Starting phenix.real_space_refine on Sat Mar 16 14:54:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5h_4352/03_2024/6g5h_4352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5h_4352/03_2024/6g5h_4352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5h_4352/03_2024/6g5h_4352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5h_4352/03_2024/6g5h_4352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5h_4352/03_2024/6g5h_4352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5h_4352/03_2024/6g5h_4352.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1665 5.49 5 S 180 5.16 5 C 40379 2.51 5 N 13707 2.21 5 O 18408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74342 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 35552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1665, 35552 Classifications: {'RNA': 1665} Modifications used: {'rna2p_pur': 128, 'rna2p_pyr': 112, 'rna3p_pur': 756, 'rna3p_pyr': 669} Link IDs: {'rna2p': 240, 'rna3p': 1424} Chain breaks: 10 Chain: "A" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1006 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "e" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 442 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "h" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 231 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "R" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 585 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 56614 SG CYS a 26 86.305 164.638 105.227 1.00 53.46 S ATOM 56997 SG CYS a 74 87.081 163.493 108.446 1.00 48.19 S ATOM 57016 SG CYS a 77 88.859 166.659 106.458 1.00 50.67 S ATOM 58031 SG CYS d 21 151.874 158.241 71.999 1.00 65.88 S ATOM 58055 SG CYS d 24 149.128 156.050 71.131 1.00 64.20 S ATOM 58202 SG CYS d 42 149.484 155.998 74.730 1.00 66.02 S ATOM 71723 SG CYS f 126 174.148 149.869 30.795 1.00152.45 S ATOM 71841 SG CYS f 141 170.759 149.310 28.670 1.00159.45 S Time building chain proxies: 29.23, per 1000 atoms: 0.39 Number of scatterers: 74342 At special positions: 0 Unit cell: (207.044, 249.32, 208.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 180 16.00 P 1665 15.00 O 18408 8.00 N 13707 7.00 C 40379 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: 28.63 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9006 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 66 sheets defined 27.9% alpha, 8.3% beta 515 base pairs and 888 stacking pairs defined. Time for finding SS restraints: 23.01 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.946A pdb=" N LEU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.876A pdb=" N TRP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.883A pdb=" N ALA A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.882A pdb=" N VAL A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 89' Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.927A pdb=" N ALA A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 removed outlier: 4.275A pdb=" N GLY A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.761A pdb=" N GLY B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.934A pdb=" N CYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.767A pdb=" N ILE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 172 " --> pdb=" O MET B 168 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 176' Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.880A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.879A pdb=" N ASP B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.022A pdb=" N GLU B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 231' Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.882A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 85 removed outlier: 4.157A pdb=" N TYR C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 4.164A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.764A pdb=" N ALA C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 159 " --> pdb=" O ILE C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 209 through 218 removed outlier: 3.804A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.871A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.009A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.935A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.717A pdb=" N LYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.516A pdb=" N TRP E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.904A pdb=" N ARG E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.949A pdb=" N LYS E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS E 63 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.778A pdb=" N LYS E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 247 through 259 removed outlier: 3.900A pdb=" N ARG E 252 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA E 258 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 47 removed outlier: 3.927A pdb=" N LYS G 46 " --> pdb=" O GLU G 43 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY G 47 " --> pdb=" O GLU G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 43 through 47' Processing helix chain 'G' and resid 140 through 145 removed outlier: 3.919A pdb=" N LEU G 144 " --> pdb=" O ARG G 140 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 140 through 145' Processing helix chain 'G' and resid 152 through 157 removed outlier: 4.255A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 230 removed outlier: 3.837A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS G 221 " --> pdb=" O MET G 217 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 removed outlier: 4.049A pdb=" N GLY H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU H 27 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU H 28 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU H 29 " --> pdb=" O GLN H 25 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 43 removed outlier: 3.563A pdb=" N LEU H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU H 43 " --> pdb=" O GLN H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 36 through 43' Processing helix chain 'H' and resid 70 through 75 removed outlier: 3.792A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 70 through 75' Processing helix chain 'H' and resid 75 through 86 removed outlier: 3.900A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 75 through 86' Processing helix chain 'H' and resid 121 through 127 removed outlier: 3.883A pdb=" N HIS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 170 removed outlier: 3.701A pdb=" N VAL H 170 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 removed outlier: 3.836A pdb=" N GLY H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU H 180 