " distance=2.03 Simple disulfide: pdb=" SG CYS A2749 " - pdb=" SG CYS A2767 " distance=2.03 Simple disulfide: pdb=" SG CYS A2761 " - pdb=" SG CYS A2776 " distance=2.02 Simple disulfide: pdb=" SG CYS A2781 " - pdb=" SG CYS A2794 " distance=2.04 Simple disulfide: pdb=" SG CYS A2789 " - pdb=" SG CYS A2807 " distance=2.03 Simple disulfide: pdb=" SG CYS A2801 " - pdb=" SG CYS A2818 " distance=2.03 Simple disulfide: pdb=" SG CYS A2823 " - pdb=" SG CYS A2836 " distance=2.04 Simple disulfide: pdb=" SG CYS A2830 " - pdb=" SG CYS A2849 " distance=2.04 Simple disulfide: pdb=" SG CYS A2843 " - pdb=" SG CYS A2860 " distance=2.03 Simple disulfide: pdb=" SG CYS A2865 " - pdb=" SG CYS A2878 " distance=2.04 Simple disulfide: pdb=" SG CYS A2872 " - pdb=" SG CYS A2891 " distance=2.03 Simple disulfide: pdb=" SG CYS A2885 " - pdb=" SG CYS A2901 " distance=2.04 Simple disulfide: pdb=" SG CYS A2908 " - pdb=" SG CYS A2920 " distance=2.03 Simple disulfide: pdb=" SG CYS A2915 " - pdb=" SG CYS A2933 " distance=2.03 Simple disulfide: pdb=" SG CYS A2927 " - pdb=" SG CYS A2945 " distance=2.03 Simple disulfide: pdb=" SG CYS A2950 " - pdb=" SG CYS A2967 " distance=2.04 Simple disulfide: pdb=" SG CYS A2957 " - pdb=" SG CYS A2980 " distance=2.04 Simple disulfide: pdb=" SG CYS A2974 " - pdb=" SG CYS A2990 " distance=2.03 Simple disulfide: pdb=" SG CYS A2995 " - pdb=" SG CYS A3007 " distance=2.04 Simple disulfide: pdb=" SG CYS A3002 " - pdb=" SG CYS A3020 " distance=2.03 Simple disulfide: pdb=" SG CYS A3014 " - pdb=" SG CYS A3029 " distance=2.04 Simple disulfide: pdb=" SG CYS A3034 " - pdb=" SG CYS A3046 " distance=2.03 Simple disulfide: pdb=" SG CYS A3041 " - pdb=" SG CYS A3059 " distance=2.02 Simple disulfide: pdb=" SG CYS A3053 " - pdb=" SG CYS A3070 " distance=2.04 Simple disulfide: pdb=" SG CYS A3077 " - pdb=" SG CYS A3089 " distance=2.03 Simple disulfide: pdb=" SG CYS A3084 " - pdb=" SG CYS A3102 " distance=2.03 Simple disulfide: pdb=" SG CYS A3096 " - pdb=" SG CYS A3111 " distance=2.03 Simple disulfide: pdb=" SG CYS A3116 " - pdb=" SG CYS A3128 " distance=2.04 Simple disulfide: pdb=" SG CYS A3124 " - pdb=" SG CYS A3137 " distance=2.03 Simple disulfide: pdb=" SG CYS A3139 " - pdb=" SG CYS A3152 " distance=2.03 Simple disulfide: pdb=" SG CYS A3158 " - pdb=" SG CYS A3169 " distance=2.03 Simple disulfide: pdb=" SG CYS A3165 " - pdb=" SG CYS A3178 " distance=2.04 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.04 Simple disulfide: pdb=" SG CYS A3313 " - pdb=" SG CYS A3321 " distance=2.03 Simple disulfide: pdb=" SG CYS A3471 " - pdb=" SG CYS A3482 " distance=2.04 Simple disulfide: pdb=" SG CYS A3478 " - pdb=" SG CYS A3493 " distance=2.03 Simple disulfide: pdb=" SG CYS A3495 " - pdb=" SG CYS A3510 " distance=2.03 Simple disulfide: pdb=" SG CYS A3514 " - pdb=" SG CYS A3527 " distance=2.03 Simple disulfide: pdb=" SG CYS A3521 " - pdb=" SG CYS A3540 " distance=2.03 Simple disulfide: pdb=" SG CYS A3534 " - pdb=" SG CYS A3550 " distance=2.04 Simple disulfide: pdb=" SG CYS A3555 " - pdb=" SG CYS A3567 " distance=2.02 Simple disulfide: pdb=" SG CYS A3562 " - pdb=" SG CYS A3580 " distance=2.04 Simple disulfide: pdb=" SG CYS A3574 " - pdb=" SG CYS A3591 " distance=2.04 Simple disulfide: pdb=" SG CYS A3596 " - pdb=" SG CYS A3608 " distance=2.03 Simple disulfide: pdb=" SG CYS A3603 " - pdb=" SG CYS A3621 " distance=2.03 Simple disulfide: pdb=" SG CYS A3615 " - pdb=" SG CYS A3632 " distance=2.03 Simple disulfide: pdb=" SG CYS A3637 " - pdb=" SG CYS A3649 " distance=2.04 Simple disulfide: pdb=" SG CYS A3644 " - pdb=" SG CYS A3662 " distance=2.03 Simple disulfide: pdb=" SG CYS A3656 " - pdb=" SG CYS A3673 " distance=2.04 Simple disulfide: pdb=" SG CYS A3680 " - pdb=" SG CYS A3694 " distance=2.02 Simple disulfide: pdb=" SG CYS A3688 " - pdb=" SG CYS A3707 " distance=2.04 Simple disulfide: pdb=" SG CYS A3701 " - pdb=" SG CYS A3716 " distance=2.04 Simple disulfide: pdb=" SG CYS A3721 " - pdb=" SG CYS A3734 " distance=2.03 Simple disulfide: pdb=" SG CYS A3729 " - pdb=" SG CYS A3747 " distance=2.03 Simple disulfide: pdb=" SG CYS A3741 " - pdb=" SG CYS A3756 " distance=2.04 Simple disulfide: pdb=" SG CYS A3761 " - pdb=" SG CYS A3773 " distance=2.03 Simple disulfide: pdb=" SG CYS A3768 " - pdb=" SG CYS A3786 " distance=2.04 Simple disulfide: pdb=" SG CYS A3780 " - pdb=" SG CYS A3795 " distance=2.03 Simple disulfide: pdb=" SG CYS A3800 " - pdb=" SG CYS A3812 " distance=2.03 Simple disulfide: pdb=" SG CYS A3807 " - pdb=" SG CYS A3825 " distance=2.04 Simple disulfide: pdb=" SG CYS A3819 " - pdb=" SG CYS A3834 " distance=2.03 Simple disulfide: pdb=" SG CYS A3844 " - pdb=" SG CYS A3856 " distance=2.01 Simple disulfide: pdb=" SG CYS A3851 " - pdb=" SG CYS A3869 " distance=2.03 Simple disulfide: pdb=" SG CYS A3863 " - pdb=" SG CYS A3880 " distance=2.04 Simple disulfide: pdb=" SG CYS A3885 " - pdb=" SG CYS A3898 " distance=2.03 Simple disulfide: pdb=" SG CYS A3893 " - pdb=" SG CYS A3911 " distance=2.05 Simple disulfide: pdb=" SG CYS A3905 " - pdb=" SG CYS A3922 " distance=2.04 Simple disulfide: pdb=" SG CYS A3930 " - pdb=" SG CYS A3942 " distance=2.03 Simple disulfide: pdb=" SG CYS A3937 " - pdb=" SG CYS A3955 " distance=2.04 Simple disulfide: pdb=" SG CYS A3949 " - pdb=" SG CYS A3964 " distance=2.04 Simple disulfide: pdb=" SG CYS A3972 " - pdb=" SG CYS A3981 " distance=2.04 Simple disulfide: pdb=" SG CYS A3977 " - pdb=" SG CYS A3991 " distance=2.02 Simple disulfide: pdb=" SG CYS A3993 " - pdb=" SG CYS A4007 " distance=2.03 Simple disulfide: pdb=" SG CYS A4013 " - pdb=" SG CYS A4023 " distance=2.03 Simple disulfide: pdb=" SG CYS A4019 " - pdb=" SG CYS A4032 " distance=2.04 Simple disulfide: pdb=" SG CYS A4034 " - pdb=" SG CYS A4049 " distance=2.03 Simple disulfide: pdb=" SG CYS A4336 " - pdb=" SG CYS A4344 " distance=2.03 Simple disulfide: pdb=" SG CYS A4340 " - pdb=" SG CYS A4353 " distance=2.04 Simple disulfide: pdb=" SG CYS A4355 " - pdb=" SG CYS A4369 " distance=2.04 Simple disulfide: pdb=" SG CYS A4383 " - pdb=" SG CYS A4391 " distance=2.04 Simple disulfide: pdb=" SG CYS A4385 " - pdb=" SG CYS A4401 " distance=2.03 Simple disulfide: pdb=" SG CYS A4403 " - pdb=" SG CYS A4412 " distance=2.04 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=44, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A4701 " - " ASN A 340 " " NAG A4702 " - " ASN A 387 " " NAG A4703 " - " ASN A 657 " " NAG A4704 " - " ASN A 865 " " NAG A4705 " - " ASN A1187 " " NAG A4706 " - " ASN A1328 " " NAG A4707 " - " ASN A1341 " " NAG A4708 " - " ASN A1384 " " NAG A4709 " - " ASN A1451 " " NAG A4710 " - " ASN A1497 " " NAG A4711 " - " ASN A1551 " " NAG A4712 " - " ASN A1676 " " NAG A4713 " - " ASN A1733 " " NAG A4714 " - " ASN A1811 " " NAG A4715 " - " ASN A2134 " " NAG A4716 " - " ASN A2225 " " NAG A4717 " - " ASN A2396 " " NAG A4718 " - " ASN A2488 " " NAG A4719 " - " ASN A2548 " " NAG A4720 " - " ASN A2782 " " NAG A4721 " - " ASN A2810 " " NAG A4722 " - " ASN A2949 " " NAG A4723 " - " ASN A2989 " " NAG A4724 " - " ASN A3127 " " NAG A4725 " - " ASN A3213 " " NAG A4726 " - " ASN A3259 " " NAG A4727 " - " ASN A3317 " " NAG A4728 " - " ASN A3357 " " NAG A4729 " - " ASN A3448 " " NAG A4730 " - " ASN A3566 " " NAG A4731 " - " ASN A3682 " " NAG A4732 " - " ASN A3840 " " NAG A4733 " - " ASN A3969 " " NAG A4734 " - " ASN A3980 " " NAG A4735 " - " ASN A4070 " " NAG A4736 " - " ASN A4329 " " NAG A4739 " - " ASN A 178 " " NAG A4804 " - " ASN A 159 " " NAG A4805 " - " ASN A 462 " " NAG B4701 " - " ASN B 340 " " NAG B4702 " - " ASN B 387 " " NAG B4703 " - " ASN B 657 " " NAG B4704 " - " ASN B 865 " " NAG B4705 " - " ASN B1187 " " NAG B4706 " - " ASN B1328 " " NAG B4707 " - " ASN B1341 " " NAG B4708 " - " ASN B1384 " " NAG B4709 " - " ASN B1451 " " NAG B4710 " - " ASN B1497 " " NAG B4711 " - " ASN B1551 " " NAG B4712 " - " ASN B1676 " " NAG B4713 " - " ASN B1733 " " NAG B4714 " - " ASN B1811 " " NAG B4715 " - " ASN B2134 " " NAG B4716 " - " ASN B2225 " " NAG B4717 " - " ASN B2396 " " NAG B4718 " - " ASN B2488 " " NAG B4719 " - " ASN B2548 " " NAG B4720 " - " ASN B2782 " " NAG B4721 " - " ASN B2810 " " NAG B4722 " - " ASN B2949 " " NAG B4723 " - " ASN B2989 " " NAG B4724 " - " ASN B3127 " " NAG B4725 " - " ASN B3213 " " NAG B4726 " - " ASN B3259 " " NAG B4727 " - " ASN B3317 " " NAG B4728 " - " ASN B3357 " " NAG B4729 " - " ASN B3448 " " NAG B4730 " - " ASN B3566 " " NAG B4731 " - " ASN B3682 " " NAG B4732 " - " ASN B3840 " " NAG B4733 " - " ASN B3969 " " NAG B4734 " - " ASN B3980 " " NAG B4735 " - " ASN B4070 " " NAG B4736 " - " ASN B4329 " " NAG B4739 " - " ASN B 178 " " NAG B4804 " - " ASN B 159 " " NAG B4805 " - " ASN B 462 " " NAG C 1 " - " ASN A2178 " " NAG D 1 " - " ASN B2178 " Number of additional bonds: simple=44, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.46 Conformation dependent library (CDL) restraints added in 6.8 seconds 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16188 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 230 sheets defined 9.9% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.999A pdb=" N ILE A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 124 through 128 removed outlier: 4.097A pdb=" N CYS A 127 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 128' Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.784A pdb=" N CYS A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.452A pdb=" N ASN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.931A pdb=" N ASP A 242 " --> pdb=" O TRP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.846A pdb=" N SER A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 1041 through 1045 removed outlier: 3.855A pdb=" N CYS A1044 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1087 removed outlier: 3.669A pdb=" N CYS A1086 " --> pdb=" O GLN A1083 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A1087 " --> pdb=" O TRP A1084 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1083 through 1087' Processing helix chain 'A' and resid 1095 through 1100 removed outlier: 4.012A pdb=" N ASN A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.987A pdb=" N CYS A1129 " --> pdb=" O GLU A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1138 through 1143 removed outlier: 4.326A pdb=" N ASN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.110A pdb=" N CYS A1169 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1183 removed outlier: 4.133A pdb=" N GLY A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 removed outlier: 4.361A pdb=" N CYS A1208 " --> pdb=" O ARG A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 removed outlier: 3.980A pdb=" N GLY A1222 " --> pdb=" O ASP A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1231 removed outlier: 3.597A pdb=" N MET A1230 " --> pdb=" O PRO A1227 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS A1231 " --> pdb=" O PRO A1228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1227 