Starting phenix.real_space_refine (version: dev) on Tue Apr 12 04:07:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt3_23975/04_2022/7mt3_23975_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.015 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "2 ARG 6": "NH1" <-> "NH2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "8 ARG 9": "NH1" <-> "NH2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "8 ARG 103": "NH1" <-> "NH2" Residue "8 ARG 126": "NH1" <-> "NH2" Residue "8 ARG 134": "NH1" <-> "NH2" Residue "8 ARG 164": "NH1" <-> "NH2" Residue "8 ARG 207": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 141": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 151": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 136": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 147942 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 446 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "7" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 120 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain breaks: 1 Chain: "8" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1704 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 66958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66958 Classifications: {'RNA': 3118} Modifications used: {'rna3p': 1, 'rna2p': 1, 'rna3p_pur': 1481, 'rna3p_pyr': 1171, 'rna2p_pur': 301, 'rna2p_pyr': 163} Link IDs: {'rna3p': 2652, 'rna2p': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna3p_pyr': 46, 'rna2p_pur': 6, 'rna3p_pur': 56, 'rna2p_pyr': 7} Link IDs: {'rna3p': 101, 'rna2p': 13} Chain breaks: 1 Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 203, 'PCIS': 1} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1075 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 537 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 560 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32620 Classifications: {'RNA': 1519} Modifications used: {'rna3p': 6, 'rna2p': 1, 'rna3p_pur': 731, 'rna3p_pyr': 568, 'rna2p_pur': 119, 'rna2p_pyr': 94} Link IDs: {'rna3p': 1304, 'rna2p': 214} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1222 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1006 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "r" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "y" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 33, 'p5*END': 1, 'rna3p_pur': 30, 'rna2p_pur': 9} Link IDs: {'rna3p': 63, 'rna2p': 13} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna2p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 298 Unusual residues: {' MG': 298} Classifications: {'undetermined': 298} Link IDs: {None: 297} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Unusual residues: {' MG': 125} Classifications: {'undetermined': 125} Link IDs: {None: 124} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 121.060 177.615 185.920 1.00 60.18 S ATOM 519 SG CYS 1 18 121.114 180.807 184.164 1.00 61.58 S ATOM 734 SG CYS 1 42 124.405 179.384 184.831 1.00 56.94 S ATOM 755 SG CYS 1 45 122.625 181.224 188.110 1.00 60.22 S ATOM 1778 SG CYS 4 11 187.229 98.337 128.400 1.00 89.13 S ATOM 1801 SG CYS 4 14 188.185 101.743 127.925 1.00 85.49 S ATOM 1911 SG CYS 4 27 189.295 99.117 124.928 1.00 84.20 S ATOM 2121 SG CYS 6 16 120.966 109.019 220.188 1.00143.29 S ATOM 2280 SG CYS 6 38 124.652 109.023 220.065 1.00134.68 S ATOM 2301 SG CYS 6 41 122.864 106.007 219.157 1.00134.22 S ATOM 94880 SG CYS X 5 93.390 200.806 123.360 1.00 50.99 S ATOM 94902 SG CYS X 8 95.270 202.758 125.800 1.00 52.30 S ATOM 95245 SG CYS X 52 93.193 199.465 127.024 1.00 53.30 S ATOM 95264 SG CYS X 55 91.320 202.547 126.995 1.00 57.56 S ATOM A0VTE SG CYS n 24 87.573 63.369 170.657 1.00 89.03 S ATOM A0VTZ SG CYS n 27 89.388 64.291 167.611 1.00 88.35 S ATOM A0VWX SG CYS n 40 86.476 66.287 168.538 1.00 84.69 S ATOM A0VXM SG CYS n 43 85.973 63.063 166.391 1.00 85.72 S ATOM A0XVT SG CYS r 20 34.104 117.876 100.439 1.00 90.44 S ATOM A0XWH SG CYS r 23 34.420 116.815 96.616 1.00 99.13 S ATOM A0Y42 SG CYS r 57 38.037 117.504 97.804 1.00 71.79 S Time building chain proxies: 61.62, per 1000 atoms: 0.42 Number of scatterers: 147942 At special positions: 0 Unit cell: (243.8, 270.3, 240.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 89 16.00 P 4835 15.00 Mg 435 11.99 O 41398 8.00 N 27678 7.00 C 73501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.91 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " Number of angles added : 24 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10234 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 160 helices and 72 sheets defined 35.7% alpha, 18.1% beta 1181 base pairs and 2724 stacking pairs defined. Time for finding SS restraints: 60.93 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 3.741A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG 0 17 " --> pdb=" O THR 0 13 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.644A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 19 removed outlier: 3.644A pdb=" N ALA 2 16 " --> pdb=" O ASN 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 28 removed outlier: 4.197A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 removed outlier: 3.911A pdb=" N ILE 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG 2 39 " --> pdb=" O SER 2 35 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS 2 40 " --> pdb=" O SER 2 36 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.850A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 46 removed outlier: 3.856A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP 3 45 " --> pdb=" O THR 3 41 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.312A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR 3 59 " --> pdb=" O THR 3 55 " (cutoff:3.500A) Processing helix chain '6' and resid 57 through 65 removed outlier: 4.580A pdb=" N PHE 6 61 " --> pdb=" O ARG 6 57 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS 6 63 " --> pdb=" O ALA 6 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG 6 64 " --> pdb=" O ARG 6 60 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR 6 65 " --> pdb=" O PHE 6 61 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 8 removed outlier: 3.506A pdb=" N LYS 7 8 " --> pdb=" O ARG 7 4 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 15 removed outlier: 3.931A pdb=" N ALA 8 11 " --> pdb=" O ALA 8 7 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA 8 12 " --> pdb=" O TYR 8 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA 8 13 " --> pdb=" O ARG 8 9 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS 8 14 " --> pdb=" O ALA 8 10 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 36 removed outlier: 3.666A pdb=" N ALA 8 27 " --> pdb=" O PRO 8 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER 8 34 " --> pdb=" O ALA 8 30 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 3.695A pdb=" N ALA 8 87 " --> pdb=" O LYS 8 83 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA 8 89 " --> pdb=" O ASP 8 85 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA 8 90 " --> pdb=" O ALA 8 86 " (cutoff:3.500A) Processing helix chain '8' and resid 99 through 107 removed outlier: 3.672A pdb=" N ILE 8 104 " --> pdb=" O LEU 8 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN 8 105 " --> pdb=" O ILE 8 101 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY 8 107 " --> pdb=" O ARG 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 122 removed outlier: 5.306A pdb=" N ALA 8 122 " --> pdb=" O PRO 8 118 " (cutoff:3.500A) Processing helix chain '8' and resid 123 through 132 removed outlier: 4.473A pdb=" N ILE 8 127 " --> pdb=" O LYS 8 123 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG 8 129 " --> pdb=" O GLY 8 125 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL 8 130 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU 8 131 " --> pdb=" O ILE 8 127 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY 8 132 " --> pdb=" O ALA 8 128 " (cutoff:3.500A) Processing helix chain '8' and resid 148 through 159 removed outlier: 3.815A pdb=" N ALA 8 152 " --> pdb=" O ASP 8 148 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL 8 153 " --> pdb=" O VAL 8 149 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA 8 154 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE 8 156 " --> pdb=" O ALA 8 152 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY 8 159 " --> pdb=" O ASP 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 3.620A pdb=" N LEU 8 185 " --> pdb=" O ASP 8 181 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA 8 186 " --> pdb=" O GLU 8 182 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE 8 193 " --> pdb=" O TYR 8 189 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP 8 194 " --> pdb=" O GLY 8 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 8 195 " --> pdb=" O ALA 8 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.526A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.014A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.009A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 4.075A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.722A pdb=" N GLN C 201 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA C 202 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 203 " --> pdb=" O GLU C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'D' and resid 58 through 63 removed outlier: 4.121A pdb=" N VAL D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 63' Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.512A pdb=" N GLY D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.705A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'E' and resid 36 through 53 removed outlier: 4.302A pdb=" N GLN E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.597A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.737A pdb=" N ALA E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.507A pdb=" N LEU E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 4.224A pdb=" N SER E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.599A pdb=" N ALA E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.538A pdb=" N ASN E 208 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 removed outlier: 3.555A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 5.056A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.622A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.542A pdb=" N LEU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.531A pdb=" N ALA F 50 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG F 52 " --> pdb=" O GLU F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.635A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.745A pdb=" N ARG G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.731A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 22 through 29' Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.514A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.540A pdb=" N ALA J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 72 removed outlier: 4.191A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.959A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.847A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.534A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.412A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 118 removed outlier: 3.738A pdb=" N ILE K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 43 removed outlier: 3.922A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.951A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.910A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 3.834A pdb=" N VAL L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 4.017A pdb=" N ARG L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.882A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS M 59 " --> pdb=" O ASN M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.620A pdb=" N ALA M 114 " --> pdb=" O ASN M 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS M 123 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.530A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.528A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.729A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.851A pdb=" N LYS N 68 " --> pdb=" O ARG N 64 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 4.061A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.798A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 4.012A pdb=" N THR O 8 " --> pdb=" O SER O 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 3.572A pdb=" N GLY O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.523A pdb=" N LEU O 82 " --> pdb=" O ARG O 78 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE O 83 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU O 85 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.720A pdb=" N GLU O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 12 removed outlier: 3.845A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS P 9 " --> pdb=" O ASP P 5 " (cutoff:3.500A) Proline residue: P 10 - end of helix No H-bonds generated for 'chain 'P' and resid 4 through 12' Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.888A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 4.302A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.654A pdb=" N GLU Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.553A pdb=" N ASN Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE Q 57 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS Q 59 " --> pdb=" O GLY Q 55 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 4.023A pdb=" N GLN Q 81 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.899A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 117 removed outlier: 3.701A pdb=" N THR Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 removed outlier: 4.707A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.964A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 4.761A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 71 removed outlier: 4.897A pdb=" N GLY S 55 " --> pdb=" O GLN S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.095A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE S 61 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA S 62 " --> pdb=" O ALA S 58 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.611A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.280A pdb=" N GLY T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 50 Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.250A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 removed outlier: 3.647A pdb=" N ARG V 23 " --> pdb=" O LYS V 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG V 24 " --> pdb=" O GLY V 20 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG V 26 " --> pdb=" O SER V 22 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG V 27 " --> pdb=" O ARG V 23 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA V 28 " --> pdb=" O ARG V 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY V 29 " --> pdb=" O ALA V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 58 removed outlier: 5.149A pdb=" N ALA V 53 " --> pdb=" O GLY V 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG V 57 " --> pdb=" O ALA V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 3.952A pdb=" N ALA X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 13 removed outlier: 3.511A pdb=" N LEU Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 6 through 13' Processing helix chain 'Y' and resid 14 through 39 removed outlier: 6.077A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.992A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE Y 57 " --> pdb=" O GLU Y 53 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 4.162A pdb=" N SER Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.679A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.789A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 4.396A pdb=" N TYR c 31 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG c 40 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.561A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 71 through 77' Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.552A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG c 87 " --> pdb=" O ALA c 83 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.582A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.696A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN c 122 " --> pdb=" O GLY c 118 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 3.532A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.317A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 6.504A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix No H-bonds generated for 'chain 'd' and resid 23 through 30' Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.785A pdb=" N LYS d 53 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.986A pdb=" N ARG d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.443A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU d 86 " --> pdb=" O GLY d 82 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.603A pdb=" N GLY d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.526A pdb=" N ALA d 109 " --> pdb=" O THR d 105 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 4.480A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 201 removed outlier: 3.949A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU d 197 " --> pdb=" O GLN d 193 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 4.187A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 4.088A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS e 148 " --> pdb=" O ALA e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 3.632A pdb=" N VAL e 168 " --> pdb=" O ALA e 164 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 3.888A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 196 removed outlier: 3.777A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 197 through 208 removed outlier: 3.543A pdb=" N LEU e 201 " --> pdb=" O PRO e 197 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA e 203 " --> pdb=" O GLY e 199 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG e 204 " --> pdb=" O MET e 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG e 205 " --> pdb=" O LEU e 201 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.794A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 3.629A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG f 31 " --> pdb=" O LEU f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 3.642A pdb=" N GLU f 74 " --> pdb=" O ALA f 70 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.532A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.777A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR g 54 " --> pdb=" O ALA g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.501A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP g 67 " --> pdb=" O LYS g 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.709A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 4.441A pdb=" N ASP g 126 " --> pdb=" O ASN g 122 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.799A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N HIS g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.552A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.774A pdb=" N ASN h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.675A pdb=" N ARG h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.570A pdb=" N GLN i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN i 67 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 4.038A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL i 76 " --> pdb=" O PRO i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.515A pdb=" N GLY i 98 " --> pdb=" O SER i 94 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA i 99 " --> pdb=" O GLY i 95 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 114 through 123 removed outlier: 4.731A pdb=" N ALA i 118 " --> pdb=" O GLU i 114 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.166A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU j 27 " --> pdb=" O ARG j 23 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR j 28 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.221A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 5.464A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 64 through 69 removed outlier: 4.889A pdb=" N SER k 68 " --> pdb=" O GLY k 64 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR k 69 " --> pdb=" O SER k 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 64 through 69' Processing helix chain 'k' and resid 70 through 88 removed outlier: 3.516A pdb=" N ALA k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU k 78 " --> pdb=" O GLN k 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA k 80 " --> pdb=" O ALA k 76 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 3.632A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN k 111 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.826A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.714A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.337A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.624A pdb=" N GLU m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA m 36 " --> pdb=" O GLU m 