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 106 through 111 removed outlier: 3.953A pdb=" N GLN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 removed outlier: 3.895A pdb=" N SER I 115 " --> pdb=" O GLN I 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 116' Processing helix chain 'I' and resid 131 through 138 removed outlier: 3.993A pdb=" N GLU I 135 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU I 137 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.999A pdb=" N LYS I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR I 149 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS I 153 " --> pdb=" O TYR I 149 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.976A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE I 166 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 removed outlier: 3.934A pdb=" N GLU I 196 " --> pdb=" O GLY I 192 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR I 198 " --> pdb=" O GLU I 194 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU I 199 " --> pdb=" O LEU I 195 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS I 201 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE I 202 " --> pdb=" O TYR I 198 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS I 203 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 29 removed outlier: 3.897A pdb=" N ASP J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 removed outlier: 3.904A pdb=" N GLY J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU J 34 " --> pdb=" O LYS J 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 29 through 34' Processing helix chain 'J' and resid 67 through 75 removed outlier: 3.962A pdb=" N PHE J 72 " --> pdb=" O PRO J 68 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY J 74 " --> pdb=" O ARG J 70 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.855A pdb=" N LEU J 81 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.562A pdb=" N ILE J 97 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.725A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.785A pdb=" N VAL J 114 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS J 116 " --> pdb=" O THR J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 132 removed outlier: 3.823A pdb=" N LEU J 129 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.614A pdb=" N GLN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 181 removed outlier: 3.927A pdb=" N ASN J 177 " --> pdb=" O VAL J 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA J 178 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'N' and resid 29 through 41 removed outlier: 3.965A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE N 37 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU N 40 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 44 No H-bonds generated for 'chain 'N' and resid 42 through 44' Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.888A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU N 54 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP N 56 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER N 57 " --> pdb=" O ILE N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.834A pdb=" N THR N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 79 removed outlier: 3.818A pdb=" N LEU N 75 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER N 77 " --> pdb=" O ARG N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 90 removed outlier: 3.891A pdb=" N HIS N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 103 removed outlier: 3.736A pdb=" N VAL N 98 " --> pdb=" O LYS N 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG N 99 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS N 100 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS N 101 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 94 through 103' Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'N' and resid 125 through 130 removed outlier: 3.775A pdb=" N TYR N 129 " --> pdb=" O LEU N 125 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 125 through 130' Processing helix chain 'N' and resid 143 through 147 removed outlier: 3.616A pdb=" N ALA N 146 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER N 147 " --> pdb=" O SER N 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 143 through 147' Processing helix chain 'O' and resid 81 through 86 removed outlier: 3.832A pdb=" N CYS O 85 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 81 through 86' Processing helix chain 'O' and resid 111 through 121 removed outlier: 3.807A pdb=" N ALA O 115 " --> pdb=" O GLY O 111 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA O 118 " --> pdb=" O SER O 114 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA O 120 " --> pdb=" O LEU O 116 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG O 121 " --> pdb=" O ARG O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 111 through 121' Processing helix chain 'V' and resid 56 through 61 Processing helix chain 'V' and resid 66 through 75 removed outlier: 3.833A pdb=" N LEU V 70 " --> pdb=" O ASP V 66 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG V 71 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA V 73 " --> pdb=" O ILE V 69 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS V 74 " --> pdb=" O LEU V 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 66 through 75' Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.855A pdb=" N ALA W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 21 removed outlier: 3.896A pdb=" N LYS W 19 " --> pdb=" O ASN W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 44 removed outlier: 3.872A pdb=" N MET W 41 " --> pdb=" O PHE W 37 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET W 42 " --> pdb=" O LEU W 38 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS W 43 " --> pdb=" O THR W 39 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 37 through 44' Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.597A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 31 removed outlier: 3.982A pdb=" N ALA X 30 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS X 31 " --> pdb=" O TYR X 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 26 through 31' Processing helix chain 'X' and resid 33 through 38 removed outlier: 3.962A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 49 removed outlier: 3.911A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU Y 44 " --> pdb=" O ILE Y 40 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 removed outlier: 3.912A pdb=" N LYS Y 83 " --> pdb=" O LEU Y 79 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS Y 84 " --> pdb=" O ASP Y 80 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN Y 85 " --> pdb=" O TYR Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 114 removed outlier: 3.930A pdb=" N GLU Y 109 " --> pdb=" O LYS Y 105 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS Y 111 " --> pdb=" O ARG Y 107 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN Y 112 " --> pdb=" O LYS Y 108 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET Y 114 " --> pdb=" O ARG Y 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 105 through 114' Processing helix chain 'a' and resid 50 through 57 removed outlier: 3.851A pdb=" N SER a 54 " --> pdb=" O VAL a 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA a 56 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 80 removed outlier: 3.905A pdb=" N ILE a 79 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 75 through 80' Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.548A pdb=" N GLY d 35 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 46 removed outlier: 3.539A pdb=" N GLN d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR d 46 " --> pdb=" O CYS d 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 41 through 46' Processing helix chain 'd' and resid 46 through 51 Processing helix chain 'e' and resid 33 through 43 removed outlier: 3.866A pdb=" N GLN e 37 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN e 39 " --> pdb=" O ARG e 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 21 removed outlier: 3.898A pdb=" N ARG h 18 " --> pdb=" O LYS h 14 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS h 19 " --> pdb=" O ARG h 15 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET h 20 " --> pdb=" O LYS h 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 removed outlier: 3.926A pdb=" N PHE D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.991A pdb=" N ASN D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU D 28 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.886A pdb=" N LEU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.844A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 3.844A pdb=" N LYS D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.908A pdb=" N CYS D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU D 123 " --> pdb=" O CYS D 119 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 removed outlier: 3.800A pdb=" N ASN D 165 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.837A pdb=" N LEU F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN F 74 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 105 removed outlier: 3.848A pdb=" N VAL F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS F 95 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA F 96 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 removed outlier: 3.828A pdb=" N ASN F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.839A pdb=" N VAL F 147 " --> pdb=" O PRO F 143 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN F 149 " --> pdb=" O ARG F 145 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS F 155 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG F 159 " --> pdb=" O CYS F 155 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 183 removed outlier: 3.887A pdb=" N ALA F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F 176 " --> pdb=" O CYS F 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA F 180 " --> pdb=" O GLU F 176 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 3.901A pdb=" N LYS F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 removed outlier: 3.939A pdb=" N LEU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER F 202 " --> pdb=" O ARG F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 192 through 202' Processing helix chain 'K' and resid 4 through 12 removed outlier: 3.885A pdb=" N ILE K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 19 removed outlier: 3.900A pdb=" N PHE K 16 " --> pdb=" O TYR K 12 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.551A pdb=" N VAL K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS K 47 " --> pdb=" O LEU K 43 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA K 48 " --> pdb=" O HIS K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 83 removed outlier: 4.115A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU K 79 " --> pdb=" O GLY K 75 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG K 80 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP K 81 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 26 removed outlier: 4.140A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 17 through 26' Processing helix chain 'M' and resid 35 through 41 removed outlier: 3.942A pdb=" N ALA M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 72 removed outlier: 3.887A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS M 69 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA M 70 " --> pdb=" O GLU M 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 removed outlier: 3.977A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 83 through 88' Processing helix chain 'M' and resid 119 through 130 removed outlier: 4.005A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU M 126 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS M 130 " --> pdb=" O GLU M 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 119 through 130' Processing helix chain 'P' and resid 22 through 28 removed outlier: 3.996A pdb=" N LEU P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 35 removed outlier: 3.604A pdb=" N LEU P 33 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 35' Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.958A pdb=" N ARG P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN P 46 " --> pdb=" O ARG P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 64 removed outlier: 3.858A pdb=" N ARG P 59 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU P 60 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS P 64 " --> pdb=" O LEU P 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 55 through 64' Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.576A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.559A pdb=" N MET P 111 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 112' Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.614A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 52 removed outlier: 3.761A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.926A pdb=" N LEU Q 57 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 removed outlier: 3.845A pdb=" N ALA Q 64 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 82 removed outlier: 3.825A pdb=" N TYR Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 99 removed outlier: 