through 1231' 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 1288 through 1292 removed outlier: 4.050A pdb=" N CYS A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A1292 " --> pdb=" O TRP A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1288 through 1292' Processing helix chain 'A' and resid 1301 through 1305 removed outlier: 3.612A pdb=" N LYS A1304 " --> pdb=" O SER A1301 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP A1305 " --> pdb=" O ASP A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1301 through 1305' Processing helix chain 'A' and resid 1330 through 1332 No H-bonds generated for 'chain 'A' and resid 1330 through 1332' Processing helix chain 'A' and resid 1346 through 1351 Processing helix chain 'A' and resid 1357 through 1361 Processing helix chain 'A' and resid 1393 through 1397 Processing helix chain 'A' and resid 1694 through 1698 removed outlier: 3.559A pdb=" N ARG A1697 " --> pdb=" O HIS A1694 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A1698 " --> pdb=" O PRO A1695 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1694 through 1698' Processing helix chain 'A' and resid 1704 through 1708 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 2331 through 2335 Processing helix chain 'A' and resid 2345 through 2354 removed outlier: 3.859A pdb=" N GLN A2349 " --> pdb=" O PRO A2346 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER A2350 " --> pdb=" O CYS A2347 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN A2351 " --> pdb=" O LEU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2654 through 2658 removed outlier: 3.518A pdb=" N GLN A2658 " --> pdb=" O PRO A2655 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2663 Processing helix chain 'A' and resid 2717 through 2721 removed outlier: 4.334A pdb=" N CYS A2720 " --> pdb=" O ASP A2717 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A2721 " --> pdb=" O TRP A2718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2717 through 2721' Processing helix chain 'A' and resid 2733 through 2738 Processing helix chain 'A' and resid 2756 through 2760 Processing helix chain 'A' and resid 2798 through 2800 No H-bonds generated for 'chain 'A' and resid 2798 through 2800' Processing helix chain 'A' and resid 2840 through 2844 removed outlier: 4.086A pdb=" N CYS A2843 " --> pdb=" O ALA A2840 " (cutoff:3.500A) Processing helix chain 'A' and resid 2856 through 2861 Processing helix chain 'A' and resid 2882 through 2887 removed outlier: 4.030A pdb=" N CYS A2885 " --> pdb=" O TYR A2882 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A2887 " --> pdb=" O PHE A2884 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2902 Processing helix chain 'A' and resid 2924 through 2926 No H-bonds generated for 'chain 'A' and resid 2924 through 2926' Processing helix chain 'A' and resid 2940 through 2948 removed outlier: 6.450A pdb=" N CYS A2945 " --> pdb=" O ARG A2942 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU A2946 " --> pdb=" O HIS A2943 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2973 No H-bonds generated for 'chain 'A' and resid 2971 through 2973' Processing helix chain 'A' and resid 2983 through 2987 Processing helix chain 'A' and resid 3011 through 3013 No H-bonds generated for 'chain 'A' and resid 3011 through 3013' Processing helix chain 'A' and resid 3050 through 3054 removed outlier: 4.019A pdb=" N CYS A3053 " --> pdb=" O LEU A3050 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A3054 " --> pdb=" O TYR A3051 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3050 through 3054' Processing helix chain 'A' and resid 3066 through 3071 Processing helix chain 'A' and resid 3093 through 3097 removed outlier: 3.860A pdb=" N CYS A3096 " --> pdb=" O GLY A3093 " (cutoff:3.500A) Processing helix chain 'A' and resid 3105 through 3110 removed outlier: 4.232A pdb=" N LYS A3109 " --> pdb=" O ASN A3105 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A3110 " --> pdb=" O SER A3106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3105 through 3110' 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: 3.730A 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 3474 through 3478 Processing helix chain 'A' and resid 3522 through 3525 removed outlier: 3.663A pdb=" N GLU A3525 " --> pdb=" O GLY A3522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3522 through 3525' 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 3575 removed outlier: 3.505A pdb=" N ALA A3572 " --> pdb=" O SER A3569 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS A3574 " --> pdb=" O GLN A3571 " (cutoff:3.500A) 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 3623 through 3627 removed outlier: 3.851A pdb=" N ASP A3626 " --> pdb=" O ASP A3623 " (cutoff:3.500A) Processing helix chain 'A' and resid 3628 through 3633 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 3669 through 3674 Processing helix chain 'A' and resid 3675 through 3679 Processing helix chain 'A' and resid 3698 through 3701 removed outlier: 3.854A pdb=" N CYS A3701 " --> pdb=" O TRP A3698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3698 through 3701' Processing helix chain 'A' and resid 3712 through 3716 removed outlier: 4.284A pdb=" N GLY A3715 " --> pdb=" O ASP A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3738 through 3742 removed outlier: 3.937A pdb=" N CYS A3741 " --> pdb=" O ARG A3738 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A3742 " --> pdb=" O TRP A3739 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3738 through 3742' Processing helix chain 'A' and resid 3750 through 3755 removed outlier: 4.400A pdb=" N SER A3755 " --> pdb=" O SER A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3777 through 3781 removed outlier: 3.929A pdb=" N CYS A3780 " --> pdb=" O ARG A3777 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP A3781 " --> pdb=" O TRP A3778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3777 through 3781' Processing helix chain 'A' and resid 3815 through 3819 removed outlier: 4.441A pdb=" N CYS A3819 " --> pdb=" O LYS A3815 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3815 through 3819' Processing helix chain 'A' and resid 3830 through 3834 removed outlier: 3.878A pdb=" N ALA A3833 " --> pdb=" O ASP A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3858 through 3862 Processing helix chain 'A' and resid 3872 through 3875 Processing helix chain 'A' and resid 3876 through 3881 removed outlier: 4.020A pdb=" N CYS A3880 " --> pdb=" O GLU A3876 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A3881 " --> pdb=" O ILE A3877 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3876 through 3881' Processing helix chain 'A' and resid 3902 through 3906 removed outlier: 3.719A pdb=" N CYS A3905 " --> pdb=" O HIS A3902 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3923 Processing helix chain 'A' and resid 3946 through 3950 removed outlier: 3.753A pdb=" N CYS A3949 " --> pdb=" O HIS A3946 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A3950 " --> pdb=" O TYR A3947 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3946 through 3950' Processing helix chain 'A' and resid 3971 through 3975 Processing helix chain 'A' and resid 4011 through 4015 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.999A pdb=" N ILE B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 61' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 124 through 128 removed outlier: 4.097A pdb=" N CYS B 127 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 128' Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.784A pdb=" N CYS B 164 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 165 " --> pdb=" O GLN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 removed outlier: 4.452A pdb=" N ASN B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 removed outlier: 3.931A pdb=" N ASP B 242 " --> pdb=" O TRP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.846A pdb=" N SER B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 1041 through 1045 removed outlier: 3.855A pdb=" N CYS B1044 " --> pdb=" O ILE B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1087 removed outlier: 3.669A pdb=" N CYS B1086 " --> pdb=" O GLN B1083 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B1087 " --> pdb=" O TRP B1084 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1083 through 1087' Processing helix chain 'B' and resid 1095 through 1100 removed outlier: 4.012A pdb=" N ASN B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1129 removed outlier: 3.987A pdb=" N CYS B1129 " --> pdb=" O GLU B1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1126 through 1129' Processing helix chain 'B' and resid 1138 through 1143 removed outlier: 4.326A pdb=" N ASN B1143 " --> pdb=" O SER B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1169 removed outlier: 4.110A pdb=" N CYS B1169 " --> pdb=" O LEU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1183 removed outlier: 4.133A pdb=" N GLY B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1209 removed outlier: 4.361A pdb=" N CYS B1208 " --> pdb=" O ARG B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1223 removed outlier: 3.980A pdb=" N GLY B1222 " --> pdb=" O ASP B1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 1227 through 1231 removed outlier: 3.597A pdb=" N MET B1230 " --> pdb=" O PRO B1227 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS B1231 " --> pdb=" O PRO B1228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1227 through 1231' 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 1288 through 1292 removed outlier: 4.050A pdb=" N CYS B1291 " --> pdb=" O SER B1288 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B1292 " --> pdb=" O TRP B1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1288 through 1292' Processing helix chain 'B' and resid 1301 through 1305 removed outlier: 3.612A pdb=" N LYS B1304 " --> pdb=" O SER B1301 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP B1305 " --> pdb=" O ASP B1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1301 through 1305' Processing helix chain 'B' and resid 1330 through 1332 No H-bonds generated for 'chain 'B' and resid 1330 through 1332' Processing helix chain 'B' and resid 1346 through 1351 Processing helix chain 'B' and resid 1357 through 1361 Processing helix chain 'B' and resid 1393 through 1397 Processing helix chain 'B' and resid 1694 through 1698 removed outlier: 3.559A pdb=" N ARG B1697 " --> pdb=" O HIS B1694 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B1698 " --> pdb=" O PRO B1695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1694 through 1698' Processing helix chain 'B' and resid 1704 through 1708 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 2331 through 2335 Processing helix chain 'B' and resid 2345 through 2354 removed outlier: 3.859A pdb=" N GLN B2349 " --> pdb=" O