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.929A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.625A pdb=" N HIS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN m 63 " --> pdb=" O TYR m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.727A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP m 77 " --> pdb=" O GLU m 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE m 82 " --> pdb=" O ILE m 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.508A pdb=" N ARG m 93 " --> pdb=" O GLY m 89 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.330A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.542A pdb=" N ASN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY n 12 " --> pdb=" O ASN n 8 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.810A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.103A pdb=" N LYS o 9 " --> pdb=" O ALA o 5 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.823A pdb=" N GLU o 41 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS o 44 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.164A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP o 74 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.544A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU o 85 " --> pdb=" O LEU o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 6.007A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER p 61 " --> pdb=" O GLN p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.789A pdb=" N LYS p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 85 removed outlier: 4.151A pdb=" N PHE p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.710A pdb=" N PHE p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA p 108 " --> pdb=" O GLU p 104 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 4.411A pdb=" N ALA r 24 " --> pdb=" O CYS r 20 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS r 25 " --> pdb=" O VAL r 21 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 20 through 26' Processing helix chain 'r' and resid 34 through 43 removed outlier: 3.526A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG r 39 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE r 42 " --> pdb=" O LEU r 38 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 34 through 43' Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.598A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.600A pdb=" N ASP r 63 " --> pdb=" O GLN r 59 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL r 74 " --> pdb=" O ASN r 70 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA r 75 " --> pdb=" O ALA r 71 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 18 removed outlier: 4.116A pdb=" N LEU s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 12 through 18' Processing helix chain 's' and resid 70 through 75 removed outlier: 3.622A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 70 through 75' Processing helix chain 't' and resid 7 through 41 removed outlier: 3.700A pdb=" N GLU t 15 " --> pdb=" O ASN t 11 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG t 16 " --> pdb=" O ARG t 12 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR t 30 " --> pdb=" O SER t 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA t 31 " --> pdb=" O SER t 27 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS t 40 " --> pdb=" O ARG t 36 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA t 41 " --> pdb=" O GLU t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 removed outlier: 6.216A pdb=" N ALA t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR t 54 " --> pdb=" O LEU t 50 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY t 65 " --> pdb=" O ALA t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.714A pdb=" N LYS t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 removed outlier: 3.525A pdb=" N VAL 0 30 " --> pdb=" O HIS 0 37 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1' and resid 8 through 13 removed outlier: 3.600A pdb=" N LYS 1 27 " --> pdb=" O PRO 1 9 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 37 through 40 Processing sheet with id= 4, first strand: chain '3' and resid 22 through 25 removed outlier: 6.390A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 6, first strand: chain '6' and resid 12 through 16 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain '8' and resid 60 through 64 Processing sheet with id= 8, first strand: chain '8' and resid 75 through 78 Processing sheet with id= 9, first strand: chain '8' and resid 169 through 176 removed outlier: 6.338A pdb=" N ALA 8 169 " --> pdb=" O LEU 8 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 8 175 " --> pdb=" O VAL 8 42 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL 8 42 " --> pdb=" O ILE 8 175 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE 8 212 " --> pdb=" O VAL 8 224 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 8 224 " --> pdb=" O ILE 8 212 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.495A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.481A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.849A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 139 through 143 removed outlier: 3.961A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.481A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.770A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.133A pdb=" N GLN D 99 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 38 through 42 removed outlier: 5.082A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR D 47 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.447A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.769A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 13 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'E' and resid 129 through 132 Processing sheet with id= 22, first strand: chain 'F' and resid 72 through 75 removed outlier: 3.597A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN F 44 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 79 through 82 removed outlier: 7.282A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 23 through 27 Processing sheet with id= 25, first strand: chain 'G' and resid 41 through 46 removed outlier: 4.638A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'G' and resid 83 through 90 removed outlier: 5.405A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 125 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.529A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 107 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL G 114 " --> pdb=" O PHE G 106 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.821A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 17 through 21 removed outlier: 5.980A pdb=" N LYS K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 10 " --> pdb=" O LYS K 17 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 31, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.174A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 33, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.586A pdb=" N SER L 142 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.858A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.766A