3.863A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS Q 90 " --> pdb=" O GLN Q 86 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA Q 91 " --> pdb=" O SER Q 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU Q 92 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA Q 94 " --> pdb=" O LYS Q 90 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 removed outlier: 3.857A pdb=" N LYS Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS Q 109 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU Q 112 " --> pdb=" O ILE Q 108 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE Q 113 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.520A pdb=" N LEU Q 119 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 29 through 34 removed outlier: 3.911A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 34' Processing helix chain 'R' and resid 34 through 38 removed outlier: 3.847A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 34 through 38' Processing helix chain 'R' and resid 43 through 51 removed outlier: 3.923A pdb=" N LYS R 49 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA R 51 " --> pdb=" O ARG R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.858A pdb=" N THR R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG R 60 " --> pdb=" O HIS R 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 60' Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 76 through 81 removed outlier: 4.016A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 76 through 81' Processing helix chain 'R' and resid 102 through 108 removed outlier: 3.943A pdb=" N LEU R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU R 108 " --> pdb=" O GLU R 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 102 through 108' Processing helix chain 'S' and resid 25 through 31 removed outlier: 3.997A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.874A pdb=" N HIS S 42 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL S 44 " --> pdb=" O TYR S 40 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG S 46 " --> pdb=" O HIS S 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 71 removed outlier: 3.987A pdb=" N GLU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG S 66 " --> pdb=" O ASP S 62 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL S 67 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE S 68 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE S 70 " --> pdb=" O ARG S 66 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET S 71 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.971A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 112 removed outlier: 3.944A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS S 106 " --> pdb=" O GLY S 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU S 107 " --> pdb=" O LEU S 103 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG S 108 " --> pdb=" O ASP S 104 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU S 109 " --> pdb=" O ASN S 105 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP S 110 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU S 111 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU S 112 " --> pdb=" O ARG S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 128 removed outlier: 3.918A pdb=" N HIS S 125 " --> pdb=" O ARG S 121 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE S 126 " --> pdb=" O GLY S 122 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP S 127 " --> pdb=" O LEU S 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.653A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 17 removed outlier: 3.954A pdb=" N VAL T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 24 removed outlier: 3.654A pdb=" N LYS T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 19 through 24' Processing helix chain 'T' and resid 59 through 64 removed outlier: 3.819A pdb=" N HIS T 63 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 59 through 64' Processing helix chain 'T' and resid 72 through 76 Processing helix chain 'T' and resid 100 through 106 removed outlier: 3.897A pdb=" N LEU T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN T 105 " --> pdb=" O ARG T 101 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 100 through 106' Processing helix chain 'T' and resid 107 through 111 Processing helix chain 'T' and resid 126 through 144 removed outlier: 3.944A pdb=" N ASP T 130 " --> pdb=" O GLN T 126 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU T 131 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP T 132 " --> pdb=" O GLN T 128 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG T 133 " --> pdb=" O ARG T 129 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA T 135 " --> pdb=" O LEU T 131 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY T 136 " --> pdb=" O ASP T 132 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL T 138 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA T 139 " --> pdb=" O ALA T 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA T 140 " --> pdb=" O GLY T 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA T 141 " --> pdb=" O GLN T 137 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN T 142 " --> pdb=" O VAL T 138 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS T 143 " --> pdb=" O ALA T 139 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS T 144 " --> pdb=" O ALA T 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 126 through 144' Processing helix chain 'U' and resid 28 through 46 Processing helix chain 'U' and resid 94 through 104 removed outlier: 3.975A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE U 101 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR U 102 " --> pdb=" O VAL U 98 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 94 through 104' Processing helix chain 'Z' and resid 51 through 59 removed outlier: 3.996A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU Z 58 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS Z 59 " --> pdb=" O TYR Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 65 Processing helix chain 'Z' and resid 69 through 77 removed outlier: 3.981A pdb=" N SER Z 74 " --> pdb=" O PRO Z 70 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU Z 75 " --> pdb=" O ALA Z 71 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG Z 76 " --> pdb=" O VAL Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 89 removed outlier: 4.031A pdb=" N ALA Z 86 " --> pdb=" O SER Z 82 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU Z 88 " --> pdb=" O ALA Z 84 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 82 through 89' Processing helix chain 'Z' and resid 89 through 95 removed outlier: 