PRO B2346 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER B2350 " --> pdb=" O CYS B2347 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN B2351 " --> pdb=" O LEU B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2654 through 2658 removed outlier: 3.518A pdb=" N GLN B2658 " --> pdb=" O PRO B2655 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2663 Processing helix chain 'B' and resid 2717 through 2721 removed outlier: 4.334A pdb=" N CYS B2720 " --> pdb=" O ASP B2717 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B2721 " --> pdb=" O TRP B2718 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2717 through 2721' Processing helix chain 'B' and resid 2733 through 2738 Processing helix chain 'B' and resid 2756 through 2760 Processing helix chain 'B' and resid 2798 through 2800 No H-bonds generated for 'chain 'B' and resid 2798 through 2800' Processing helix chain 'B' and resid 2840 through 2844 removed outlier: 4.086A pdb=" N CYS B2843 " --> pdb=" O ALA B2840 " (cutoff:3.500A) Processing helix chain 'B' and resid 2856 through 2861 Processing helix chain 'B' and resid 2882 through 2887 removed outlier: 4.030A pdb=" N CYS B2885 " --> pdb=" O TYR B2882 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY B2887 " --> pdb=" O PHE B2884 " (cutoff:3.500A) Processing helix chain 'B' and resid 2898 through 2902 Processing helix chain 'B' and resid 2924 through 2926 No H-bonds generated for 'chain 'B' and resid 2924 through 2926' Processing helix chain 'B' and resid 2940 through 2948 removed outlier: 6.450A pdb=" N CYS B2945 " --> pdb=" O ARG B2942 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU B2946 " --> pdb=" O HIS B2943 " (cutoff:3.500A) Processing helix chain 'B' and resid 2971 through 2973 No H-bonds generated for 'chain 'B' and resid 2971 through 2973' Processing helix chain 'B' and resid 2983 through 2987 Processing helix chain 'B' and resid 3011 through 3013 No H-bonds generated for 'chain 'B' and resid 3011 through 3013' Processing helix chain 'B' and resid 3050 through 3054 removed outlier: 4.019A pdb=" N CYS B3053 " --> pdb=" O LEU B3050 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B3054 " --> pdb=" O TYR B3051 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3050 through 3054' Processing helix chain 'B' and resid 3066 through 3071 Processing helix chain 'B' and resid 3093 through 3097 removed outlier: 3.860A pdb=" N CYS B3096 " --> pdb=" O GLY B3093 " (cutoff:3.500A) Processing helix chain 'B' and resid 3105 through 3110 removed outlier: 4.232A pdb=" N LYS B3109 " --> pdb=" O ASN B3105 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B3110 " --> pdb=" O SER B3106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3105 through 3110' 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: 3.730A 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 3474 through 3478 Processing helix chain 'B' and resid 3522 through 3525 removed outlier: 3.663A pdb=" N GLU B3525 " --> pdb=" O GLY B3522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3522 through 3525' 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 3575 removed outlier: 3.505A pdb=" N ALA B3572 " --> pdb=" O SER B3569 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B3574 " --> pdb=" O GLN B3571 " (cutoff:3.500A) 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 3623 through 3627 removed outlier: 3.851A pdb=" N ASP B3626 " --> pdb=" O ASP B3623 " (cutoff:3.500A) Processing helix chain 'B' and resid 3628 through 3633 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 3669 through 3674 Processing helix chain 'B' and resid 3675 through 3679 Processing helix chain 'B' and resid 3698 through 3701 removed outlier: 3.854A pdb=" N CYS B3701 " --> pdb=" O TRP B3698 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3698 through 3701' Processing helix chain 'B' and resid 3712 through 3716 removed outlier: 4.284A pdb=" N GLY B3715 " --> pdb=" O ASP B3712 " (cutoff:3.500A) Processing helix chain 'B' and resid 3738 through 3742 removed outlier: 3.937A pdb=" N CYS B3741 " --> pdb=" O ARG B3738 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B3742 " --> pdb=" O TRP B3739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3738 through 3742' Processing helix chain 'B' and resid 3750 through 3755 removed outlier: 4.400A pdb=" N SER B3755 " --> pdb=" O SER B3751 " (cutoff:3.500A) Processing helix chain 'B' and resid 3777 through 3781 removed outlier: 3.929A pdb=" N CYS B3780 " --> pdb=" O ARG B3777 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B3781 " --> pdb=" O TRP B3778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3777 through 3781' Processing helix chain 'B' and resid 3815 through 3819 removed outlier: 4.441A pdb=" N CYS B3819 " --> pdb=" O LYS B3815 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3815 through 3819' Processing helix chain 'B' and resid 3830 through 3834 removed outlier: 3.878A pdb=" N ALA B3833 " --> pdb=" O ASP B3830 " (cutoff:3.500A) Processing helix chain 'B' and resid 3858 through 3862 Processing helix chain 'B' and resid 3872 through 3875 Processing helix chain 'B' and resid 3876 through 3881 removed outlier: 4.020A pdb=" N CYS B3880 " --> pdb=" O GLU B3876 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE B3881 " --> pdb=" O ILE B3877 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3876 through 3881' Processing helix chain 'B' and resid 3902 through 3906 removed outlier: 3.719A pdb=" N CYS B3905 " --> pdb=" O HIS B3902 " (cutoff:3.500A) Processing helix chain 'B' and resid 3918 through 3923 Processing helix chain 'B' and resid 3946 through 3950 removed outlier: 3.753A pdb=" N CYS B3949 " --> pdb=" O HIS B3946 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B3950 " --> pdb=" O TYR B3947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3946 through 3950' Processing helix chain 'B' and resid 3971 through 3975 Processing helix chain 'B' and resid 4011 through 4015 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 4.323A pdb=" N CYS A 35 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 7.495A 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 73 Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 115 removed outlier: 3.565A pdb=" N CYS A 115 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 190 Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 229 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.767A pdb=" N ARG A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AB1, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AB3, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AB4, first strand: chain 'A' and resid 413 through 415 Processing sheet with id=AB5, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.801A pdb=" N GLY A 427 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 474 removed outlier: 6.829A pdb=" N ILE A 490 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.062A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 537 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 561 through 564 removed outlier: 6.719A pdb=" N ILE A 580 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 603 through 609 removed outlier: 6.390A pdb=" N THR A 616 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 606 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 614 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 608 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 623 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 672 through 677 Processing sheet with id=AC2, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AC3, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.647A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 742 through 748 removed outlier: 4.271A pdb=" N GLY A 744 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 764 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 785 through 791 removed outlier: 3.985A pdb=" N CYS A 787 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 807 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 827 through 833 removed outlier: 3.827A pdb=" N SER A 829 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG A 852 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TRP A 854 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 860 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 871 through 877 removed outlier: 4.253A pdb=" N VAL A 886 " --> pdb=" O ASN A 872 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 874 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR A 884 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 876 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 882 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 915 through 921 removed outlier: 3.883A pdb=" N GLY A 917 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 935 " --> pdb=" O VAL A 949 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 986 through 990 Processing sheet with id=AD1, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id=AD2, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AD3, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id=AD4, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 3.551A pdb=" N MET A1121 " --> pdb=" O CYS A1117 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 3.965A pdb=" N ARG A1161 " --> pdb=" O CYS A1157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1438 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A1689 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1192 through 1193 Processing sheet with id=AD7, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id=AD8, first strand: chain 'A' and resid 1276 through 1278 Processing sheet with id=AD9, first strand: chain 'A' and resid 1317 through 1319 Processing sheet with id=AE1, first strand: chain 'A' and resid 1364 through 1366 Processing sheet with id=AE2, first strand: chain 'A' and resid 1380 through 1382 Processing sheet with id=AE3, first strand: chain 'A' and resid 1404 through 1408 Processing sheet with id=AE4, first strand: chain 'A' and resid 1420 through 1422 Processing sheet with id=AE5, first strand: chain 'A' and resid 1469 through 1475 removed outlier: 4.026A pdb=" N ALA A1471 " --> pdb=" O SER A1484 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A1490 " --> pdb=" O ASP A1485 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1491 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1515 through 1517 removed outlier: 6.827A pdb=" N ILE A1534 " --> pdb=" O LEU A1547 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1555 through 1561 removed outlier: 3.982A pdb=" N GLY A1557 " --> pdb=" O SER A1572 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A1580 " --> pdb=" O ILE A1593 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1601 through 1607 removed outlier: 5.783A pdb=" N MET A1616 " --> pdb=" O CYS A1602 