pdb=" N ALA N 108 " --> pdb=" O ARG N 103 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N MET N 110 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.608A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.668A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS P 28 " --> pdb=" O HIS P 82 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.801A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR P 59 " --> pdb=" O ARG P 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR P 57 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.708A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 21 through 25 removed outlier: 4.315A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU R 34 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'R' and resid 67 through 71 removed outlier: 3.851A pdb=" N GLY R 67 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLN R 93 " --> pdb=" O GLY R 71 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.807A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 83 through 89 removed outlier: 4.897A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.315A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.877A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.881A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 40 through 46 removed outlier: 3.513A pdb=" N ALA V 33 " --> pdb=" O GLN V 43 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 120 through 125 removed outlier: 3.540A pdb=" N VAL V 180 " --> pdb=" O LEU V 121 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL V 176 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 127 through 132 removed outlier: 5.799A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 51, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.749A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER X 19 " --> pdb=" O ARG X 23 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.409A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR Z 7 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.346A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 165 through 170 removed outlier: 3.649A pdb=" N GLY c 148 " --> pdb=" O TYR c 203 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR c 191 " --> pdb=" O GLY c 194 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'd' and resid 136 through 139 removed outlier: 4.253A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.808A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA e 66 " --> pdb=" O GLY e 82 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 115 through 119 removed outlier: 3.529A pdb=" N VAL e 125 " --> pdb=" O GLY e 118 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE e 154 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 35 through 38 removed outlier: 3.727A pdb=" N GLU f 38 " --> pdb=" O ASP f 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL f 65 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA f 67 " --> pdb=" O ARG f 2 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE f 9 " --> pdb=" O ARG f 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'f' and resid 39 through 44 removed outlier: 4.275A pdb=" N LYS f 39 " --> pdb=" O ASP f 64 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP f 64 " --> pdb=" O LYS f 39 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'f' and resid 45 through 48 removed outlier: 3.566A pdb=" N GLY f 58 " --> pdb=" O ARG f 46 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.435A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.638A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE h 62 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 125 through 128 removed outlier: 6.192A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.504A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU i 42 " --> pdb=" O ILE i 27 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY i 31 " --> pdb=" O VAL i 38 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY i 89 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG i 39 " --> pdb=" O HIS i 87 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS i 87 " --> pdb=" O ARG i 39 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE i 85 " --> pdb=" O ARG i 41 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'j' and resid 69 through 76 removed outlier: 4.992A pdb=" N ARG j 7 " --> pdb=" O GLN j 101 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 39 through 46 removed outlier: 4.086A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY k 118 " --> pdb=" O VAL k 92 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL k 94 " --> pdb=" O GLY k 118 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'l' and resid 29 through 33 removed outlier: 3.546A pdb=" N VAL l 80 " --> pdb=" O GLY l 32 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.962A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR l 38 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU l 57 " --> pdb=" O VAL l 61 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'p' and resid 5 through 11 removed outlier: 5.353A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG p 39 " --> pdb=" O GLU p 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU p 50 " --> pdb=" O ARG p 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU p 48 " --> pdb=" O HIS p 41 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 59 through 63 removed outlier: 3.924A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'q' and resid 71 through 82 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 's' and resid 30 through 33 removed outlier: 3.956A pdb=" N ILE s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2888 hydrogen bonds 4654 hydrogen bond angles 0 basepair planarities 1181 basepair parallelities 2724 stacking parallelities Total time for adding SS restraints: 344.63 Time building geometry restraints manager: 57.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12032 1.30 - 1.43: 72998 1.43 - 1.56: 65716 1.56 - 1.69: 9668 1.69 - 1.82: 148 Bond restraints: 160562 Sorted by residual: bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.150 1.446 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.805 1.592 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C8 G7M a 518 " pdb=" N7 G7M a 518 " ideal model delta sigma weight residual 1.348 1.507 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 1.348 1.504 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" N7 G7M a 518 " pdb=" C5 G7M a 518 " ideal model delta sigma weight residual 1.329 1.441 -0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 160557 not shown) Histogram of bond angle deviations from ideal: 97.91 - 106.01: 27556 106.01 - 114.12: 102219 114.12 - 122.22: 77201 122.22 - 130.33: 32178 130.33 - 138.43: 1808 Bond angle restraints: 240962 Sorted by residual: angle pdb=" C ASN Q 72 " pdb=" N ASP Q 73 " pdb=" CA ASP Q 73 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CA ARG K 110 " pdb=" CB ARG K 110 " pdb=" CG ARG K 110 " ideal model delta sigma weight residual 114.10 124.78 -10.68 2.00e+00 2.50e-01 2.85e+01 