Starting phenix.real_space_refine (version: dev) on Sat May 21 00:48:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/05_2022/7nfx_12303_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/05_2022/7nfx_12303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/05_2022/7nfx_12303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/05_2022/7nfx_12303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/05_2022/7nfx_12303_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/05_2022/7nfx_12303_neut_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.006 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 "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 148232 Number of models: 1 Model: "" Number of chains: 62 Chain: "1" Number of atoms: 5341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 5341 Classifications: {'RNA': 249} Modifications used: {'rna3p_pyr': 101, 'rna2p_pur': 12, 'rna3p_pur': 124, 'rna2p_pyr': 12} Link IDs: {'rna3p': 224, 'rna2p': 24} Chain breaks: 3 Chain: "5" Number of atoms: 74854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3493, 74854 Classifications: {'RNA': 3493} Modifications used: {'5*END': 1, 'rna2p_pur': 325, 'rna3p_pur': 1579, 'rna2p_pyr': 214, 'rna3p_pyr': 1374} Link IDs: {'rna3p': 2953, 'rna2p': 539} Chain breaks: 15 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 6, 'rna3p_pyr': 53} Link IDs: {'rna3p': 107, 'rna2p': 12} Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'rna3p_pyr': 67, 'rna2p_pur': 14, 'rna3p_pur': 62, 'rna2p_pyr': 13, '5*END': 1} Link IDs: {'rna3p': 129, 'rna2p': 26} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "r" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "t" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "u" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1637 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain: "v" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1455 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Chain: "w" Number of atoms: 623 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 617 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 617 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 621 Chain: "x" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3236 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 10, 'TRANS': 406} Chain breaks: 1 Chain: "y" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1133 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "z" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 161 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 5, 'TRANS': 13} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GNP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0NW4 SG CYS g 46 59.310 120.371 111.920 1.00 26.61 S ATOM A0NWL SG CYS g 49 58.613 118.736 115.335 1.00 28.99 S ATOM A0O3W SG CYS g 83 58.475 116.594 112.270 1.00 25.18 S ATOM A0O4G SG CYS g 86 55.862 119.270 112.685 1.00 26.45 S ATOM A0PU7 SG CYS j 19 107.649 141.850 86.862 1.00 16.45 S ATOM A0PUZ SG CYS j 22 111.021 143.664 86.815 1.00 12.78 S ATOM A0PXI SG CYS j 34 108.198 144.958 88.968 1.00 15.07 S ATOM A0PY1 SG CYS j 37 108.029 145.263 85.173 1.00 16.57 S ATOM A0R6J SG CYS m 96 154.212 197.458 177.169 1.00 24.69 S ATOM A0R79 SG CYS m 99 155.028 193.799 176.575 1.00 23.47 S ATOM A0R9R SG CYS m 110 157.793 196.064 177.663 1.00 25.02 S ATOM A0RAZ SG CYS m 115 156.352 196.402 174.168 1.00 23.66 S ATOM A0RMN SG CYS o 12 98.752 236.607 88.385 1.00 29.84 S ATOM A0RNB SG CYS o 15 97.474 239.431 86.234 1.00 29.12 S ATOM A0S0C SG CYS o 72 95.245 237.989 89.049 1.00 27.99 S ATOM A0S1D SG CYS o 77 96.027 236.034 85.814 1.00 29.97 S ATOM A0SG3 SG CYS p 39 54.129 129.736 125.390 1.00 15.59 S ATOM A0SGQ SG CYS p 42 53.880 126.304 127.094 1.00 17.02 S ATOM A0SK4 SG CYS p 57 57.009 127.377 125.102 1.00 15.86 S ATOM A0SKK SG CYS p 60 53.610 126.353 123.526 1.00 17.83 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS w 39 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS w 39 " occ=0.50 Time building chain proxies: 60.09, per 1000 atoms: 0.41 Number of scatterers: 148232 At special positions: 0 Unit cell: (255.942, 309.042, 270.81, 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 5 29.99 S 290 16.00 P 4021 15.00 Mg 2 11.99 O 38559 8.00 N 27743 7.00 C 77612 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: 55.84 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " Number of angles added : 30 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14376 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: 270 helices and 67 sheets defined 44.7% alpha, 13.2% beta 1236 base pairs and 1953 stacking pairs defined. Time for finding SS restraints: 63.82 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.815A pdb=" N ARG A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 13' Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.727A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.830A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.971A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.010A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.876A pdb=" N CYS B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.480A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.947A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.481A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.742A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.013A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 49 removed outlier: 4.046A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 133 removed outlier: 4.039A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 141 removed outlier: 3.587A pdb=" N GLY C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 4.281A pdb=" N GLY C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 176 through 187 removed outlier: 4.008A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 216 through 223 removed outlier: 4.887A pdb=" N ASN C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 Proline residue: C 242 - end of helix Processing helix chain 'C' and resid 253 through 264 removed outlier: 4.303A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.511A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 4.049A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.533A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 363 removed outlier: 4.177A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 5.298A pdb=" N GLN C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER C 63 " --> pdb=" O HIS C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 63' Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 4.082A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.493A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.805A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 removed outlier: 6.573A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.577A pdb=" N ASN D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 230' Processing helix chain 'D' and resid 232 through 250 removed outlier: 3.518A pdb=" N MET D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 294 removed outlier: 4.435A pdb=" N ARG D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.566A pdb=" N MET E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 removed outlier: 5.332A pdb=" N ILE E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 removed outlier: 4.170A pdb=" N LYS E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 258 removed outlier: 3.716A pdb=" N LYS E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 262 through 270 removed outlier: 4.976A pdb=" N VAL E 270 " --> pdb=" O TYR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 5.154A pdb=" N VAL E 283 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'F' and