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A1604 " --> pdb=" O TYR A1614 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR A1614 " --> pdb=" O LEU A1604 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A1606 " --> pdb=" O LEU A1612 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A1612 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE A1625 " --> pdb=" O GLN A1635 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLN A1635 " --> pdb=" O PHE A1625 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP A1627 " --> pdb=" O ARG A1633 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A1633 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 1646 through 1652 removed outlier: 4.025A pdb=" N ALA A1648 " --> pdb=" O THR A1659 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A1666 " --> pdb=" O VAL A1680 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1713 through 1716 Processing sheet with id=AF2, first strand: chain 'A' and resid 1732 through 1734 Processing sheet with id=AF3, first strand: chain 'A' and resid 1756 through 1761 removed outlier: 4.455A pdb=" N GLY A2007 " --> pdb=" O VAL A1752 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1781 through 1787 removed outlier: 4.151A pdb=" N ASP A1783 " --> pdb=" O VAL A1796 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1826 through 1830 removed outlier: 3.931A pdb=" N GLY A1826 " --> pdb=" O THR A1839 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A1846 " --> pdb=" O LEU A1861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1874 through 1880 removed outlier: 6.755A pdb=" N ILE A1901 " --> pdb=" O LEU A1914 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1922 through 1928 removed outlier: 4.448A pdb=" N VAL A1924 " --> pdb=" O ALA A1937 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A1944 " --> pdb=" O LEU A1957 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1967 through 1970 removed outlier: 6.943A pdb=" N ILE A1984 " --> pdb=" O PHE A1998 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 2033 through 2036 Processing sheet with id=AG1, first strand: chain 'A' and resid 2050 through 2052 Processing sheet with id=AG2, first strand: chain 'A' and resid 2091 through 2092 Processing sheet with id=AG3, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 4.088A pdb=" N HIS A2100 " --> pdb=" O CYS A2113 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A2125 " --> pdb=" O ILE A2138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 2147 through 2154 removed outlier: 5.622A pdb=" N ILE A2148 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A2165 " --> pdb=" O ILE A2148 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A2150 " --> pdb=" O THR A2163 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A2170 " --> pdb=" O LYS A2187 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A2187 " --> pdb=" O THR A2170 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A2172 " --> pdb=" O LEU A2185 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 4.018A pdb=" N HIS A2195 " --> pdb=" O ALA A2208 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A2230 " --> pdb=" O ILE A2216 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG A2218 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL A2228 " --> pdb=" O ARG A2218 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 3.624A pdb=" N GLY A2239 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A2248 " --> pdb=" O ASP A2243 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 3.800A pdb=" N GLY A2283 " --> pdb=" O VAL A2294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A2300 " --> pdb=" O ASP A2295 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A2301 " --> pdb=" O ILE A2317 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 2357 through 2358 Processing sheet with id=AG9, first strand: chain 'A' and resid 2375 through 2376 Processing sheet with id=AH1, first strand: chain 'A' and resid 2416 through 2417 Processing sheet with id=AH2, first strand: chain 'A' and resid 2421 through 2428 removed outlier: 5.544A pdb=" N ALA A2422 " --> pdb=" O LYS A2439 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A2439 " --> pdb=" O ALA A2422 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A2424 " --> pdb=" O THR A2437 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A2433 " --> pdb=" O ASP A2428 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG A2444 " --> pdb=" O LEU A2440 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE A2447 " --> pdb=" O SER A2464 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER A2464 " --> pdb=" O ILE A2447 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR A2449 " --> pdb=" O LEU A2462 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A2462 " --> pdb=" O TYR A2449 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN A2451 " --> pdb=" O THR A2460 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR A2460 " --> pdb=" O ASN A2451 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 2469 through 2475 removed outlier: 4.018A pdb=" N GLY A2471 " --> pdb=" O SER A2484 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER A2493 " --> pdb=" O VAL A2503 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL A2503 " --> pdb=" O SER A2493 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA A2495 " --> pdb=" O ARG A2501 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG A2501 " --> pdb=" O ALA A2495 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 2513 through 2516 removed outlier: 6.727A pdb=" N ILE A2533 " --> pdb=" O ILE A2546 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 2554 through 2560 removed outlier: 3.708A pdb=" N GLY A2556 " --> pdb=" O ALA A2569 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A2576 " --> pdb=" O VAL A2589 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 2599 through 2602 Processing sheet with id=AH7, first strand: chain 'A' and resid 2667 through 2668 removed outlier: 3.983A pdb=" N GLU A2675 " --> pdb=" O ALA A2668 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 2705 through 2707 Processing sheet with id=AH9, first strand: chain 'A' and resid 2747 through 2748 removed outlier: 3.624A pdb=" N VAL A2755 " --> pdb=" O PHE A2747 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A' and resid 2786 through 2788 Processing sheet with id=AI2, first strand: chain 'A' and resid 2827 through 2829 Processing sheet with id=AI3, first strand: chain 'A' and resid 2869 through 2870 Processing sheet with id=AI4, first strand: chain 'A' and resid 2912 through 2914 Processing sheet with id=AI5, first strand: chain 'A' and resid 2954 through 2956 Processing sheet with id=AI6, first strand: chain 'A' and resid 2999 through 3002 removed outlier: 3.587A pdb=" N ARG A3006 " --> pdb=" O CYS A3002 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 3038 through 3041 removed outlier: 3.717A pdb=" N GLN A3045 " --> pdb=" O CYS A3041 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 3081 through 3083 Processing sheet with id=AI9, first strand: chain 'A' and resid 3127 through 3130 Processing sheet with id=AJ1, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id=AJ2, first strand: chain 'A' and resid 3168 through 3172 Processing sheet with id=AJ3, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AJ4, first strand: chain 'A' and resid 3221 through 3226 removed outlier: 6.663A pdb=" N ILE A3211 " --> pdb=" O ILE A3224 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A3455 " --> pdb=" O SER A3206 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'A' and resid 3231 through 3237 removed outlier: 4.100A pdb=" N ALA A3233 " --> pdb=" O ILE A3246 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A3253 " --> pdb=" O ILE A3266 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 3.867A pdb=" N SER A3276 " --> pdb=" O LEU A3289 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A3296 " --> pdb=" O LEU A3309 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 5.731A pdb=" N ALA A3340 " --> pdb=" O ARG A3326 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A3328 " --> pdb=" O TYR A3338 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A3338 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU A3330 " --> pdb=" O TYR A3336 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR A3336 " --> pdb=" O LEU A3330 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A3348 " --> pdb=" O ILE A3361 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'A' and resid 3369 through 3375 removed outlier: 4.238A pdb=" N ALA A3371 " --> pdb=" O ALA A3384 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A3384 " --> pdb=" O ALA A3371 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A3391 " --> pdb=" O VAL A3404 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'A' and resid 3412 through 3418 removed outlier: 4.673A pdb=" N ALA A3414 " --> pdb=" O THR A3425 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A3434 " --> pdb=" O VAL A3445 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL A3445 " --> pdb=" O LYS A3434 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A3436 " --> pdb=" O ARG A3443 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG A3443 " --> pdb=" O ASN A3436 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'A' and resid 3481 through 3484 Processing sheet with id=AK2, first strand: chain 'A' and resid 3499 through 3503 Processing sheet with id=AK3, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id=AK4, first strand: chain 'A' and resid 3560 through 3561 Processing sheet with id=AK5, first strand: chain 'A' and resid 3600 through 3603 removed outlier: 3.721A pdb=" N ARG A3607 " --> pdb=" O CYS A3603 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'A' and resid 3641 through 3644 removed outlier: 3.757A pdb=" N ARG A3648 " --> pdb=" O CYS A3644 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'A' and resid 3685 through 3687 Processing sheet with id=AK8, first strand: chain 'A' and resid 3726 through 3729 removed outlier: 3.596A pdb=" N HIS A3733 " --> pdb=" O CYS A3729 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'A' and resid 3765 through 3767 Processing sheet with id=AL1, first strand: chain 'A' and resid 3804 through 3807 Processing sheet with id=AL2, first strand: chain 'A' and resid 3849 through 3851 removed outlier: 3.688A pdb=" N VAL A3855 " --> pdb=" O CYS A3851 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'A' and resid 3890 through 3892 Processing sheet with id=AL4, first strand: chain 'A' and resid 3934 through 3937 removed outlier: 3.801A pdb=" N ASN A3941 " --> pdb=" O CYS A3937 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'A' and resid 3981 through 3983 Processing sheet with id=AL6, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id=AL7, first strand: chain 'A' and resid 4022 through 4026 Processing sheet