angle pdb=" C VAL U 38 " pdb=" N ASN U 39 " pdb=" CA ASN U 39 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" CA LEU V 47 " pdb=" CB LEU V 47 " pdb=" CG LEU V 47 " ideal model delta sigma weight residual 116.30 134.03 -17.73 3.50e+00 8.16e-02 2.57e+01 angle pdb=" C SER 6 3 " pdb=" N ASP 6 4 " pdb=" CA ASP 6 4 " ideal model delta sigma weight residual 121.54 131.13 -9.59 1.91e+00 2.74e-01 2.52e+01 ... (remaining 240957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 82717 35.93 - 71.86: 2532 71.86 - 107.79: 146 107.79 - 143.72: 8 143.72 - 179.65: 25 Dihedral angle restraints: 85428 sinusoidal: 69501 harmonic: 15927 Sorted by residual: dihedral pdb=" O4' C A 882 " pdb=" C1' C A 882 " pdb=" N1 C A 882 " pdb=" C2 C A 882 " ideal model delta sinusoidal sigma weight residual -160.00 16.47 -176.47 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A3060 " pdb=" C1' C A3060 " pdb=" N1 C A3060 " pdb=" C2 C A3060 " ideal model delta sinusoidal sigma weight residual 200.00 23.92 176.08 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A 739 " pdb=" C1' C A 739 " pdb=" N1 C A 739 " pdb=" C2 C A 739 " ideal model delta sinusoidal sigma weight residual 200.00 24.54 175.46 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 85425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 28928 0.084 - 0.168: 1808 0.168 - 0.252: 94 0.252 - 0.336: 10 0.336 - 0.419: 2 Chirality restraints: 30842 Sorted by residual: chirality pdb=" CB VAL g 75 " pdb=" CA VAL g 75 " pdb=" CG1 VAL g 75 " pdb=" CG2 VAL g 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB VAL Z 50 " pdb=" CA VAL Z 50 " pdb=" CG1 VAL Z 50 " pdb=" CG2 VAL Z 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ASN U 39 " pdb=" N ASN U 39 " pdb=" C ASN U 39 " pdb=" CB ASN U 39 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 30839 not shown) Planarity restraints: 12605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 959 " -0.001 2.00e-02 2.50e+03 5.73e-01 7.40e+03 pdb=" C4' 2MG a 959 " 0.447 2.00e-02 2.50e+03 pdb=" O4' 2MG a 959 " 0.757 2.00e-02 2.50e+03 pdb=" C3' 2MG a 959 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG a 959 " -0.514 2.00e-02 2.50e+03 pdb=" C2' 2MG a 959 " -0.260 2.00e-02 2.50e+03 pdb=" O2' 2MG a 959 " 0.833 2.00e-02 2.50e+03 pdb=" C1' 2MG a 959 " 0.205 2.00e-02 2.50e+03 pdb=" N9 2MG a 959 " -0.881 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.018 2.00e-02 2.50e+03 5.49e-01 6.77e+03 pdb=" C4' OMG A2791 " 0.420 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.616 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.519 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.228 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.866 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.824 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a 960 " -0.034 2.00e-02 2.50e+03 5.00e-01 5.63e+03 pdb=" C4' 5MC a 960 " 0.421 2.00e-02 2.50e+03 pdb=" O4' 5MC a 960 " 0.570 2.00e-02 2.50e+03 pdb=" C3' 5MC a 960 " -0.563 2.00e-02 2.50e+03 pdb=" O3' 5MC a 960 " -0.407 2.00e-02 2.50e+03 pdb=" C2' 5MC a 960 " -0.270 2.00e-02 2.50e+03 pdb=" O2' 5MC a 960 " 0.765 2.00e-02 2.50e+03 pdb=" C1' 5MC a 960 " 0.255 2.00e-02 2.50e+03 pdb=" N1 5MC a 960 " -0.736 2.00e-02 2.50e+03 ... (remaining 12602 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 1 2.02 - 2.74: 19496 2.74 - 3.46: 175460 3.46 - 4.18: 468204 4.18 - 4.90: 645168 Nonbonded interactions: 1308329 Sorted by model distance: nonbonded pdb="MG MG A3329 " pdb="MG MG A3489 " model vdw 1.298 1.300 nonbonded pdb=" OP2 U A2920 " pdb="MG MG A3339 " model vdw 2.033 2.170 nonbonded pdb=" OP2 A A1119 " pdb="MG MG A3285 " model vdw 2.037 2.170 nonbonded pdb=" OP1 A A2959 " pdb="MG MG A3339 " model vdw 2.037 2.170 nonbonded pdb=" OP1 G A 880 " pdb="MG MG A3204 " model vdw 2.037 2.170 ... (remaining 1308324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 4835 5.49 5 Mg 435 5.21 5 S 89 5.16 5 C 73501 2.51 5 N 27678 2.21 5 O 41398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 17.880 Check model and map are aligned: 1.680 Convert atoms to be neutral: 0.980 Process input model: 653.990 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 694.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 0.296 160562 Z= 0.451 Angle : 0.791 17.730 240962 Z= 0.396 Chirality : 0.043 0.419 30842 Planarity : 0.011 0.573 12605 Dihedral : 13.620 179.652 75194 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.52 (0.09), residues: 5512 helix: -4.61 (0.05), residues: 1502 sheet: -1.87 (0.15), residues: 999 loop : -2.52 (0.09), residues: 3011 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1047 time to evaluate : 6.290 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 outliers start: 6 outliers final: 3 residues processed: 1051 average time/residue: 2.5366 time to fit residues: 3725.8543 Evaluate side-chains 749 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 746 time to evaluate : 6.337 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.0442 time to fit residues: 8.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 860 optimal weight: 0.9990 chunk 772 optimal weight: 20.0000 chunk 428 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 520 optimal weight: 20.0000 chunk 412 optimal weight: 3.9990 chunk 798 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 485 optimal weight: 0.2980 chunk 594 optimal weight: 3.9990 chunk 925 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 HIS 1 31 ASN 1 49 GLN 2 12 ASN 3 25 GLN 3 28 ASN 4 34 GLN 4 36 GLN 7 17 ASN ** 8 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 231 ASN C 96 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 47 GLN E 190 ASN E 214 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN J 94 GLN J 147 GLN M 14 HIS M 57 HIS P 79 ASN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN U 62 GLN V 91 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 HIS ** d 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN d 77 GLN e 163 ASN h 121 GLN i 65 HIS i 66 GLN k 126 GLN o 51 HIS p 15 ASN q 70 GLN s 23 ASN s 29 GLN t 14 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 160562 Z= 0.195 Angle : 0.602 18.346 240962 Z= 0.313 Chirality : 0.036 0.601 30842 Planarity : 0.006 0.117 12605 Dihedral : 13.546 179.957 64279 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.99 % Favored : 93.90 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.25 (0.10), residues: 5512 helix: -2.75 (0.10), residues: 1583 sheet: -1.43 (0.15), residues: 1012 loop : -2.05 (0.10), residues: 2917 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 786 time to evaluate : 6.367 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 46 residues processed: 832 average time/residue: 2.2649 time to fit residues: 2730.8404 Evaluate side-chains 769 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 723 time to evaluate : 6.332 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 18 residues processed: 29 average time/residue: 1.5927 time to fit residues: 81.1918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 514 optimal weight: 0.0270 chunk 287 optimal weight: 60.0000 chunk 