resid 26 through 81 removed outlier: 3.520A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.272A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 199 removed outlier: 4.079A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 211 removed outlier: 5.002A pdb=" N TRP F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 250 removed outlier: 4.891A pdb=" N ASN F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG F 244 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.645A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 5.211A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 4.042A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 123 removed outlier: 3.750A pdb=" N LYS G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 150 Processing helix chain 'G' and resid 167 through 178 Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.720A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS G 195 " --> pdb=" O CYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 226 removed outlier: 4.658A pdb=" N GLY G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 262 removed outlier: 3.917A pdb=" N LEU G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 86 removed outlier: 3.996A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.141A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.073A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.128A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.067A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 Processing helix chain 'I' and resid 144 through 160 removed outlier: 3.911A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 removed outlier: 4.315A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 4.149A pdb=" N HIS I 213 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.525A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY J 116 " --> pdb=" O HIS J 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 116' Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.703A pdb=" N ASP J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'L' and resid 17 through 22 removed outlier: 3.786A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.863A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 3.592A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 124 removed outlier: 3.908A pdb=" N LEU L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 147 removed outlier: 3.963A pdb=" N GLU L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 139 through 147' Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 177 through 192 Processing helix chain 'L' and resid 193 through 211 removed outlier: 3.586A pdb=" N LYS L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS L 211 " --> pdb=" O VAL L 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 56 removed outlier: 4.013A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 removed outlier: 6.464A pdb=" N VAL M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG M 74 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 removed outlier: 5.392A pdb=" N ARG M 90 " --> pdb=" O TRP M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 Processing helix chain 'M' and resid 106 through 139 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.929A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.713A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.969A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.710A pdb=" N GLY N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.110A pdb=" N ASN N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.615A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'N' and resid 147 through 152 removed outlier: 4.547A pdb=" N TRP N 150 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE N 151 " --> pdb=" O THR N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.717A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU O 29 " --> pdb=" O LYS O 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 removed outlier: 5.322A pdb=" N ARG O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.709A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.540A pdb=" N MET O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 5.095A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 150 through 190 removed outlier: 5.492A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE O 189 " --> pdb=" O VAL O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 removed outlier: 3.775A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS O 199 " --> pdb=" O VAL O 195 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.455A pdb=" N LYS P 74 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 22 through 39 removed outlier: 3.571A pdb=" N ARG Q 26 " --> pdb=" O ASP Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 54 removed outlier: 4.225A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.858A pdb=" N LEU Q 72 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.276A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY Q 153 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 146 through 153' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 6.509A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.758A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.830A pdb=" N ILE R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.600A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.502A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 120 through 125 removed outlier: 5.096A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 147 removed outlier: 4.622A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP S 147 " --> pdb=" O LYS S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 166 Proline residue: S 165 - end of helix No H-bonds generated for 'chain 'S' and resid 161 through 166' Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.529A pdb=" N PHE T 15 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 11 through 16' Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.388A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 59 removed outlier: 3.652A pdb=" N HIS T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 54 through 59' Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.078A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS T 97 " --> pdb=" O ILE T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 99 through 121 removed outlier: 4.259A pdb=" N ASP T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 4.882A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU U 30 " --> pdb=" O THR U 26 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP U 31 " --> pdb=" O HIS U 27 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY U 32 " --> pdb=" O PRO U 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 25 through 32' Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 55 through 60 removed outlier: 5.142A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 55 through 60' Processing helix chain 'U' and resid 79 through 95 removed outlier: 4.182A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 5.395A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 130 Proline residue: V 130 - end of helix Processing helix chain 'V' and resid 131 through 136 Processing helix chain 'W' and resid 33 through 43 removed outlier: 3.694A pdb=" N LYS W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 50 removed outlier: 4.053A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASN W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 45 through 50' Processing helix chain 'W' and resid 52 through 60 Processing helix chain 'X' and resid 72 through 78 removed outlier: 3.910A pdb=" N ILE X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 93 Processing helix chain 'X' and resid 105 through 117 Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 22 through 31 removed outlier: 4.321A pdb=" N SER Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.026A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 134 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.498A pdb=" N ILE Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.655A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N MET Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 3.560A pdb=" N VAL Z 96 " --> pdb=" O ASP Z 92 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 98 through 104 removed outlier: 4.930A pdb=" N ARG Z 102 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP Z 103 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) Proline residue: Z 104 - end of helix No H-bonds generated for 'chain 'Z' and resid 98 through 104' Processing helix chain 'Z' and resid 105 through 124 removed outlier: 3.802A pdb=" N LYS Z 123 " --> pdb=" O GLU Z 119 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.743A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 133' Processing helix chain 'a' and resid 2 through 7 removed outlier: 5.363A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 48 Processing helix chain 'a' and resid 64 through 69 removed outlier: 3.936A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.792A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER a 83 " --> pdb=" O TRP a 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 91 removed outlier: 3.890A pdb=" N ALA a 90 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 20 removed outlier: 4.224A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY b 20 " --> pdb=" O TRP b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 51 removed outlier: 4.629A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 76 Processing helix chain 'c' and resid 13 through 24 removed outlier: 3.885A pdb=" N ARG c 17 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 removed outlier: 4.014A pdb=" N THR c 34 " --> pdb=" O GLY c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 28 through 34 removed outlier: 3.857A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 57 removed outlier: 3.663A pdb=" N ARG d 41 " --> pdb=" O GLY d 37 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA d 42 " --> pdb=" O PHE d 38 " (cutoff:3.500A) Proline residue: d 43 - end of helix Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 3.631A pdb=" N TYR e 28 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL e 29 " --> pdb=" O SER e 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 24 through 29' Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 81 through 90 removed outlier: 4.344A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU e 89 " --> pdb=" O LEU e 85 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.579A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 40 removed outlier: 4.046A pdb=" N THR f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 35 through 40' Processing helix chain 'g' and resid 60 through 68 removed outlier: 3.610A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER g 68 " --> pdb=" O LEU g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.296A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 Processing helix chain 'h' and resid 40 through 74 removed outlier: 3.554A pdb=" N LYS h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 85 Proline residue: h 85 - end of helix Processing helix chain 'h' and resid 88 through 94 removed outlier: 3.883A pdb=" N ARG h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG h 94 " --> pdb=" O ALA h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 103 removed outlier: 6.377A pdb=" N GLU h 100 " --> pdb=" O ASN h 96 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS h 103 " --> pdb=" O GLU h 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 115 Proline residue: h 115 - end of helix Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.278A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.652A pdb=" N VAL i 47 " --> pdb=" O MET i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.519A pdb=" N VAL i 63 " --> pdb=" O GLU i 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 Processing helix chain 'i' and resid 79 through 103 removed outlier: 4.301A pdb=" N LYS i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.592A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.823A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.327A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.782A pdb=" N ARG k 17 " --> pdb=" O LEU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 60 removed outlier: 3.620A pdb=" N ALA k 53 " --> pdb=" O ASP k 49 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU k 60 " --> pdb=" O LEU k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.598A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.416A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.629A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.811A pdb=" N ARG n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 19 through 35 removed outlier: 4.116A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 19 through 24 removed outlier: 4.232A pdb=" N LEU q 23 " --> pdb=" O TYR q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 45 through 57 removed outlier: 3.566A pdb=" N ASP q 51 " --> pdb=" O THR q 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL q 52 " --> pdb=" O GLU q 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA q 55 " --> pdb=" O ASP q 51 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL q 56 " --> pdb=" O VAL q 52 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 80 removed outlier: 5.423A pdb=" N GLY q 80 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 117 removed outlier: 3.975A pdb=" N VAL q 104 " --> pdb=" O SER q 100 " (cutoff:3.500A) Proline residue: q 113 - end of helix removed outlier: 3.646A pdb=" N LYS q 116 " --> pdb=" O ILE q 112 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 13 removed outlier: 4.130A pdb=" N GLN r 6 " --> pdb=" O SER r 2 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN r 12 " --> pdb=" O MET r 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS r 13 " --> pdb=" O VAL r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 98 removed outlier: 6.060A pdb=" N THR r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU r 90 " --> pdb=" O ALA r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 122 removed outlier: 4.010A pdb=" N ARG r 107 " --> pdb=" O HIS r 103 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET r 108 " --> pdb=" O PRO r 104 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS r 122 " --> pdb=" O LEU r 118 " (cutoff:3.500A) Processing helix chain 't' and resid 5 through 22 removed outlier: 3.537A pdb=" N THR t 11 " --> pdb=" O GLU t 7 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG t 21 " --> pdb=" O PHE t 17 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR t 22 " --> pdb=" O GLN t 18 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 91 removed outlier: 4.218A pdb=" N MET t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA t 82 " --> pdb=" O LYS t 78 " (cutoff:3.500A) Processing helix chain 'u' and resid 61 through 74 removed outlier: 3.525A pdb=" N GLN u 72 " --> pdb=" O GLU u 68 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY u 74 " --> pdb=" O GLN u 70 " (cutoff:3.500A) Processing helix chain 'u' and resid 79 through 99 removed outlier: 3.636A pdb=" N TYR u 83 " --> pdb=" O ASP u 79 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 119 removed outlier: 3.968A pdb=" N LEU u 118 " --> pdb=" O THR u 114 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR u 119 " --> pdb=" O GLU u 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 