with id=AL8, first strand: chain 'A' and resid 4038 through 4040 Processing sheet with id=AL9, first strand: chain 'A' and resid 4075 through 4081 removed outlier: 6.631A pdb=" N ILE A4066 " --> pdb=" O TYR A4079 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'A' and resid 4086 through 4092 removed outlier: 3.909A pdb=" N ALA A4088 " --> pdb=" O THR A4106 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'A' and resid 4146 through 4152 removed outlier: 6.927A pdb=" N ILE A4168 " --> pdb=" O LEU A4181 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 3.758A pdb=" N ALA A4191 " --> pdb=" O THR A4204 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A4212 " --> pdb=" O LEU A4225 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'A' and resid 4233 through 4238 removed outlier: 3.582A pdb=" N GLY A4235 " --> pdb=" O SER A4249 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A4256 " --> pdb=" O ILE A4269 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 4.396A pdb=" N SER A4278 " --> pdb=" O VAL A4289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A4289 " --> pdb=" O SER A4278 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A4295 " --> pdb=" O ALA A4290 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A4296 " --> pdb=" O LEU A4310 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id=AM7, first strand: chain 'A' and resid 4390 through 4393 Processing sheet with id=AM8, first strand: chain 'B' and resid 32 through 36 removed outlier: 4.323A pdb=" N CYS B 35 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR B 39 " --> pdb=" O CYS B 35 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AN1, first strand: chain 'B' and resid 112 through 115 removed outlier: 3.565A pdb=" N CYS B 115 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AN3, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AN4, first strand: chain 'B' and resid 226 through 229 Processing sheet with id=AN5, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AN6, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.767A pdb=" N ARG B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AN8, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AN9, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AO1, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AO2, first strand: chain 'B' and resid 413 through 415 Processing sheet with id=AO3, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.801A pdb=" N GLY B 427 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'B' and resid 470 through 474 removed outlier: 6.829A pdb=" N ILE B 490 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'B' and resid 513 through 517 removed outlier: 4.062A pdb=" N GLY B 513 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 537 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'B' and resid 561 through 564 removed outlier: 6.719A pdb=" N ILE B 580 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'B' and resid 603 through 609 removed outlier: 6.390A pdb=" N THR B 616 " --> pdb=" O PHE B 604 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 606 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 614 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU B 608 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 623 " --> pdb=" O TYR B 637 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'B' and resid 672 through 677 Processing sheet with id=AO9, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AP1, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.647A pdb=" N HIS B 958 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'B' and resid 742 through 748 removed outlier: 4.271A pdb=" N GLY B 744 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 764 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'B' and resid 785 through 791 removed outlier: 3.985A pdb=" N CYS B 787 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 807 " --> pdb=" O ILE B 820 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'B' and resid 827 through 833 removed outlier: 3.827A pdb=" N SER B 829 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG B 852 " --> pdb=" O PRO B 862 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TRP B 854 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 860 " --> pdb=" O TRP B 854 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'B' and resid 871 through 877 removed outlier: 4.253A pdb=" N VAL B 886 " --> pdb=" O ASN B 872 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 874 " --> pdb=" O TYR B 884 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR B 884 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 876 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG B 882 " --> pdb=" O ILE B 876 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'B' and resid 915 through 921 removed outlier: 3.883A pdb=" N GLY B 917 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 935 " --> pdb=" O VAL B 949 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'B' and resid 986 through 990 Processing sheet with id=AP8, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id=AP9, first strand: chain 'B' and resid 1029 through 1031 Processing sheet with id=AQ1, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AQ2, first strand: chain 'B' and resid 1114 through 1117 removed outlier: 3.551A pdb=" N MET B1121 " --> pdb=" O CYS B1117 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'B' and resid 1155 through 1157 removed outlier: 3.965A pdb=" N ARG B1161 " --> pdb=" O CYS B1157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B1438 " --> pdb=" O ILE B1693 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B1689 " --> pdb=" O ALA B1442 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'B' and resid 1192 through 1193 Processing sheet with id=AQ5, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AQ6, first strand: chain 'B' and resid 1276 through 1278 Processing sheet with id=AQ7, first strand: chain 'B' and resid 1317 through 1319 Processing sheet with id=AQ8, first strand: chain 'B' and resid 1364 through 1366 Processing sheet with id=AQ9, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id=AR1, first strand: chain 'B' and resid 1404 through 1408 Processing sheet with id=AR2, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id=AR3, first strand: chain 'B' and resid 1469 through 1475 removed outlier: 4.026A pdb=" N ALA B1471 " --> pdb=" O SER B1484 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B1490 " --> pdb=" O ASP B1485 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR B1491 " --> pdb=" O VAL B1504 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'B' and resid 1515 through 1517 removed outlier: 6.827A pdb=" N ILE B1534 " --> pdb=" O LEU B1547 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 3.982A pdb=" N GLY B1557 " --> pdb=" O SER B1572 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B1580 " --> pdb=" O ILE B1593 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 5.783A pdb=" N MET B1616 " --> pdb=" O CYS B1602 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B1604 " --> pdb=" O TYR B1614 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B1614 " --> pdb=" O LEU B1604 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B1606 " --> pdb=" O LEU B1612 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B1612 " --> pdb=" O ILE B1606 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B1625 " --> pdb=" O GLN B1635 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLN B1635 " --> pdb=" O PHE B1625 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP B1627 " --> pdb=" O ARG B1633 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG B1633 " --> pdb=" O ASP B1627 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'B' and resid 1646 through 1652 removed outlier: 4.025A pdb=" N ALA B1648 " --> pdb=" O THR B1659 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B1666 " --> pdb=" O VAL B1680 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id=AR9, first strand: chain 'B' and resid 1732 through 1734 Processing sheet with id=AS1, first strand: chain 'B' and resid 1756 through 1761 removed outlier: 4.455A pdb=" N GLY B2007 " --> pdb=" O VAL B1752 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'B' and resid 1781 through 1787 removed outlier: 4.151A pdb=" N ASP B1783 " --> pdb=" O VAL B1796 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'B' and resid 1826 through 1830 removed outlier: 3.931A pdb=" N GLY B1826 " --> pdb=" O THR B1839 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B1846 " --> pdb=" O LEU B1861 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'B' and resid 1874 through 1880 removed outlier: 6.755A pdb=" N ILE B1901 " --> pdb=" O LEU B1914 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'B' and resid 1922 through 1928 removed outlier: 4.448A pdb=" N VAL B1924 " --> pdb=" O ALA B1937 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B1944 " --> pdb=" O LEU B1957 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'B' and resid 1967 through 1970 removed outlier: 6.943A pdb=" N ILE B1984 " --> pdb=" O PHE B1998 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'B' and resid 2033 through 2036 Processing sheet with id=AS8, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id=AS9, first strand: chain 'B' and resid 2091 through 2092 Processing sheet with id=AT1, first strand: chain 'B' and resid 2098 through 2104 removed outlier: 4.088A pdb=" N HIS B2100 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B2125 " --> pdb=" O ILE B2138 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'B' and resid 2147 through 2154 removed outlier: 5.622A pdb=" N ILE B2148 " --> pdb=" O ALA B2165 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B2165 " --> pdb=" O ILE B2148 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B2150 " --> pdb=" O THR B2163 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B2170 " --> pdb=" O LYS B2187 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS B2187 " --> pdb=" O THR B2170 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B2172 " --> pdb=" O LEU B2185 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 4.018A pdb=" N HIS B2195 " --> pdb=" O ALA B2208 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B2230 " --> pdb=" O ILE B2216 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG B2218 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B2228 " --> pdb=" O ARG B2218 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 3.624A pdb=" N GLY B2239 " --> pdb=" O VAL B2252 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B2248 " --> pdb=" O ASP B2243 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 3.800A pdb=" N GLY B2283 " --> pdb=" O VAL B2294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B2300 " --> pdb=" O ASP B2295 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B2301 " --> pdb=" O ILE B2317 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'B' and resid 2357 through 2358 Processing sheet with id=AT7, first strand: chain 'B' and resid 2375 through 2376 Processing sheet with id=AT8, first strand: chain 'B' and resid 2416 through 2417 Processing sheet with id=AT9, first strand: chain 'B' and resid 2421 through 2428 removed outlier: 5.544A pdb=" N ALA B2422 " --> pdb=" O LYS B2439 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS B2439 " --> pdb=" O ALA B2422 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B2424 " --> pdb=" O THR B2437 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B2433 " --> pdb=" O ASP B2428 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B2444 " --> pdb=" O LEU B2440 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE B2447 " --> pdb=" O SER B2464 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER B2464 " --> pdb=" O ILE B2447 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B2449 " --> pdb=" O LEU B2462 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B2462 " --> pdb=" O TYR B2449 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN B2451 " --> pdb=" O THR B2460 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B2460 " --> pdb=" O ASN B2451 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'B' and resid 2469 through 2475 removed outlier: 4.018A pdb=" N GLY B2471 " --> pdb=" O SER B2484 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B2493 " --> pdb=" O VAL B2503 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B2503 " --> pdb=" O SER B2493 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA B2495 " --> pdb=" O ARG B2501 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG B2501 " --> pdb=" O ALA B2495 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'B' and resid 2513 through 2516 removed outlier: 6.727A pdb=" N ILE B2533 " --> pdb=" O ILE B2546 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 3.708A pdb=" N GLY B2556 " --> pdb=" O ALA B2569 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B2576 " --> pdb=" O VAL B2589 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'B' and resid 2599 through 2602 Processing sheet with id=AU5, first strand: chain 'B' and resid 2667 through 2668 removed outlier: 3.983A pdb=" N GLU B2675 " --> pdb=" O ALA B2668 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'B' and resid 2705 through 2707 Processing sheet with id=AU7, first strand: chain 'B' and resid 2747 through 2748 removed outlier: 3.624A pdb=" N VAL B2755 " --> pdb=" O PHE B2747 " (cutoff:3.500A) Processing sheet with id=AU8, first strand: chain 'B' and resid 2786 through 2788 Processing sheet with id=AU9, first strand: chain 'B' and resid 2827 through 2829 Processing sheet with id=AV1, first strand: chain 'B' and resid 2869 through 2870 Processing sheet with id=AV2, first strand: chain 'B' and resid 2912 through 2914 Processing sheet with id=AV3, first strand: chain 'B' and resid 2954 through 2956 Processing sheet with id=AV4, first strand: chain 'B' and resid 2999 through 3002 removed outlier: 3.587A pdb=" N ARG B3006 " --> pdb=" O CYS B3002 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'B' and resid 3038 through 3041 removed outlier: 3.717A pdb=" N GLN B3045 " --> pdb=" O CYS B3041 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'B' and resid 3081 through 3083 Processing sheet with id=AV7, first strand: chain 'B' and resid 3127 through 3130 Processing sheet with id=AV8, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id=AV9, first strand: chain 'B' and resid 3168 through 3172 Processing sheet with id=AW1, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id=AW2, first strand: chain 'B' and resid 3221 through 3226 removed outlier: 6.663A pdb=" N ILE B3211 " --> pdb=" O ILE B3224 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B3455 " --> pdb=" O SER B3206 " (cutoff:3.500A) Processing sheet with id=AW3, first strand: chain 'B' and resid 3231 through 3237 removed outlier: 4.100A pdb=" N ALA B3233 " --> pdb=" O ILE B3246 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B3253 " --> pdb=" O ILE B3266 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 3.867A pdb=" N SER B3276 " --> pdb=" O LEU B3289 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B3296 " --> pdb=" O LEU B3309 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 5.731A pdb=" N ALA B3340 " --> pdb=" O ARG B3326 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B3328 " --> pdb=" O TYR B3338 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B3338 " --> pdb=" O ILE B3328 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU B3330 " --> pdb=" O TYR B3336 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR B3336 " --> pdb=" O LEU B3330 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B3348 " --> pdb=" O ILE B3361 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'B' and resid 3369 through 3375 removed outlier: 4.238A pdb=" N ALA B3371 " --> pdb=" O ALA B3384 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B3384 " --> pdb=" O ALA B3371 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B3391 " --> pdb=" O VAL B3404 " (cutoff:3.500A) Processing sheet with id=AW7, first strand: chain 'B' and resid 3412 through 3418 removed outlier: 4.673A pdb=" N ALA B3414 " --> pdb=" O THR B3425 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS B3434 " --> pdb=" O VAL B3445 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL B3445 " --> pdb=" O LYS B3434 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN B3436 " --> pdb=" O ARG B3443 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG B3443 " --> pdb=" O ASN B3436 " (cutoff:3.500A) Processing sheet with id=AW8, first strand: chain 'B' and resid 3481 through 3484 Processing sheet with id=AW9, first strand: chain 'B' and resid 3499 through 3503 Processing sheet with id=AX1, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id=AX2, first strand: chain 'B' and resid 3560 through 3561 Processing sheet with id=AX3, first strand: chain 'B' and resid 3600 through 3603 removed outlier: 3.721A pdb=" N ARG B3607 " --> pdb=" O CYS B3603 " (cutoff:3.500A) Processing sheet with id=AX4, first strand: chain 'B' and resid 3641 through 3644 removed outlier: 3.757A pdb=" N ARG B3648 " --> pdb=" O CYS B3644 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'B' and resid 3685 through 3687 Processing sheet with id=AX6, first strand: chain 'B' and resid 3726 through 3729 removed outlier: 3.596A pdb=" N HIS B3733 " --> pdb=" O CYS B3729 " (cutoff:3.500A) Processing sheet with id=AX7, first strand: chain 'B' and resid 3765 through 3767 Processing sheet with id=AX8, first strand: chain 'B' and resid 3804 through 3807 Processing sheet with id=AX9, first strand: chain 'B' and resid 3849 through 3851 removed outlier: 3.688A pdb=" N VAL B3855 " --> pdb=" O CYS B3851 " (cutoff:3.500A) Processing sheet with id=AY1, first strand: chain 'B' and resid 3890 through 3892 Processing sheet with id=AY2, first strand: chain 'B' and resid 3934 through 3937 removed outlier: 3.801A pdb=" N ASN B3941 " --> pdb=" O CYS B3937 " (cutoff:3.500A) Processing sheet with id=AY3, first strand: chain 'B' and resid 3981 through 3983 Processing sheet with id=AY4, first strand: chain 'B' and resid 3997 through 3999 Processing sheet with id=AY5, first strand: chain 'B' and resid 4022 through 4026 Processing sheet with id=AY6, first strand: chain 'B' and resid 4038 through 4040 Processing sheet with id=AY7, first strand: chain 'B' and resid 4075 through 4081 removed outlier: 6.631A pdb=" N ILE B4066 " --> pdb=" O TYR B4079 " (cutoff:3.500A) Processing sheet with id=AY8, first strand: chain 'B' and resid 4086 through 4092 removed outlier: 3.909A pdb=" N ALA B4088 " --> pdb=" O THR B4106 " (cutoff:3.500A) Processing sheet with id=AY9, first strand: chain 'B' and resid 4146 through 4152 removed outlier: 6.927A pdb=" N ILE B4168 " --> pdb=" O LEU B4181 " (cutoff:3.500A) Processing sheet with id=AZ1, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 3.758A pdb=" N ALA B4191 " --> pdb=" O THR B4204 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B4212 " --> pdb=" O LEU B4225 " (cutoff:3.500A) Processing sheet with id=AZ2, first strand: chain 'B' and resid 4233 through 4238 removed outlier: 3.582A pdb=" N GLY B4235 " --> pdb=" O SER B4249 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B4256 " --> pdb=" O ILE B4269 " (cutoff:3.500A) Processing sheet with id=AZ3, first strand: chain 'B' and resid 4276 through 4282 removed outlier: 4.396A pdb=" N SER B4278 " --> pdb=" O VAL B4289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B4289 " --> pdb=" O SER B4278 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B4295 " --> pdb=" O ALA B4290 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B4296 " --> pdb=" O LEU B4310 " (cutoff:3.500A) Processing sheet with id=AZ4, first strand: chain 'B' and resid 4343 through 4347 Processing sheet with id=AZ5, first strand: chain 'B' and resid 4390 through 4393 1818 hydrogen bonds defined for protein. 4278 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: 87.60 Time building geometry restraints manager: 16.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 12038 1.32 - 1.45: 21312 1.45 - 1.59: 34868 1.59 - 1.72: 0 1.72 - 1.85: 872 Bond restraints: 69090 Sorted by residual: bond pdb=" C PRO B1000 " pdb=" O PRO B1000 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.18e-02 7.18e+03 1.48e+01 bond pdb=" C PRO A1000 " pdb=" O PRO A1000 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.18e-02 7.18e+03 1.48e+01 bond pdb=" C VAL A 996 " pdb=" O VAL A 996 " ideal model delta sigma weight residual 1.235 1.269 -0.034 9.90e-03 1.02e+04 1.17e+01 bond pdb=" C VAL B 996 " pdb=" O VAL B 996 " ideal model delta sigma weight residual 1.235 1.269 -0.034 9.90e-03 1.02e+04 1.17e+01 bond pdb=" N VAL A2694 " pdb=" CA VAL A2694 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 ... (remaining 69085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 87282 2.38 - 4.77: 6176 4.77 - 7.15: 624 7.15 - 9.53: 76 9.53 - 11.92: 14 Bond angle restraints: 94172 Sorted by residual: angle pdb=" N ASN B2989 " pdb=" CA ASN B2989 " pdb=" C ASN B2989 " ideal model delta sigma weight residual 111.28 116.62 -5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" N ASN A2989 " pdb=" CA ASN A2989 " pdb=" C ASN A2989 " ideal model delta sigma weight residual 111.28 116.62 -5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" CA LYS A1270 " pdb=" C LYS A1270 " pdb=" O LYS A1270 " ideal model delta sigma weight residual 121.56 116.23 5.33 1.09e+00 8.42e-01 2.39e+01 angle pdb=" CA LYS B1270 " pdb=" C LYS B1270 " pdb=" O LYS B1270 " ideal model delta sigma weight residual 121.56 116.23 5.33 1.09e+00 8.42e-01 2.39e+01 angle pdb=" CA PRO A 64 " pdb=" C PRO A 64 " pdb=" O PRO A 64 " ideal