770 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 chunk 927 optimal weight: 5.9990 chunk 1001 optimal weight: 8.9990 chunk 825 optimal weight: 7.9990 chunk 919 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 743 optimal weight: 8.9990 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 1 49 GLN 3 25 GLN 8 168 GLN C 130 ASN D 34 ASN D 135 GLN E 47 GLN E 190 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS J 94 GLN ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Q 122 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN d 121 ASN k 126 GLN q 70 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 14 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 160562 Z= 0.448 Angle : 0.695 14.172 240962 Z= 0.351 Chirality : 0.042 0.309 30842 Planarity : 0.006 0.122 12605 Dihedral : 13.643 179.809 64279 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.57 (0.10), residues: 5512 helix: -1.76 (0.12), residues: 1589 sheet: -1.19 (0.16), residues: 1044 loop : -1.84 (0.11), residues: 2879 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 728 time to evaluate : 6.388 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 outliers start: 163 outliers final: 83 residues processed: 810 average time/residue: 2.2443 time to fit residues: 2634.4075 Evaluate side-chains 801 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 718 time to evaluate : 6.376 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 33 residues processed: 50 average time/residue: 1.3645 time to fit residues: 124.4014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 915 optimal weight: 0.0000 chunk 696 optimal weight: 10.0000 chunk 481 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 442 optimal weight: 7.9990 chunk 622 optimal weight: 0.9980 chunk 930 optimal weight: 10.0000 chunk 984 optimal weight: 20.0000 chunk 486 optimal weight: 0.9990 chunk 881 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 47 GLN E 190 ASN F 142 GLN J 94 GLN O 48 ASN ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN k 111 GLN r 56 ASN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 8 GLN t 70 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 160562 Z= 0.177 Angle : 0.548 15.029 240962 Z= 0.287 Chirality : 0.034 0.268 30842 Planarity : 0.005 0.115 12605 Dihedral : 13.425 179.827 64279 Min Nonbonded Distance : 1.128 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.99 (0.11), residues: 5512 helix: -1.11 (0.13), residues: 1603 sheet: -0.88 (0.16), residues: 1043 loop : -1.57 (0.11), residues: 2866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 706 time to evaluate : 6.331 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: 141 outliers final: 73 residues processed: 780 average time/residue: 2.1250 time to fit residues: 2441.2809 Evaluate side-chains 740 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 667 time to evaluate : 5.791 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 39 residues processed: 35 average time/residue: 1.4658 time to fit residues: 92.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 820 optimal weight: 1.9990 chunk 559 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 733 optimal weight: 8.9990 chunk 406 optimal weight: 7.9990 chunk 840 optimal weight: 3.9990 chunk 680 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 502 optimal weight: 6.9990 chunk 884 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 47 GLN E 53 GLN E 190 ASN J 94 GLN Q 122 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN i 96 GLN r 56 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 160562 Z= 0.360 Angle : 0.628 14.569 240962 Z= 0.320 Chirality : 0.039 0.277 30842 Planarity : 0.006 0.119 12605 Dihedral : 13.452 179.855 64279 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.75 % Favored : 93.18 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.83 (0.11), residues: 5512 helix: -0.89 (0.13), residues: 1617 sheet: -0.78 (0.16), residues: 1052 loop : -1.54 (0.11), residues: 2843 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 679 time to evaluate : 6.427 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 outliers start: 165 outliers final: 99 residues processed: 762 average time/residue: 2.1861 time to fit residues: 2445.9109 Evaluate side-chains 773 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 674 time to evaluate : 6.306 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 52 residues processed: 49 average time/residue: 1.4445 time to fit residues: 127.8209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 331 optimal weight: 9.9990 chunk 887 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 578 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 985 optimal weight: 0.2980 chunk 818 optimal weight: 0.0970 chunk 456 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 326 optimal weight: 10.0000 chunk 517 optimal weight: 0.6980 overall best weight: 2.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 47 GLN E 190 ASN J 94 GLN P 28 HIS Q 122 ASN U 62 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN i 96 GLN k 85 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 160562 Z= 0.212 Angle : 0.563 14.884 240962 Z= 0.292 Chirality : 0.035 0.269 30842 Planarity : 0.005 0.117 12605 Dihedral : 13.395 179.980 64279 Min Nonbonded Distance : 1.098 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.60 (0.11), residues: 5512 helix: -0.60 (0.13), residues: 1606 sheet: -0.71 (0.16), residues: 1075 loop : -1.43 (0.11), residues: 2831 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 667 time to evaluate : 6.365 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 outliers start: 144 outliers final: 85 residues processed: 758 average time/residue: 2.1868 time to fit residues: 2416.9609 Evaluate side-chains 761 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 676 time to evaluate : 6.408 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 58 residues processed: 30 average time/residue: 1.3946 time to fit residues: 80.2663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 950 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 561 optimal weight: 7.9990 chunk 719 optimal weight: 10.0000 chunk 557 optimal weight: 6.9990 chunk 829 optimal weight: 20.0000 chunk 550 optimal weight: 10.0000 chunk 982 optimal weight: 20.0000 chunk 614 optimal weight: 6.9990 chunk 598 optimal weight: 5.9990 chunk 453 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 47 GLN F 134 ASN J 94 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN g 153 HIS ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.085 160562 Z= 0.530 Angle : 0.734 14.265 240962 Z= 0.366 Chirality : 0.044 0.321 30842 Planarity : 0.006 0.122 12605 Dihedral : 13.610 179.639 64279 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.67 (0.11), residues: 5512 helix: -0.65 (0.13), residues: 1610 sheet: -0.65 (0.16), residues: 1054 loop : -1.53 (0.11), residues: 2848 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 696 time to evaluate : 6.