114 through 119' Processing helix chain 'u' and resid 122 through 149 removed outlier: 3.768A pdb=" N LEU u 126 " --> pdb=" O ARG u 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL u 127 " --> pdb=" O TYR u 123 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN u 146 " --> pdb=" O LYS u 142 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR u 147 " --> pdb=" O GLN u 143 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU u 148 " --> pdb=" O GLU u 144 " (cutoff:3.500A) Proline residue: u 149 - end of helix Processing helix chain 'u' and resid 150 through 175 removed outlier: 4.137A pdb=" N HIS u 154 " --> pdb=" O ARG u 150 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL u 163 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS u 164 " --> pdb=" O ARG u 160 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU u 174 " --> pdb=" O GLU u 170 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER u 175 " --> pdb=" O ARG u 171 " (cutoff:3.500A) Processing helix chain 'u' and resid 179 through 202 removed outlier: 4.247A pdb=" N LYS u 183 " --> pdb=" O ASP u 179 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU u 184 " --> pdb=" O ALA u 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU u 185 " --> pdb=" O LYS u 181 " (cutoff:3.500A) Processing helix chain 'u' and resid 204 through 226 removed outlier: 3.651A pdb=" N GLU u 209 " --> pdb=" O LYS u 205 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR u 226 " --> pdb=" O ALA u 222 " (cutoff:3.500A) Processing helix chain 'u' and resid 227 through 252 removed outlier: 3.509A pdb=" N VAL u 231 " --> pdb=" O GLU u 227 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU u 232 " --> pdb=" O GLU u 228 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR u 233 " --> pdb=" O GLN u 229 " (cutoff:3.500A) Proline residue: u 242 - end of helix removed outlier: 4.320A pdb=" N ILE u 251 " --> pdb=" O CYS u 247 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY u 252 " --> pdb=" O ALA u 248 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 86 removed outlier: 3.565A pdb=" N LEU v 84 " --> pdb=" O LEU v 80 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU v 85 " --> pdb=" O PHE v 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 124 through 133 removed outlier: 3.502A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG v 131 " --> pdb=" O GLN v 127 " (cutoff:3.500A) Processing helix chain 'v' and resid 147 through 152 removed outlier: 3.659A pdb=" N GLU v 151 " --> pdb=" O ALA v 147 " (cutoff:3.500A) Processing helix chain 'v' and resid 153 through 169 removed outlier: 3.984A pdb=" N LEU v 169 " --> pdb=" O ASP v 165 " (cutoff:3.500A) Processing helix chain 'v' and resid 189 through 207 removed outlier: 3.547A pdb=" N THR v 203 " --> pdb=" O LYS v 199 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL v 206 " --> pdb=" O ASN v 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 233 through 238 Proline residue: v 238 - end of helix Processing helix chain 'v' and resid 260 through 271 removed outlier: 5.468A pdb=" N GLU v 264 " --> pdb=" O ILE v 260 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS v 265 " --> pdb=" O GLN v 261 " (cutoff:3.500A) Processing helix chain 'v' and resid 251 through 256 removed outlier: 4.196A pdb=" N ASP v 254 " --> pdb=" O GLY v 251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL v 255 " --> pdb=" O ARG v 252 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY v 256 " --> pdb=" O GLY v 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 251 through 256' Processing helix chain 'w' and resid 6 through 22 removed outlier: 3.555A pdb=" N ASP w 21 " --> pdb=" O LEU w 17 " (cutoff:3.500A) Proline residue: w 22 - end of helix Processing helix chain 'w' and resid 55 through 76 removed outlier: 4.579A pdb=" N VAL w 59 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS w 60 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS w 61 " --> pdb=" O GLN w 57 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS w 76 " --> pdb=" O LEU w 72 " (cutoff:3.500A) Processing helix chain 'x' and resid 3 through 20 removed outlier: 6.612A pdb=" N GLY x 7 " --> pdb=" O LEU x 3 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG x 8 " --> pdb=" O ALA x 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA x 13 " --> pdb=" O LYS x 9 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN x 19 " --> pdb=" O ARG x 15 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA x 20 " --> pdb=" O SER x 16 " (cutoff:3.500A) Processing helix chain 'x' and resid 24 through 43 Processing helix chain 'x' and resid 45 through 61 removed outlier: 4.338A pdb=" N ASP x 61 " --> pdb=" O LYS x 57 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 88 Processing helix chain 'x' and resid 113 through 129 Processing helix chain 'x' and resid 143 through 156 Processing helix chain 'x' and resid 167 through 183 Processing helix chain 'x' and resid 198 through 213 Processing helix chain 'x' and resid 227 through 240 removed outlier: 4.762A pdb=" N ALA x 231 " --> pdb=" O GLN x 227 " (cutoff:3.500A) Processing helix chain 'x' and resid 257 through 267 removed outlier: 4.056A pdb=" N SER x 261 " --> pdb=" O GLY x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 287 through 296 removed outlier: 4.874A pdb=" N ILE x 291 " --> pdb=" O THR x 287 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY x 296 " --> pdb=" O SER x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 299 through 311 removed outlier: 4.268A pdb=" N LEU x 303 " --> pdb=" O ASP x 299 " (cutoff:3.500A) Processing helix chain 'x' and resid 314 through 325 removed outlier: 5.463A pdb=" N LEU x 318 " --> pdb=" O ASP x 314 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE x 319 " --> pdb=" O ASN x 315 " (cutoff:3.500A) Processing helix chain 'x' and resid 328 through 343 removed outlier: 4.137A pdb=" N GLY x 343 " --> pdb=" O ILE x 339 " (cutoff:3.500A) Processing helix chain 'x' and resid 363 through 382 removed outlier: 5.316A pdb=" N GLU x 367 " --> pdb=" O GLY x 363 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER x 381 " --> pdb=" O THR x 377 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET x 382 " --> pdb=" O ILE x 378 " (cutoff:3.500A) Processing helix chain 'x' and resid 383 through 389 Processing helix chain 'x' and resid 391 through 400 removed outlier: 3.678A pdb=" N LYS x 398 " --> pdb=" O LYS x 394 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN x 399 " --> pdb=" O VAL x 395 " (cutoff:3.500A) Proline residue: x 400 - end of helix Processing helix chain 'x' and resid 401 through 410 removed outlier: 3.637A pdb=" N GLY x 409 " --> pdb=" O ARG x 405 " (cutoff:3.500A) Processing helix chain 'x' and resid 413 through 437 removed outlier: 3.539A pdb=" N VAL x 417 " --> pdb=" O SER x 413 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN x 418 " --> pdb=" O THR x 414 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE x 437 " --> pdb=" O LYS x 433 " (cutoff:3.500A) Processing helix chain 'y' and resid 27 through 38 removed outlier: 4.005A pdb=" N ALA y 31 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU y 32 " --> pdb=" O PRO y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 94 removed outlier: 4.091A pdb=" N LYS y 81 " --> pdb=" O THR y 77 " (cutoff:3.500A) Processing helix chain 'y' and resid 95 through 101 removed outlier: 3.847A pdb=" N GLN y 100 " --> pdb=" O THR y 96 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN y 101 " --> pdb=" O GLU y 97 " (cutoff:3.500A) Processing helix chain 'y' and resid 102 through 110 removed outlier: 4.283A pdb=" N LEU y 106 " --> pdb=" O SER y 102 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR y 110 " --> pdb=" O LEU y 106 " (cutoff:3.500A) Processing helix chain 'y' and resid 113 through 129 Processing helix chain 'z' and resid 562 through 569 Proline residue: z 568 - end of helix Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.545A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.859A pdb=" N THR A 111 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.125A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.709A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 53 through 59 removed outlier: 6.760A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.683A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 286 through 290 removed outlier: 3.579A pdb=" N LYS B 286 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 76 through 80 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.059A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 6 through 10 removed outlier: 5.165A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 226 through 232 removed outlier: 3.904A pdb=" N THR C 228 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 60 through 66 Processing sheet with id= 15, first strand: chain 'E' and resid 143 through 149 removed outlier: 4.005A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 142 through 146 removed outlier: 5.445A pdb=" N PHE F 120 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 180 through 185 removed outlier: 3.913A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.837A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 20, first strand: chain 'H' and resid 102 through 106 removed outlier: 6.672A pdb=" N LEU H 111 " --> pdb=" O GLN H 106 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER H 110 " --> pdb=" O MET H 128 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.039A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.261A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR I 140 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 95 through 98 removed outlier: 3.628A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 189 through 192 removed outlier: 5.501A pdb=" N ARG I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 48 through 52 removed outlier: 3.677A pdb=" N VAL J 49 " --> pdb=" O HIS J 71 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N CYS J 25 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY J 127 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 10 through 16 removed outlier: 4.116A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS M 23 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU M 37 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY M 40 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG M 46 " --> pdb=" O GLY M 40 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 113 through 116 removed outlier: 6.855A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 29, first strand: chain 'P' and resid 14 through 20 removed outlier: 6.592A pdb=" N ILE P 149 " --> pdb=" O GLU P 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 57 through 60 removed outlier: 3.609A pdb=" N PHE P 60 " --> pdb=" O GLN P 80 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLN P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 32, first strand: chain 'P' and resid 124 through 130 removed outlier: 4.117A pdb=" N MET P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 34, first strand: chain 'S' and resid 27 through 33 removed outlier: 6.806A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 92 through 99 removed outlier: 4.055A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.596A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 39 through 42 removed outlier: 4.088A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 73 through 80 removed outlier: 3.897A pdb=" N LYS T 83 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 61 through 65 removed outlier: 4.171A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU U 112 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE U 115 " --> pdb=" O TRP U 99 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TRP U 99 " --> pdb=" O PHE U 115 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 24 through 27 removed outlier: 4.364A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 59 through 64 removed outlier: 4.277A pdb=" N ASP V 59 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP V 100 " --> pdb=" O ARG V 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG V 85 " --> pdb=" O ASP V 100 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 87 through 90 removed outlier: 4.473A pdb=" N VAL V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.559A pdb=" N GLU W 4 " --> pdb=" O LYS W 12 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS W 12 " --> pdb=" O GLU W 4 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS W 6 " --> pdb=" O GLY W 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 18 through 22 Processing sheet with id= 45, first strand: chain 'X' and resid 95 through 100 Processing sheet with id= 46, first strand: chain 'Y' and resid 53 through 56 removed outlier: 4.711A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Y' and resid 71 through 75 Processing sheet with id= 48, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.009A pdb=" N VAL Y 85 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Z' and resid 9 through 14 removed outlier: 4.817A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 51, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.627A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 20 through 27 removed outlier: 4.269A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR d 103 " --> pdb=" O LYS d 91 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 54, first strand: chain 'f' and resid 9 through 12 removed outlier: 6.657A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 6 through 12 removed outlier: 4.222A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 20 through 24 Processing sheet with id= 57, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.540A pdb=" N ARG k 3 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL k 32 " --> pdb=" O ILE k 47 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS k 67 " --> pdb=" O VAL k 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE k 25 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'm' and resid 100 through 104 removed outlier: 4.432A pdb=" N ALA m 101 " --> pdb=" O CYS m 96 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS m 93 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ASN m 120 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'o' and resid 7 through 10 removed outlier: 5.362A pdb=" N VAL o 67 " --> pdb=" O TYR o 26 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.260A pdb=" N LYS p 46 " --> pdb=" O GLY p 58 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 15 through 18 removed outlier: 3.699A pdb=" N GLN q 85 " --> pdb=" O ASN q 59 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN q 59 " --> pdb=" O GLN q 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'r' and resid 48 through 53 removed outlier: 4.786A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N SER r 76 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 27 through 32 Processing sheet with id= 64, first strand: chain 'v' and resid 97 through 105 removed outlier: 7.364A pdb=" N THR v 97 " --> pdb=" O PRO v 119 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN v 111 " --> pdb=" O VAL v 105 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG v 65 " --> pdb=" O SER v 112 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU v 118 " --> pdb=" O LEU v 69 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY v 71 " --> pdb=" O LEU v 118 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'w' and resid 26 through 32 Processing sheet with id= 66, first strand: chain 'x' and resid 158 through 161 removed outlier: 4.709A pdb=" N PHE x 106 " --> pdb=" O VAL x 189 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR x 191 " --> pdb=" O PHE x 106 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY x 108 " --> pdb=" O THR x 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN x 216 " --> pdb=" O VAL x 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'y' and resid 3 through 7 2502 hydrogen bonds defined for protein. 