3.668A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 removed outlier: 4.001A pdb=" N TYR f 105 " --> pdb=" O ALA f 101 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR f 106 " --> pdb=" O VAL f 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 101 through 106' Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.847A pdb=" N TYR A 39 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.685A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER A 75 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 7.300A pdb=" N VAL B 33 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LYS B 46 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR B 31 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU B 48 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP B 29 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.902A pdb=" N LYS B 83 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 104 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 85 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 102 " --> pdb=" O LYS B 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 123 removed outlier: 3.850A pdb=" N ILE B 121 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 141 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 123 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS B 139 " --> pdb=" O ALA B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.852A pdb=" N ALA C 126 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS C 142 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.879A pdb=" N VAL C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 163 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 205 Processing sheet with id=AA9, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.257A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 42 through 43 removed outlier: 3.613A pdb=" N LEU E 42 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.909A pdb=" N GLY E 132 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 162 through 163 removed outlier: 3.705A pdb=" N LYS E 168 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 180 through 182 removed outlier: 3.746A pdb=" N CYS E 181 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY E 193 " --> pdb=" O CYS E 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 210 through 211 removed outlier: 3.852A pdb=" N VAL E 210 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE E 218 " --> pdb=" O VAL E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 56 through 57 removed outlier: 6.767A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 72 through 73 removed outlier: 3.910A pdb=" N VAL G 73 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL G 97 " --> pdb=" O VAL G 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 49 through 52 removed outlier: 3.922A pdb=" N LYS H 49 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE H 61 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 51 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA H 59 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 155 through 158 removed outlier: 7.133A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.829A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.809A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.884A pdb=" N ARG I 74 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE I 65 " --> pdb=" O ARG I 74 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR I 76 " --> pdb=" O GLY I 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY I 63 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AC5, first strand: chain 'L' and resid 76 through 77 Processing sheet with id=AC6, first strand: chain 'L' and resid 85 through 86 removed outlier: 3.860A pdb=" N ILE L 86 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL L 111 " --> pdb=" O ILE L 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 91 through 93 removed outlier: 3.939A pdb=" N TYR L 92 " --> pdb=" O ARG L 105 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG L 105 " --> pdb=" O TYR L 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 128 through 130 Processing sheet with id=AC9, first strand: chain 'O' and resid 28 through 31 removed outlier: 5.981A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 42 through 45 removed outlier: 4.275A pdb=" N CYS O 54 " --> pdb=" O VAL O 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 36 through 39 removed outlier: 3.915A pdb=" N VAL V 36 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS V 51 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 24 through 25 removed outlier: 3.892A pdb=" N VAL W 25 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL W 63 " --> pdb=" O VAL W 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'W' and resid 80 through 81 Processing sheet with id=AD5, first strand: chain 'W' and resid 104 through 105 removed outlier: 3.856A pdb=" N LEU W 104 " --> pdb=" O MET W 111 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET W 111 " --> pdb=" O LEU W 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'X' and resid 47 through 50 removed outlier: 3.851A pdb=" N ALA X 47 " --> pdb=" O VAL X 102 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL X 102 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY X 49 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL X 100 " --> pdb=" O GLY X 49 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE X 81 " --> pdb=" O VAL X 72 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL X 72 " --> pdb=" O ILE X 81 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA X 83 " --> pdb=" O VAL X 70 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL X 70 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG X 67 " --> pdb=" O VAL X 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL X 57 " --> pdb=" O ARG X 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 124 through 125 Processing sheet with id=AD8, first strand: chain 'Y' and resid 7 through 9 removed outlier: 3.886A pdb=" N ARG Y 8 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP Y 26 " --> pdb=" O ARG Y 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.834A pdb=" N ILE a 21 " --> pdb=" O VAL a 30 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL a 30 " --> pdb=" O ILE a 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'a' and resid 36 through 43 removed outlier: 3.877A pdb=" N ILE a 36 " --> pdb=" O TYR a 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR a 73 " --> pdb=" O ILE a 36 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS a 38 " --> pdb=" O LEU a 71 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU a 71 " --> pdb=" O LYS a 38 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL a 40 " --> pdb=" O VAL a 69 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL a 69 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG a 42 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU a 67 " --> pdb=" O ARG a 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AE3, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE4, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.917A pdb=" N GLU D 38 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 49 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG D 40 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 47 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.882A pdb=" N CYS D 134 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP D 154 " --> pdb=" O CYS D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.611A pdb=" N LYS D 185 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 139 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY D 183 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 182 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL D 175 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 184 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.673A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AE9, first strand: chain 'F' and resid 123 through 124 removed outlier: 3.922A pdb=" N ASP F 124 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL F 139 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'M' and resid 76 through 79 removed outlier: 3.724A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU M 52 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL M 79 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL M 111 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL M 51 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL M 109 " --> pdb=" O VAL M 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AF3, first strand: chain 'Q' and resid 26 through 27 removed outlier: 3.972A pdb=" N LYS Q 26 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP Q 67 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'Q' and resid 33 through 34 Processing sheet with id=AF5, first strand: chain 'R' and resid 96 through 98 removed outlier: 3.982A pdb=" N GLN R 118 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 98 " --> pdb=" O GLN R 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'S' and resid 12 through 14 removed outlier: 3.916A pdb=" N LEU S 13 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE S 20 " --> pdb=" O LEU S 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'T' and resid 81 through 83 removed outlier: 3.950A pdb=" N GLY T 81 " --> pdb=" O SER T 93 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER T 93 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN T 83 " --> pdb=" O HIS T 91 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS T 91 " --> pdb=" O GLN T 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'T' and resid 113 through 115 removed outlier: 3.933A pdb=" N GLU T 114 " --> pdb=" O LYS T 122 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS T 122 " --> pdb=" O GLU T 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'U' and resid 54 through 55 removed outlier: 3.899A pdb=" N PHE U 80 " --> pdb=" O ILE U 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE U 63 " --> pdb=" O PHE U 80 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE U 84 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS U 59 " --> pdb=" O ILE U 84 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 54 through 55 removed outlier: 3.511A pdb=" N HIS U 85 " --> pdb=" O SER U 26 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER U 26 " --> pdb=" O HIS U 85 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG U 87 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU U 24 " --> pdb=" O ARG U 87 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE U 89 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE U 22 " --> pdb=" O ILE U 89 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG U 21 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR U 115 " --> pdb=" O ARG U 21 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR U 23 " --> pdb=" O GLU U 113 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU U 113 " --> pdb=" O THR U 23 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR U 25 " --> pdb=" O GLU U 111 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU U 111 " --> pdb=" O THR U 25 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.369A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER Z 101 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE Z 108 " --> pdb=" O SER Z 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'c' and resid 10 through 11 removed outlier: 3.967A pdb=" N LYS c 10 " --> pdb=" O LEU c 58 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU c 58 " --> pdb=" O LYS c 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'c' and resid 17 through 19 removed outlier: 6.625A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL c 30 " --> pdb=" O ARG c 44 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG c 44 " --> pdb=" O VAL c 30 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 139 through 140 Processing sheet with id=AG6, first strand: chain 'g' and resid 4 through 11 removed outlier: 6.369A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA g 300 " --> pdb=" O ARG g 308 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 32 through 33 removed outlier: 3.881A pdb=" N SER g 33 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE g 41 " --> pdb=" O SER g 33 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 70 through 71 Processing sheet with id=AG9, first strand: chain 'g' and resid 112 through 113 removed outlier: 3.882A pdb=" N ALA g 112 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL g 121 " --> pdb=" O ALA g 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'g' and resid 153 through 157 removed outlier: 4.451A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE g 164 " --> pdb=" O SER g 157 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE g 165 " --> pdb=" O TRP g 177 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP g 177 " --> pdb=" O ILE g 165 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER g 167 " --> pdb=" O LYS g 175 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS g 175 " --> pdb=" O SER g 167 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 199 through 200 removed outlier: 3.970A pdb=" N CYS g 207 " --> pdb=" O TRP g 219 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP g 219 " --> pdb=" O CYS g 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS g 225 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 247 through 249 removed outlier: 3.964A pdb=" N LEU g 248 " --> pdb=" O TRP g 259 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP g 259 " --> pdb=" O LEU g 248 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1283 hydrogen bonds 2054 hydrogen bond angles 0 basepair planarities 515 basepair parallelities 888 stacking parallelities Total time for adding SS restraints: 48.11 Time building geometry restraints manager: 31.