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 97 residues processed: 778 average time/residue: 2.2719 time to fit residues: 2585.1401 Evaluate side-chains 781 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 684 time to evaluate : 6.394 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 56 residues processed: 43 average time/residue: 1.3017 time to fit residues: 106.2809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 607 optimal weight: 3.9990 chunk 392 optimal weight: 2.9990 chunk 586 optimal weight: 0.9990 chunk 295 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 624 optimal weight: 7.9990 chunk 669 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 771 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 47 GLN E 190 ASN F 134 ASN J 94 GLN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN V 38 HIS ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN i 96 GLN i 147 GLN k 85 GLN ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 57 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.156 160562 Z= 0.287 Angle : 0.623 15.853 240962 Z= 0.321 Chirality : 0.037 0.309 30842 Planarity : 0.006 0.119 12605 Dihedral : 13.531 179.621 64279 Min Nonbonded Distance : 1.060 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.55 (0.11), residues: 5512 helix: -0.51 (0.13), residues: 1623 sheet: -0.57 (0.16), residues: 1050 loop : -1.50 (0.11), residues: 2839 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 689 time to evaluate : 6.132 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 outliers start: 121 outliers final: 86 residues processed: 769 average time/residue: 2.1942 time to fit residues: 2467.1149 Evaluate side-chains 763 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 677 time to evaluate : 6.275 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 63 residues processed: 25 average time/residue: 1.3801 time to fit residues: 65.8835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 893 optimal weight: 0.0060 chunk 940 optimal weight: 5.9990 chunk 858 optimal weight: 4.9990 chunk 915 optimal weight: 0.4980 chunk 550 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 718 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 827 optimal weight: 9.9990 chunk 865 optimal weight: 5.9990 chunk 912 optimal weight: 0.7980 overall best weight: 2.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN F 134 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN i 96 GLN i 147 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.143 160562 Z= 0.185 Angle : 0.549 16.836 240962 Z= 0.285 Chirality : 0.033 0.280 30842 Planarity : 0.005 0.115 12605 Dihedral : 13.335 179.639 64279 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.28 (0.11), residues: 5512 helix: -0.17 (0.13), residues: 1626 sheet: -0.50 (0.16), residues: 1043 loop : -1.37 (0.11), residues: 2843 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 687 time to evaluate : 6.359 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 outliers start: 99 outliers final: 69 residues processed: 759 average time/residue: 2.1967 time to fit residues: 2455.1481 Evaluate side-chains 727 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 658 time to evaluate : 6.410 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 60 residues processed: 10 average time/residue: 1.4932 time to fit residues: 31.8003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 601 optimal weight: 1.9990 chunk 967 optimal weight: 5.9990 chunk 590 optimal weight: 1.9990 chunk 459 optimal weight: 0.0000 chunk 672 optimal weight: 20.0000 chunk 1015 optimal weight: 10.0000 chunk 934 optimal weight: 9.9990 chunk 808 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 chunk 624 optimal weight: 3.9990 chunk 495 optimal weight: 5.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 214 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN J 94 GLN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN i 96 GLN i 147 GLN j 4 GLN k 85 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.168 160562 Z= 0.197 Angle : 0.544 15.740 240962 Z= 0.282 Chirality : 0.033 0.261 30842 Planarity : 0.005 0.116 12605 Dihedral : 13.236 179.158 64279 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.03 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.06 (0.11), residues: 5512 helix: 0.10 (0.13), residues: 1622 sheet: -0.43 (0.16), residues: 1047 loop : -1.26 (0.11), residues: 2843 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11024 Ramachandran restraints generated. 5512 Oldfield, 0 Emsley, 5512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 673 time to evaluate : 6.346 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 outliers start: 83 outliers final: 67 residues processed: 739 average time/residue: 2.1781 time to fit residues: 2363.9726 Evaluate side-chains 726 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 659 time to evaluate : 6.066 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 58 residues processed: 9 average time/residue: 1.4107 time to fit residues: 27.8624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 642 optimal weight: 4.9990 chunk 861 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 745 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 809 optimal weight: 7.9990 chunk 338 optimal weight: 10.0000 chunk 831 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN D 135 GLN E 47 GLN E 214 ASN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN ** e 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 121 GLN i 96 GLN i 147 GLN k 85 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.078714 restraints weight = 216067.088| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.04 r_work: 0.2827 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 1.00 restraints_weight: 0.2500 r_work: 0.2805 rms_B_bonded: 1.07 restraints_weight: 0.1250 r_work: 0.2794 rms_B_bonded: 1.17 restraints_weight: 0.0625 r_work: 0.2781 rms_B_bonded: 1.30 restraints_weight: 0.0312 r_work: 0.2768 rms_B_bonded: 1.47 restraints_weight: 0.0156 r_work: 0.2752 rms_B_bonded: 1.67 restraints_weight: 0.0078 r_work: 0.2735 rms_B_bonded: 1.92 restraints_weight: 0.0039 r_work: 0.2716 rms_B_bonded: 2.20 restraints_weight: 0.0020 r_work: 0.2694 rms_B_bonded: 2.54 restraints_weight: 0.0010 r_work: 0.2669 rms_B_bonded: 2.94 restraints_weight: 0.0005 r_work: 0.2641 rms_B_bonded: 3.41 restraints_weight: 0.0002 r_work: 0.2609 rms_B_bonded: 3.97 restraints_weight: 0.0001 r_work: 0.2571 rms_B_bonded: 4.62 restraints_weight: 0.0001 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.469 160562 Z= 0.486 Angle : 0.697 37.506 240962 Z= 0.349 Chirality : 0.042 0.299 30842 Planarity : 0.006 0.121 12605 Dihedral : 13.446 179.501 64279 Min Nonbonded Distance : 1.025 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.98 % Favored : 92.92 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.23 (0.11), residues: 5512 helix: -0.09 (0.13), residues: 1609 sheet: -0.45 (0.16), residues: 1062 loop : -1.36 (0.11), residues: 2841 =============================================================================== Job complete usr+sys time: 38080.94 seconds wall clock time: 656 minutes 9.73 seconds (39369.73 seconds total)