7417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3237 hydrogen bonds 5548 hydrogen bond angles 0 basepair planarities 1236 basepair parallelities 1953 stacking parallelities Total time for adding SS restraints: 314.49 Time building geometry restraints manager: 61.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19751 1.33 - 1.45: 63387 1.45 - 1.57: 67900 1.57 - 1.69: 8020 1.69 - 1.81: 463 Bond restraints: 159521 Sorted by residual: bond pdb=" N GLU x 226 " pdb=" CA GLU x 226 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.41e+01 bond pdb=" N3B GNP x 601 " pdb=" PG GNP x 601 " ideal model delta sigma weight residual 1.801 1.710 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" O5' GNP x 601 " pdb=" PA GNP x 601 " ideal model delta sigma weight residual 1.660 1.573 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" N ILE x 157 " pdb=" CA ILE x 157 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.70e-03 1.32e+04 1.89e+01 bond pdb=" N LYS x 286 " pdb=" CA LYS x 286 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.16e+01 ... (remaining 159516 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.72: 24994 106.72 - 113.60: 94015 113.60 - 120.47: 61565 120.47 - 127.35: 45767 127.35 - 134.22: 8443 Bond angle restraints: 234784 Sorted by residual: angle pdb=" N PRO y 245 " pdb=" CA PRO y 245 " pdb=" CB PRO y 245 " ideal model delta sigma weight residual 103.25 110.84 -7.59 1.05e+00 9.07e-01 5.23e+01 angle pdb=" CA PHE x 285 " pdb=" C PHE x 285 " pdb=" O PHE x 285 " ideal model delta sigma weight residual 120.51 113.11 7.40 1.43e+00 4.89e-01 2.68e+01 angle pdb=" C3' A 55061 " pdb=" O3' A 55061 " pdb=" P G 55062 " ideal model delta sigma weight residual 120.20 127.81 -7.61 1.50e+00 4.44e-01 2.58e+01 angle pdb=" CA ILE x 187 " pdb=" C ILE x 187 " pdb=" O ILE x 187 " ideal model delta sigma weight residual 122.63 118.39 4.24 8.70e-01 1.32e+00 2.37e+01 angle pdb=" N ASP x 5 " pdb=" CA ASP x 5 " pdb=" C ASP x 5 " ideal model delta sigma weight residual 113.12 107.37 5.75 1.25e+00 6.40e-01 2.11e+01 ... (remaining 234779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 84259 35.97 - 71.94: 2823 71.94 - 107.91: 303 107.91 - 143.87: 46 143.87 - 179.84: 99 Dihedral angle restraints: 87530 sinusoidal: 65253 harmonic: 22277 Sorted by residual: dihedral pdb=" CA GLY x 298 " pdb=" C GLY x 298 " pdb=" N ASP x 299 " pdb=" CA ASP x 299 " ideal model delta harmonic sigma weight residual 180.00 122.89 57.11 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" C4' U 55022 " pdb=" C3' U 55022 " pdb=" C2' U 55022 " pdb=" C1' U 55022 " ideal model delta sinusoidal sigma weight residual -35.00 33.61 -68.61 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C5' U 55022 " pdb=" C4' U 55022 " pdb=" C3' U 55022 " pdb=" O3' U 55022 " ideal model delta sinusoidal sigma weight residual 147.00 79.03 67.97 1 8.00e+00 1.56e-02 9.37e+01 ... (remaining 87527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 27862 0.075 - 0.150: 1227 0.150 - 0.225: 120 0.225 - 0.300: 6 0.300 - 0.375: 1 Chirality restraints: 29216 Sorted by residual: chirality pdb=" C3' U 55022 " pdb=" C4' U 55022 " pdb=" O3' U 55022 " pdb=" C2' U 55022 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE x 135 " pdb=" N ILE x 135 " pdb=" C ILE x 135 " pdb=" CB ILE x 135 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL x 240 " pdb=" CA VAL x 240 " pdb=" CG1 VAL x 240 " pdb=" CG2 VAL x 240 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 29213 not shown) Planarity restraints: 14749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER i 92 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C SER i 92 " 0.076 2.00e-02 2.50e+03 pdb=" O SER i 92 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL i 93 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER i 91 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C SER i 91 " 0.063 2.00e-02 2.50e+03 pdb=" O SER i 91 " -0.024 2.00e-02 2.50e+03 pdb=" N SER i 92 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR f 106 " -0.055 5.00e-02 4.00e+02 8.42e-02 1.14e+01 pdb=" N PRO f 107 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO f 107 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 107 " -0.045 5.00e-02 4.00e+02 ... (remaining 14746 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 5162 2.66 - 3.22: 127054 3.22 - 3.78: 285213 3.78 - 4.34: 374631 4.34 - 4.90: 527811 Nonbonded interactions: 1319871 Sorted by model distance: nonbonded pdb=" O6 G 52624 " pdb=" O2 U 52632 " model vdw 2.097 2.432 nonbonded pdb=" OG SER v 95 " pdb="MG MG v 300 " model vdw 2.106 2.170 nonbonded pdb=" O1B GNP x 601 " pdb="MG MG x 602 " model vdw 2.108 2.170 nonbonded pdb=" O2' U 55022 " pdb=" O5' C 55023 " model vdw 2.111 2.440 nonbonded pdb=" OP2 A 51326 " pdb=" O2' U 54445 " model vdw 2.116 2.440 ... (remaining 1319866 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 5 6.06 5 P 4021 5.49 5 Mg 2 5.21 5 S 290 5.16 5 C 77612 2.51 5 N 27743 2.21 5 O 38559 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=0.50 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: 4.260 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: 0.130 Extract box with map and model: 28.840 Check model and map are aligned: 1.600 Convert atoms to be neutral: 0.950 Process input model: 629.720 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 671.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.002 0.091 159521 Z= 0.151 Angle : 0.526 10.910 234784 Z= 0.304 Chirality : 0.032 0.375 29216 Planarity : 0.003 0.084 14749 Dihedral : 15.771 179.842 73154 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.96 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.10), residues: 7563 helix: 1.93 (0.10), residues: 2783 sheet: -0.16 (0.16), residues: 1049 loop : -0.98 (0.10), residues: 3731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2075 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1813 time to evaluate : 7.455 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 outliers start: 262 outliers final: 71 residues processed: 1977 average time/residue: 1.6252 time to fit residues: 5340.6851 Evaluate side-chains 1193 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1122 time to evaluate : 7.192 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 1.1988 time to fit residues: 164.7257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 966 optimal weight: 8.9990 chunk 867 optimal weight: 9.9990 chunk 481 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 585 optimal weight: 3.9990 chunk 463 optimal weight: 10.0000 chunk 897 optimal weight: 0.8980 chunk 347 optimal weight: 10.0000 chunk 545 optimal weight: 0.0980 chunk 667 optimal weight: 4.9990 chunk 1039 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 95 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 3 HIS B 184 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 376 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 215 ASN C 299 GLN D 9 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 241 GLN G 112 GLN G 149 ASN ** G 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 HIS H 39 ASN H 78 GLN J 65 ASN J 98 ASN J 104 ASN N 196 ASN O 42 ASN O 180 GLN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Q 125 GLN