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8966 1.31 - 1.44: 30569 1.44 - 1.57: 36078 1.57 - 1.70: 3314 1.70 - 1.82: 273 Bond restraints: 79200 Sorted by residual: bond pdb=" C SER E 237 " pdb=" N LEU E 238 " ideal model delta sigma weight residual 1.335 1.214 0.121 1.43e-02 4.89e+03 7.14e+01 bond pdb=" C VAL T 87 " pdb=" N MET T 88 " ideal model delta sigma weight residual 1.331 1.226 0.105 1.48e-02 4.57e+03 5.01e+01 bond pdb=" C VAL D 172 " pdb=" O VAL D 172 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.04e-02 9.25e+03 2.23e+01 bond pdb=" C1' G 2 432 " pdb=" N9 G 2 432 " ideal model delta sigma weight residual 1.475 1.409 0.066 1.50e-02 4.44e+03 1.94e+01 bond pdb=" C1' U 2 658 " pdb=" N1 U 2 658 " ideal model delta sigma weight residual 1.470 1.408 0.062 1.50e-02 4.44e+03 1.71e+01 ... (remaining 79195 not shown) Histogram of bond angle deviations from ideal: 93.10 - 101.99: 1802 101.99 - 110.88: 38824 110.88 - 119.77: 40522 119.77 - 128.66: 31635 128.66 - 137.56: 2085 Bond angle restraints: 114868 Sorted by residual: angle pdb=" O2' C 2 37 " pdb=" C2' C 2 37 " pdb=" C1' C 2 37 " ideal model delta sigma weight residual 108.40 93.10 15.30 1.50e+00 4.44e-01 1.04e+02 angle pdb=" N VAL d 23 " pdb=" CA VAL d 23 " pdb=" C VAL d 23 " ideal model delta sigma weight residual 110.72 120.87 -10.15 1.01e+00 9.80e-01 1.01e+02 angle pdb=" N LYS H 85 " pdb=" CA LYS H 85 " pdb=" C LYS H 85 " ideal model delta sigma weight residual 111.28 121.46 -10.18 1.09e+00 8.42e-01 8.71e+01 angle pdb=" C4' C 2 37 " pdb=" C3' C 2 37 " pdb=" O3' C 2 37 " ideal model delta sigma weight residual 113.00 126.41 -13.41 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N GLY B 64 " pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 112.73 123.00 -10.27 1.20e+00 6.94e-01 7.33e+01 ... (remaining 114863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 45679 35.64 - 71.29: 4154 71.29 - 106.93: 527 106.93 - 142.58: 22 142.58 - 178.22: 46 Dihedral angle restraints: 50428 sinusoidal: 36465 harmonic: 13963 Sorted by residual: dihedral pdb=" CA ASN F 165 " pdb=" C ASN F 165 " pdb=" N ILE F 166 " pdb=" CA ILE F 166 " ideal model delta harmonic sigma weight residual 180.00 -125.06 -54.94 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA ILE Q 42 " pdb=" C ILE Q 42 " pdb=" N GLU Q 43 " pdb=" CA GLU Q 43 " ideal model delta harmonic sigma weight residual -180.00 -126.35 -53.65 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ALA F 40 " pdb=" C ALA F 40 " pdb=" N VAL F 41 " pdb=" CA VAL F 41 " ideal model delta harmonic sigma weight residual -180.00 -128.78 -51.22 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 50425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 13257 0.120 - 0.241: 845 0.241 - 0.361: 64 0.361 - 0.482: 17 0.482 - 0.602: 2 Chirality restraints: 14185 Sorted by residual: chirality pdb=" C1' A 2 25 " pdb=" O4' A 2 25 " pdb=" C2' A 2 25 " pdb=" N9 A 2 25 " both_signs ideal model delta sigma weight residual False 2.46 1.86 0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CA ASN C 134 " pdb=" N ASN C 134 " pdb=" C ASN C 134 " pdb=" CB ASN C 134 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA LYS H 85 " pdb=" N LYS H 85 " pdb=" C LYS H 85 " pdb=" CB LYS H 85 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 14182 not shown) Planarity restraints: 8389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 38 " -0.076 2.00e-02 2.50e+03 3.67e-02 3.71e+01 pdb=" N9 A 2 38 " 0.072 2.00e-02 2.50e+03 pdb=" C8 A 2 38 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A 2 38 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A 2 38 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A 2 38 " -0.043 2.00e-02 2.50e+03 pdb=" N6 A 2 38 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A 2 38 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A 2 38 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 38 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 38 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 25 " 0.078 2.00e-02 2.50e+03 3.14e-02 2.71e+01 pdb=" N9 A 2 25 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A 2 25 " -0.030 2.00e-02 2.50e+03 pdb=" N7 A 2 25 " -0.007 2.00e-02 2.50e+03 pdb=" C5 A 2 25 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A 2 25 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A 2 25 " 0.031 2.00e-02 2.50e+03 pdb=" N1 A 2 25 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A 2 25 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A 2 25 " -0.022 2.00e-02 2.50e+03 pdb=" C4 A 2 25 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 61 " 0.045 2.00e-02 2.50e+03 3.11e-02 2.66e+01 pdb=" N9 A 2 61 " -0.081 2.00e-02 2.50e+03 pdb=" C8 A 2 61 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A 2 61 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A 2 61 " 0.042 2.00e-02 2.50e+03 pdb=" C6 A 2 61 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 2 61 " -0.001 2.00e-02 2.50e+03 pdb=" N1 A 2 61 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A 2 61 " -0.012 2.00e-02 2.50e+03 pdb=" N3 A 2 61 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 61 " 0.009 2.00e-02 2.50e+03 ... (remaining 8386 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 3 2.19 - 2.87: 25367 2.87 - 3.54: 103200 3.54 - 4.22: 209844 4.22 - 4.90: 300987 Nonbonded interactions: 639401 Sorted by model distance: nonbonded pdb=" NZ LYS B 63 " pdb=" O GLU B 89 " model vdw 1.511 2.520 nonbonded pdb=" NE1 TRP d 8 " pdb=" CB HIS K 28 " model vdw 2.047 3.520 nonbonded pdb=" O LYS B 63 " pdb=" CG2 THR B 88 " model vdw 2.163 3.460 nonbonded pdb=" O2' C 21415 " pdb=" OD2 ASP T 132 " model vdw 2.197 2.440 nonbonded pdb=" OP1 U 2 688 " pdb=" OG1 THR H 121 " model vdw 2.215 2.440 ... (remaining 639396 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 12.810 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 196.630 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.011 0.125 79200 Z= 0.668 Angle : 1.335 15.303 114868 Z= 0.717 Chirality : 0.066 0.602 14185 Planarity : 0.008 0.093 8389 Dihedral : 22.390 178.224 41422 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.62 % Favored : 91.21 % Rotamer: Outliers : 1.22 % Allowed : 3.89 % Favored : 94.