model delta sigma weight residual 121.23 116.05 5.18 1.07e+00 8.73e-01 2.34e+01 ... (remaining 94167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 39789 17.95 - 35.90: 2460 35.90 - 53.86: 417 53.86 - 71.81: 123 71.81 - 89.76: 42 Dihedral angle restraints: 42831 sinusoidal: 17603 harmonic: 25228 Sorted by residual: dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual -86.00 -167.87 81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A2663 " pdb=" SG CYS A2663 " pdb=" SG CYS A2676 " pdb=" CB CYS A2676 " ideal model delta sinusoidal sigma weight residual -86.00 -163.86 77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A3124 " pdb=" SG CYS A3124 " pdb=" SG CYS A3137 " pdb=" CB CYS A3137 " ideal model delta sinusoidal sigma weight residual -86.00 -156.45 70.45 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 42828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 9418 0.114 - 0.228: 1008 0.228 - 0.342: 42 0.342 - 0.455: 4 0.455 - 0.569: 4 Chirality restraints: 10476 Sorted by residual: chirality pdb=" C1 NAG A4708 " pdb=" ND2 ASN A1384 " pdb=" C2 NAG A4708 " pdb=" O5 NAG A4708 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" C1 NAG B4708 " pdb=" ND2 ASN B1384 " pdb=" C2 NAG B4708 " pdb=" O5 NAG B4708 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" C1 NAG A4723 " pdb=" ND2 ASN A2989 " pdb=" C2 NAG A4723 " pdb=" O5 NAG A4723 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 10473 not shown) Planarity restraints: 12518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NGA B4747 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NGA B4747 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NGA B4747 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NGA B4747 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NGA B4747 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NGA A4747 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NGA A4747 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NGA A4747 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NGA A4747 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NGA A4747 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4732 " 0.338 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A4732 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A4732 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A4732 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG A4732 " 0.091 2.00e-02 2.50e+03 ... (remaining 12515 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1083 2.59 - 3.17: 59337 3.17 - 3.74: 101750 3.74 - 4.32: 151272 4.32 - 4.90: 245628 Nonbonded interactions: 559070 Sorted by model distance: nonbonded pdb=" SG CYS B3844 " pdb=" SG CYS B3856 " model vdw 2.011 3.760 nonbonded pdb=" SG CYS B3977 " pdb=" SG CYS B3991 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS B1361 " pdb=" SG CYS B1374 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS B1032 " pdb=" SG CYS B1050 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS B 999 " pdb=" SG CYS B1012 " model vdw 2.020 3.760 ... (remaining 559065 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 47.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.070 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 322.960 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 385.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 69090 Z= 0.453 Angle : 1.282 11.917 94172 Z= 0.749 Chirality : 0.071 0.569 10476 Planarity : 0.014 0.304 12438 Dihedral : 12.127 89.758 26160 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.43 % Allowed : 5.10 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.09), residues: 8748 helix: -4.03 (0.16), residues: 242 sheet: 0.37 (0.10), residues: 2458 loop : -0.86 (0.08), residues: 6048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.008 TRP A 85 HIS 0.043 0.006 HIS A1075 PHE 0.070 0.008 PHE A2787 TYR 0.074 0.009 TYR A2482 ARG 0.072 0.005 ARG B3350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 5.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2630 MET cc_start: 0.5938 (mmm) cc_final: 0.5736 (mmm) REVERT: B 2630 MET cc_start: 0.5936 (mmm) cc_final: 0.5735 (mmm) outliers start: 30 outliers final: 10 residues processed: 303 average time/residue: 1.4787 time to fit residues: 613.8210 Evaluate side-chains 158 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3072 THR Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain B residue 2676 CYS Chi-restraints excluded: chain B residue 3072 THR Chi-restraints excluded: chain B residue 3076 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 738 optimal weight: 20.0000 chunk 662 optimal weight: 0.8980 chunk 367 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 446 optimal weight: 10.0000 chunk 353 optimal weight: 20.0000 chunk 685 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 416 optimal weight: 0.7980 chunk 509 optimal weight: 8.9990 chunk 793 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 431 HIS A 826 ASN A 833 HIS A1363 HIS A1505 HIS A1673 HIS A2263 HIS A3854 HIS A4145 GLN A4185 GLN A4206 GLN B 129 HIS B 226 GLN B 431 HIS B 826 ASN B 833 HIS B1363 HIS B1505 HIS B1673 HIS B1712 HIS B2263 HIS B2677 GLN B3854 HIS B3951 ASN B4005 ASN B4145 GLN B4185 GLN B4206 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 69090 Z= 0.352 Angle : 0.720 9.704 94172 Z= 0.384 Chirality : 0.050 0.385 10476 Planarity : 0.005 0.055 12438 Dihedral : 6.999 56.547 12086 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.52 % Allowed : 7.17 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.09), residues: 8748 helix: -3.52 (0.21), residues: 208 sheet: 0.16 (0.10), residues: 2500 loop : -0.20 (0.08), residues: 6040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B2527 HIS 0.006 0.001 HIS B2195 PHE 0.024 0.002 PHE B2884 TYR 0.016 0.002 TYR B2692 ARG 0.006 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 148 time to evaluate : 5.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 22 residues processed: 237 average time/residue: 1.2857 time to fit residues: 435.4844 Evaluate side-chains 160 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 2494 MET Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 2494 MET Chi-restraints excluded: chain B residue 2690 ASN Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 441 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 660 optimal weight: 3.9990 chunk 540 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 795 optimal weight: 20.0000 chunk 858 optimal weight: 0.6980 chunk 708 optimal weight: 20.0000 chunk 788 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 637 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN B 796 ASN B3378 ASN B3387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 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 0.091 69090 Z= 0.358 Angle : 0.662 11.029 94172 Z= 0.350 Chirality : 0.048 0.283 10476 Planarity : 0.005 0.060 12438 Dihedral : 6.552 57.544 12079 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.40 % Allowed : 8.62 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.09), residues: 8748 helix: -3.19 (0.24), residues: 220 sheet: 0.10 (0.10), residues: 2370 loop : -0.11 (0.08), residues: 6158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 930 HIS 0.006 0.001 HIS A2195 PHE 0.019 0.002 PHE A2884 TYR 0.018 0.002 TYR A 765 ARG 0.006 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 138 time to evaluate : 5.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 29 residues processed: 225 average time/residue: 1.2547 time to fit residues: 400.3363 Evaluate side-chains 163 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3485 LYS Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1871 VAL Chi-restraints excluded: chain B residue 2951 SER Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3094 THR Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 785 optimal weight: 10.0000 chunk 597 optimal weight: 8.9990 chunk 412 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 379 optimal weight: 4.9990 chunk 533 optimal weight: 0.9990 chunk 797 optimal weight: 0.0570 chunk 844 optimal weight: 1.9990 chunk 416 optimal weight: 0.7980 chunk 756 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A3387 HIS B2808 HIS B3378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 69090 Z= 0.154 Angle : 0.576 9.429 94172 Z= 0.303 Chirality : 0.046 0.288 10476 Planarity : 0.004 0.046 12438 Dihedral : 6.275 58.603 12079 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.04 % Allowed : 9.33 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 8748 helix: -3.02 (0.25), residues: 256 sheet: 0.12 (0.10), residues: 2390 loop : -0.00 (0.09), residues: 6102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B2527 HIS 0.003 0.001 HIS B1363 PHE 0.016 0.001 PHE A2884 TYR 0.015 0.001 TYR A3136 ARG 0.004 0.000 ARG B1444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 148 time to evaluate : 5.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 30 residues processed: 215 average time/residue: 1.2358 time to fit residues: 378.7989 Evaluate side-chains 166 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2690 ASN Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3495 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 703 optimal weight: 10.0000 chunk 479 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 629 optimal weight: 40.0000 chunk 348 optimal weight: 5.9990 chunk 720 optimal weight: 20.0000 chunk 583 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 431 optimal weight: 8.9990 chunk 758 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 819 GLN A2107 ASN A2808 HIS B 435 HIS B 819 GLN B2107 ASN B3057 ASN B3378 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 69090 Z= 0.408 Angle : 0.641 10.665 94172 Z= 0.336 Chirality : 0.048 0.291 10476 Planarity : 0.004 0.082 12438 Dihedral : 6.445 57.440 12079 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.58 % Allowed : 9.83 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 8748 helix: -2.93 (0.27), residues: 242 sheet: -0.31 (0.10), residues: 2660 loop : -0.07 (0.09), residues: 5846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 930 HIS 0.006 0.001 HIS A2195 PHE 0.016 0.002 PHE A 840 TYR 0.018 0.002 TYR B 765 ARG 0.009 0.001 ARG A3083 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 135 time to evaluate : 5.