R 130 ASN S 66 GLN T 3 ASN T 66 ASN U 38 ASN W 30 GLN W 45 ASN X 105 ASN Y 86 GLN Z 78 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN e 102 ASN f 80 ASN h 30 GLN h 62 ASN j 76 HIS ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN r 21 ASN ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 100 ASN ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 19 ASN x 76 GLN x 338 ASN y 45 ASN y 87 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.131 159521 Z= 0.246 Angle : 0.599 15.642 234784 Z= 0.303 Chirality : 0.036 0.340 29216 Planarity : 0.005 0.131 14749 Dihedral : 16.118 179.740 56869 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 7563 helix: 1.80 (0.10), residues: 2789 sheet: -0.17 (0.16), residues: 1043 loop : -1.03 (0.10), residues: 3731 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1170 time to evaluate : 7.604 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: 209 outliers final: 120 residues processed: 1302 average time/residue: 1.3816 time to fit residues: 3103.2422 Evaluate side-chains 1157 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1037 time to evaluate : 7.537 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 0 residues processed: 120 average time/residue: 1.1680 time to fit residues: 272.6899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 577 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 865 optimal weight: 0.1980 chunk 708 optimal weight: 1.9990 chunk 286 optimal weight: 20.0000 chunk 1041 optimal weight: 5.9990 chunk 1125 optimal weight: 20.0000 chunk 927 optimal weight: 8.9990 chunk 1032 optimal weight: 10.0000 chunk 355 optimal weight: 20.0000 chunk 835 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 162 ASN B 209 GLN C 94 ASN D 63 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS E 207 HIS E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN J 104 ASN L 104 ASN N 37 HIS O 72 HIS ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN R 39 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN S 92 ASN T 69 GLN U 50 ASN X 73 HIS X 111 GLN Y 56 GLN Y 86 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN e 126 ASN h 30 GLN l 19 GLN l 33 ASN o 51 GLN r 21 ASN r 31 ASN ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 159521 Z= 0.242 Angle : 0.597 16.150 234784 Z= 0.303 Chirality : 0.036 0.353 29216 Planarity : 0.005 0.139 14749 Dihedral : 16.205 179.770 56869 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.62 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 7563 helix: 1.66 (0.10), residues: 2784 sheet: -0.15 (0.16), residues: 1035 loop : -1.09 (0.10), residues: 3744 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1092 time to evaluate : 7.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 187 outliers final: 97 residues processed: 1216 average time/residue: 1.4166 time to fit residues: 2970.7209 Evaluate side-chains 1109 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1012 time to evaluate : 7.424 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 1.1768 time to fit residues: 221.8806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1029 optimal weight: 10.0000 chunk 783 optimal weight: 0.9980 chunk 540 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 497 optimal weight: 6.9990 chunk 699 optimal weight: 0.8980 chunk 1045 optimal weight: 20.0000 chunk 1106 optimal weight: 20.0000 chunk 546 optimal weight: 0.0020 chunk 990 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 ASN E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN J 65 ASN J 104 ASN N 37 HIS ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN T 114 GLN X 73 HIS ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN h 30 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN p 56 HIS q 50 GLN ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.061 159521 Z= 0.139 Angle : 0.532 15.014 234784 Z= 0.272 Chirality : 0.033 0.250 29216 Planarity : 0.004 0.133 14749 Dihedral : 16.141 179.938 56869 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7563 helix: 1.88 (0.10), residues: 2787 sheet: -0.08 (0.16), residues: 1041 loop : -0.99 (0.10), residues: 3735 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1054 time to evaluate : 7.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 65 residues processed: 1153 average time/residue: 1.3840 time to fit residues: 2766.4272 Evaluate side-chains 1059 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 994 time to evaluate : 7.287 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 1.1025 time to fit residues: 145.6478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 921 optimal weight: 0.9990 chunk 628 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 824 optimal weight: 4.9990 chunk 456 optimal weight: 9.9990 chunk 944 optimal weight: 8.9990 chunk 765 optimal weight: 10.0000 chunk 1 optimal weight: 40.0000 chunk 565 optimal weight: 10.0000 chunk 993 optimal weight: 4.9990 chunk 279 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 21 ASN D 9 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 112 GLN J 65 ASN J 104 ASN L 115 GLN N 37 HIS ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN R 39 GLN S 37 HIS S 50 GLN T 98 HIS T 114 GLN U 50 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN g 28 ASN h 30 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN m 117 HIS ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 8 GLN ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 ASN y 45 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 159521 Z= 0.290 Angle : 0.640 14.519 234784 Z= 0.325 Chirality : 0.038 0.348 29216 Planarity : 0.006 0.131 14749 Dihedral : 16.301 179.916 56869 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.07 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7563 helix: 1.62 (0.10), residues: 2785 sheet: -0.14 (0.16), residues: 1043 loop : -1.09 (0.10), residues: 3735 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1040 time to evaluate : 7.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 95 residues processed: 1133 average time/residue: 1.4278 time to fit residues: 2812.7592 Evaluate side-chains 1105 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1010 time to evaluate : 7.583 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 1.1487 time to fit residues: 217.2407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 372 optimal weight: 9.9990 chunk 996 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 649 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 1107 optimal weight: 5.9990 chunk 919 optimal weight: 10.0000 chunk 512 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 366 optimal weight: 10.0000 chunk 581 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN D 9 ASN D 122 GLN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN J 65 ASN J 104 ASN M 33 GLN M 125 ASN N 37 HIS P 34 GLN Q 57 ASN Q 125 GLN S 108 GLN T 114 GLN U 44 GLN ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN a 93 ASN ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 HIS e 57 ASN g 28 ASN h 30 GLN h 98 HIS ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 44 ASN y 45 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.151 159521 Z= 0.484 Angle : 0.813 15.788 234784 Z= 0.409 Chirality : 0.047 0.371 29216 Planarity : 0.007 0.123 14749 Dihedral : 16.790 179.801 56869 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.69 % Favored : 93.21 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 7563 helix: 0.92 (0.10), residues: 2799 sheet: -0.47 (0.16), residues: 1033 loop : -1.43 (0.10), residues: 3731 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1029 time to evaluate : 7.