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3146 MET cc_start: 0.7861 (mmm) cc_final: 0.7638 (mmm) REVERT: B 3146 MET cc_start: 0.7889 (mmm) cc_final: 0.7685 (mmm) outliers start: 109 outliers final: 39 residues processed: 234 average time/residue: 1.2054 time to fit residues: 409.9763 Evaluate side-chains 171 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 2690 ASN Chi-restraints excluded: chain B residue 2951 SER Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3495 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3808 THR Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 284 optimal weight: 2.9990 chunk 760 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 496 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 845 optimal weight: 1.9990 chunk 701 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 279 optimal weight: 7.9990 chunk 443 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN A2403 HIS B 767 GLN ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69090 Z= 0.257 Angle : 0.578 10.140 94172 Z= 0.302 Chirality : 0.046 0.249 10476 Planarity : 0.004 0.048 12438 Dihedral : 6.150 56.903 12078 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.14 % Allowed : 10.54 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 8748 helix: -2.88 (0.27), residues: 242 sheet: -0.32 (0.10), residues: 2624 loop : -0.03 (0.09), residues: 5882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 930 HIS 0.005 0.001 HIS B1363 PHE 0.014 0.001 PHE B3393 TYR 0.017 0.001 TYR A 765 ARG 0.008 0.000 ARG A3334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 138 time to evaluate : 5.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 34 residues processed: 210 average time/residue: 1.2345 time to fit residues: 374.6366 Evaluate side-chains 169 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 2690 ASN Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3495 CYS Chi-restraints excluded: chain B residue 3795 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3808 THR Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 815 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 481 optimal weight: 0.7980 chunk 617 optimal weight: 9.9990 chunk 478 optimal weight: 6.9990 chunk 711 optimal weight: 20.0000 chunk 472 optimal weight: 6.9990 chunk 842 optimal weight: 7.9990 chunk 527 optimal weight: 6.9990 chunk 513 optimal weight: 9.9990 chunk 388 optimal weight: 0.3980 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS B1351 GLN ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 69090 Z= 0.364 Angle : 0.617 11.756 94172 Z= 0.319 Chirality : 0.047 0.342 10476 Planarity : 0.004 0.048 12438 Dihedral : 6.185 58.825 12078 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 10.95 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.09), residues: 8748 helix: -2.81 (0.28), residues: 242 sheet: -0.45 (0.10), residues: 2614 loop : -0.11 (0.09), residues: 5892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 930 HIS 0.007 0.001 HIS B1505 PHE 0.013 0.002 PHE A3393 TYR 0.018 0.001 TYR B 765 ARG 0.007 0.000 ARG A3334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 135 time to evaluate : 5.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 47 residues processed: 223 average time/residue: 1.1855 time to fit residues: 382.2989 Evaluate side-chains 180 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1793 ILE Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3637 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1793 ILE Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 2175 ILE Chi-restraints excluded: chain B residue 2690 ASN Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3795 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3808 THR Chi-restraints excluded: chain B residue 3860 PHE Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 521 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 503 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 535 optimal weight: 0.4980 chunk 573 optimal weight: 3.9990 chunk 416 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 662 optimal weight: 0.8980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS A3921 HIS ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 69090 Z= 0.199 Angle : 0.570 10.570 94172 Z= 0.295 Chirality : 0.045 0.338 10476 Planarity : 0.004 0.049 12438 Dihedral : 5.964 58.300 12078 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.13 % Allowed : 11.27 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.09), residues: 8748 helix: -2.61 (0.30), residues: 230 sheet: -0.39 (0.10), residues: 2598 loop : -0.08 (0.09), residues: 5920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 930 HIS 0.004 0.001 HIS A2403 PHE 0.014 0.001 PHE A3393 TYR 0.016 0.001 TYR A 765 ARG 0.005 0.000 ARG B3334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 137 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3146 MET cc_start: 0.7572 (mmm) cc_final: 0.7195 (mmm) REVERT: A 3674 MET cc_start: 0.6527 (mmm) cc_final: 0.6188 (mmp) REVERT: B 3146 MET cc_start: 0.7678 (mmm) cc_final: 0.7446 (mmm) outliers start: 78 outliers final: 36 residues processed: 206 average time/residue: 1.2982 time to fit residues: 381.5527 Evaluate side-chains 166 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2951 SER Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2175 ILE Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3795 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3860 PHE Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 766 optimal weight: 2.9990 chunk 807 optimal weight: 1.9990 chunk 736 optimal weight: 0.0270 chunk 785 optimal weight: 9.9990 chunk 806 optimal weight: 20.0000 chunk 472 optimal weight: 8.9990 chunk 341 optimal weight: 10.0000 chunk 616 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 709 optimal weight: 9.9990 chunk 742 optimal weight: 10.0000 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2084 HIS B2403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 69090 Z= 0.377 Angle : 0.632 10.877 94172 Z= 0.325 Chirality : 0.047 0.387 10476 Planarity : 0.004 0.053 12438 Dihedral : 6.157 59.444 12078 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.91 % Allowed : 11.67 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 8748 helix: -2.50 (0.30), residues: 230 sheet: -0.56 (0.10), residues: 2596 loop : -0.19 (0.09), residues: 5922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 930 HIS 0.007 0.001 HIS A2195 PHE 0.016 0.002 PHE A4277 TYR 0.017 0.002 TYR A 765 ARG 0.004 0.000 ARG B 678 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 132 time to evaluate : 5.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3146 MET cc_start: 0.7653 (mmm) cc_final: 0.7317 (mmm) REVERT: A 3674 MET cc_start: 0.6660 (mmm) cc_final: 0.6433 (mmp) REVERT: B 3146 MET cc_start: 0.7709 (mmm) cc_final: 0.7488 (mmm) outliers start: 63 outliers final: 42 residues processed: 190 average time/residue: 1.3448 time to fit residues: 360.5674 Evaluate side-chains 171 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 1793 ILE Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 2951 SER Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3637 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 1793 ILE Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 2175 ILE Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3795 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3860 PHE Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 782 optimal weight: 20.0000 chunk 515 optimal weight: 7.9990 chunk 830 optimal weight: 8.9990 chunk 506 optimal weight: 2.9990 chunk 393 optimal weight: 0.0870 chunk 577 optimal weight: 10.0000 chunk 870 optimal weight: 0.9990 chunk 801 optimal weight: 5.9990 chunk 693 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 535 optimal weight: 10.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2403 HIS ** B 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69090 Z= 0.250 Angle : 0.593 12.121 94172 Z= 0.304 Chirality : 0.046 0.605 10476 Planarity : 0.004 0.052 12438 Dihedral : 5.998 59.871 12078 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.70 % Allowed : 11.98 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.09), residues: 8748 helix: -2.37 (0.32), residues: 206 sheet: -0.52 (0.10), residues: 2584 loop : -0.15 (0.09), residues: 5958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 930 HIS 0.005 0.001 HIS B1723 PHE 0.015 0.001 PHE B4033 TYR 0.017 0.001 TYR A 765 ARG 0.005 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 5.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3146 MET cc_start: 0.7643 (mmm) cc_final: 0.7313 (mmm) REVERT: B 3674 MET cc_start: 0.6419 (mmm) cc_final: 0.6119 (mmp) outliers start: 48 outliers final: 34 residues processed: 174 average time/residue: 1.4106 time to fit residues: 343.9220 Evaluate side-chains 164 residues out of total 7716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 7.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 1073 CYS Chi-restraints excluded: chain A residue 1175 CYS Chi-restraints excluded: chain A residue 1214 CYS Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1710 CYS Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2676 CYS Chi-restraints excluded: chain A residue 2713 CYS Chi-restraints excluded: chain A residue 3076 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3637 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 4224 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 1279 CYS Chi-restraints excluded: chain B residue 1416 CYS Chi-restraints excluded: chain B residue 1552 VAL Chi-restraints excluded: chain B residue 2175 ILE Chi-restraints excluded: chain B residue 3076 THR Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3795 CYS Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3860 PHE Chi-restraints excluded: chain B residue 3916 ASP Chi-restraints excluded: chain B residue 4224 VAL Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 874 random chunks: chunk 425 optimal weight: 1.9990 chunk 550 optimal weight: 0.0670 chunk 738 optimal weight: 0.1980 chunk 212 optimal weight: 0.9990 chunk 639 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 192 optimal weight: 0.0170 chunk 694 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 713 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 833 HIS A2403 HIS A3594 HIS A4145 GLN B2403 HIS B4145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.059922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.042227 restraints weight = 396423.843| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.24 r_work: 0.2949 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 69090 Z= 0.134 Angle : 0.566 13.673 94172 Z= 0.288 Chirality : 0.045 0.508 10476 Planarity : 0.004 0.052 12438 Dihedral : 5.643 57.928 12078 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.55 % Allowed : 12.09 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 8748 helix: -2.39 (0.31), residues: 206 sheet: -0.31 (0.11), residues: 2300 loop : -0.10 (0.08), residues: 6242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 930 HIS 0.003 0.001 HIS B1723 PHE 0.015 0.001 PHE A3393 TYR 0.033 0.001 TYR A2692 ARG 0.004 0.000 ARG B4048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13792.89 seconds wall clock time: 242 minutes 0.20 seconds (14520.20 seconds total)