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 95 residues processed: 1134 average time/residue: 1.4186 time to fit residues: 2792.4698 Evaluate side-chains 1074 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 979 time to evaluate : 7.700 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 1.1530 time to fit residues: 214.5552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1068 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 631 optimal weight: 4.9990 chunk 809 optimal weight: 7.9990 chunk 626 optimal weight: 9.9990 chunk 932 optimal weight: 0.8980 chunk 618 optimal weight: 5.9990 chunk 1103 optimal weight: 4.9990 chunk 690 optimal weight: 4.9990 chunk 672 optimal weight: 20.0000 chunk 509 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS D 9 ASN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN N 37 HIS Q 125 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN U 50 ASN X 94 ASN X 105 ASN X 111 GLN ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN g 28 ASN h 30 GLN l 33 ASN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 25 GLN p 56 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.287 159521 Z= 0.279 Angle : 0.660 23.001 234784 Z= 0.339 Chirality : 0.039 0.332 29216 Planarity : 0.005 0.136 14749 Dihedral : 16.598 179.922 56869 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.76 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.37 (0.10), residues: 7563 helix: 1.19 (0.10), residues: 2792 sheet: -0.37 (0.16), residues: 1022 loop : -1.35 (0.10), residues: 3749 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1018 time to evaluate : 7.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 45 residues processed: 1066 average time/residue: 1.4172 time to fit residues: 2629.8878 Evaluate side-chains 1026 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 981 time to evaluate : 7.680 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 1.1790 time to fit residues: 108.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 682 optimal weight: 0.9980 chunk 440 optimal weight: 1.9990 chunk 659 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 701 optimal weight: 1.9990 chunk 751 optimal weight: 2.9990 chunk 545 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 867 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 354 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN J 65 ASN J 104 ASN M 125 ASN N 37 HIS Q 125 GLN S 108 GLN X 105 ASN X 111 GLN ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN e 101 HIS e 102 ASN h 30 GLN j 13 ASN j 66 HIS ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 44 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.211 159521 Z= 0.189 Angle : 0.583 16.349 234784 Z= 0.300 Chirality : 0.035 0.292 29216 Planarity : 0.005 0.108 14749 Dihedral : 16.401 179.730 56869 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.23 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.09 (0.10), residues: 7563 helix: 1.48 (0.10), residues: 2790 sheet: -0.27 (0.16), residues: 1039 loop : -1.22 (0.10), residues: 3734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1021 time to evaluate : 7.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 26 residues processed: 1053 average time/residue: 1.5000 time to fit residues: 2756.3111 Evaluate side-chains 1002 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 976 time to evaluate : 7.615 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 1.1643 time to fit residues: 66.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1003 optimal weight: 7.9990 chunk 1057 optimal weight: 8.9990 chunk 964 optimal weight: 7.9990 chunk 1028 optimal weight: 0.7980 chunk 1056 optimal weight: 5.9990 chunk 618 optimal weight: 9.9990 chunk 448 optimal weight: 9.9990 chunk 807 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 929 optimal weight: 0.9980 chunk 972 optimal weight: 4.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 354 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN J 104 ASN M 125 ASN N 37 HIS Q 125 GLN U 38 ASN X 105 ASN X 111 GLN a 67 GLN ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN h 30 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 165 HIS ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.198 159521 Z= 0.262 Angle : 0.627 17.268 234784 Z= 0.321 Chirality : 0.038 0.308 29216 Planarity : 0.005 0.124 14749 Dihedral : 16.424 179.863 56869 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.82 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.14 (0.10), residues: 7563 helix: 1.44 (0.10), residues: 2783 sheet: -0.26 (0.16), residues: 1033 loop : -1.26 (0.10), residues: 3747 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 994 time to evaluate : 7.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 1019 average time/residue: 1.4250 time to fit residues: 2522.0442 Evaluate side-chains 999 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 967 time to evaluate : 7.665 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 1.2446 time to fit residues: 82.2758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1024 optimal weight: 5.9990 chunk 675 optimal weight: 3.9990 chunk 1087 optimal weight: 1.9990 chunk 663 optimal weight: 2.9990 chunk 515 optimal weight: 0.6980 chunk 755 optimal weight: 0.9990 chunk 1140 optimal weight: 0.0170 chunk 1049 optimal weight: 2.9990 chunk 908 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 701 optimal weight: 4.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN T 114 GLN U 50 ASN X 105 ASN X 111 GLN a 67 GLN d 100 ASN e 57 ASN h 30 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.476 159521 Z= 0.186 Angle : 0.564 23.567 234784 Z= 0.292 Chirality : 0.034 0.263 29216 Planarity : 0.005 0.222 14749 Dihedral : 16.299 179.977 56869 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7563 helix: 1.68 (0.10), residues: 2782 sheet: -0.13 (0.16), residues: 1037 loop : -1.14 (0.10), residues: 3744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1018 time to evaluate : 7.674 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 1031 average time/residue: 1.4068 time to fit residues: 2515.1855 Evaluate side-chains 986 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 978 time to evaluate : 7.332 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.1006 time to fit residues: 25.9546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 556 optimal weight: 7.9990 chunk 721 optimal weight: 8.9990 chunk 967 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 837 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 909 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 934 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS Q 125 GLN X 111 GLN e 57 ASN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 109 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124371 restraints weight = 253093.173| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.15 r_work: 0.3451 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work: 0.3415 rms_B_bonded: 1.59 restraints_weight: 0.1250 r_work: 0.3391 rms_B_bonded: 2.03 restraints_weight: 0.0625 r_work: 0.3361 rms_B_bonded: 2.65 restraints_weight: 0.0312 r_work: 0.3320 rms_B_bonded: 3.54 restraints_weight: 0.0156 r_work: 0.3262 rms_B_bonded: 4.88 restraints_weight: 0.0078 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.424 159521 Z= 0.406 Angle : 0.684 73.897 234784 Z= 0.338 Chirality : 0.040 0.366 29216 Planarity : 0.005 0.221 14749 Dihedral : 16.260 179.924 56869 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.10), residues: 7563 helix: 1.55 (0.10), residues: 2782 sheet: -0.11 (0.16), residues: 1035 loop : -1.17 (0.10), residues: 3746 =============================================================================== Job complete usr+sys time: 41192.36 seconds wall clock time: 710 minutes 11.67 seconds (42611.67 seconds total)