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.10), residues: 4790 helix: -4.33 (0.11), residues: 877 sheet: -3.59 (0.17), residues: 618 loop : -2.18 (0.09), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP K 64 HIS 0.021 0.004 HIS F 51 PHE 0.052 0.005 PHE I 65 TYR 0.044 0.005 TYR g 302 ARG 0.024 0.002 ARG X 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1542 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6600 (tp-100) REVERT: A 156 TYR cc_start: 0.8162 (m-80) cc_final: 0.7534 (m-80) REVERT: B 59 SER cc_start: 0.8021 (p) cc_final: 0.7704 (t) REVERT: B 192 SER cc_start: 0.8618 (t) cc_final: 0.8301 (p) REVERT: B 229 MET cc_start: 0.6468 (mmp) cc_final: 0.5722 (tpp) REVERT: C 276 THR cc_start: 0.6899 (m) cc_final: 0.6488 (m) REVERT: E 105 THR cc_start: 0.7834 (m) cc_final: 0.7540 (m) REVERT: E 149 TYR cc_start: 0.8667 (m-10) cc_final: 0.8357 (m-10) REVERT: E 194 VAL cc_start: 0.9493 (t) cc_final: 0.9253 (m) REVERT: E 225 ILE cc_start: 0.8660 (tt) cc_final: 0.8335 (tt) REVERT: G 59 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7444 (mp10) REVERT: G 121 ILE cc_start: 0.8279 (mt) cc_final: 0.8050 (tp) REVERT: G 211 LYS cc_start: 0.7670 (tttt) cc_final: 0.7029 (mtpt) REVERT: G 217 MET cc_start: 0.6469 (mmp) cc_final: 0.6013 (ptt) REVERT: H 63 PHE cc_start: 0.6486 (m-80) cc_final: 0.6050 (m-10) REVERT: H 106 ARG cc_start: 0.5489 (mtt-85) cc_final: 0.4995 (ttm170) REVERT: H 138 GLU cc_start: 0.4750 (mt-10) cc_final: 0.3247 (pm20) REVERT: I 146 GLN cc_start: 0.6338 (pt0) cc_final: 0.6137 (pt0) REVERT: I 147 LYS cc_start: 0.7022 (tmtp) cc_final: 0.6767 (mmtt) REVERT: I 154 LYS cc_start: 0.7155 (mttt) cc_final: 0.6553 (mtpt) REVERT: I 189 VAL cc_start: 0.7612 (t) cc_final: 0.7350 (p) REVERT: I 206 LYS cc_start: 0.7427 (mtmm) cc_final: 0.7166 (mmmt) REVERT: J 13 TYR cc_start: 0.8957 (p90) cc_final: 0.8736 (p90) REVERT: J 14 VAL cc_start: 0.9260 (t) cc_final: 0.9059 (p) REVERT: J 143 ASN cc_start: 0.7894 (t0) cc_final: 0.7650 (t0) REVERT: N 25 TRP cc_start: 0.8375 (p90) cc_final: 0.8038 (p90) REVERT: O 62 VAL cc_start: 0.8878 (t) cc_final: 0.8541 (m) REVERT: O 119 LEU cc_start: 0.8025 (pp) cc_final: 0.7408 (mt) REVERT: O 124 MET cc_start: 0.8548 (mmm) cc_final: 0.7891 (mmm) REVERT: V 20 SER cc_start: 0.8313 (p) cc_final: 0.8103 (t) REVERT: V 61 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7953 (mtt90) REVERT: W 54 ASP cc_start: 0.7959 (t0) cc_final: 0.7759 (t0) REVERT: W 76 SER cc_start: 0.9163 (t) cc_final: 0.8881 (t) REVERT: X 50 ILE cc_start: 0.8567 (mt) cc_final: 0.8357 (tp) REVERT: Y 107 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (ptt90) REVERT: a 8 ASN cc_start: 0.7949 (m-40) cc_final: 0.7712 (m-40) REVERT: a 10 ARG cc_start: 0.8683 (ttm170) cc_final: 0.8428 (ttm-80) REVERT: e 24 LYS cc_start: 0.6663 (ptpt) cc_final: 0.6446 (tptt) REVERT: h 4 LYS cc_start: 0.7273 (ttmt) cc_final: 0.7019 (ttpp) REVERT: D 57 ASN cc_start: 0.6392 (m-40) cc_final: 0.5465 (m-40) REVERT: F 45 TYR cc_start: 0.8427 (m-80) cc_final: 0.8101 (m-80) REVERT: F 95 HIS cc_start: 0.6476 (m-70) cc_final: 0.5924 (m-70) REVERT: F 139 VAL cc_start: 0.7167 (m) cc_final: 0.6802 (m) REVERT: F 142 SER cc_start: 0.7014 (m) cc_final: 0.6696 (m) REVERT: F 188 TYR cc_start: 0.6948 (t80) cc_final: 0.6606 (t80) REVERT: K 64 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.5815 (m-10) REVERT: K 89 ILE cc_start: 0.6169 (mm) cc_final: 0.5890 (mt) REVERT: M 93 LYS cc_start: 0.6200 (mttt) cc_final: 0.5828 (mtmm) REVERT: P 52 LYS cc_start: 0.8384 (mttt) cc_final: 0.8102 (tptp) REVERT: P 60 LEU cc_start: 0.8451 (mt) cc_final: 0.7871 (pp) REVERT: P 85 ILE cc_start: 0.8369 (mt) cc_final: 0.7519 (mt) REVERT: P 88 GLU cc_start: 0.7691 (mp0) cc_final: 0.7310 (pt0) REVERT: P 103 ASN cc_start: 0.5601 (m110) cc_final: 0.5137 (t0) REVERT: P 130 ARG cc_start: 0.6949 (ptt180) cc_final: 0.6748 (mmp80) REVERT: Q 81 ILE cc_start: 0.8349 (mt) cc_final: 0.7880 (mt) REVERT: S 28 PHE cc_start: 0.6958 (m-80) cc_final: 0.6638 (m-80) REVERT: S 34 LYS cc_start: 0.7834 (mttt) cc_final: 0.7109 (mttt) REVERT: S 49 ASP cc_start: 0.8006 (t0) cc_final: 0.7740 (m-30) REVERT: S 54 LYS cc_start: 0.7159 (mttt) cc_final: 0.6569 (mmtt) REVERT: T 83 GLN cc_start: 0.7537 (tp40) cc_final: 0.7218 (tp40) REVERT: T 112 MET cc_start: 0.8007 (mtp) cc_final: 0.7713 (mtp) REVERT: U 38 ASP cc_start: 0.7312 (t0) cc_final: 0.6996 (t0) REVERT: U 93 SER cc_start: 0.6079 (p) cc_final: 0.5663 (t) REVERT: U 99 LYS cc_start: 0.8383 (tttt) cc_final: 0.7984 (mptt) REVERT: c 16 LYS cc_start: 0.7720 (mtpt) cc_final: 0.7375 (mmtt) REVERT: c 38 THR cc_start: 0.6867 (m) cc_final: 0.6144 (p) REVERT: f 83 LYS cc_start: 0.4569 (tptt) cc_final: 0.3873 (pttm) REVERT: f 132 MET cc_start: 0.4406 (mtp) cc_final: 0.3714 (mtm) REVERT: g 18 VAL cc_start: 0.7887 (t) cc_final: 0.7589 (t) outliers start: 51 outliers final: 19 residues processed: 1573 average time/residue: 0.8523 time to fit residues: 2162.3532 Evaluate side-chains 973 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 952 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain U residue 27 ARG Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 34 LYS Chi-restraints excluded: chain U residue 36 CYS Chi-restraints excluded: chain c residue 34 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 539 optimal weight: 0.8980 chunk 484 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 chunk 258 optimal weight: 9.9990 chunk 500 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 580 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 92 GLN B 177 GLN E 8 HIS E 17 HIS E 50 ASN E 98 ASN E 179 ASN E 201 HIS G 70 HIS G 227 GLN H 73 GLN I 7 ASN I 87 ASN I 116 HIS I 165 GLN I 181 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 HIS ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 65 ASN L 100 ASN N 58 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 GLN V 21 ASN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN W 82 GLN W 92 ASN W 98 GLN X 46 HIS a 72 HIS d 3 HIS e 15 GLN e 58 ASN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN F 179 ASN K 77 GLN M 19 GLN Q 77 HIS R 31 ASN R 116 ASN S 10 GLN S 19 ASN S 85 ASN S 125 HIS U 47 ASN U 85 HIS Z 103 HIS ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN f 139 HIS g 4 GLN g 62 HIS g 64 HIS g 181 ASN ** g 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 79200 Z= 0.184 Angle : 0.702 9.853 114868 Z= 0.361 Chirality : 0.041 0.360 14185 Planarity : 0.005 0.063 8389 Dihedral : 24.502 179.972 31423 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 3.63 % Allowed : 13.90 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.10), residues: 4790 helix: -4.06 (0.10), residues: 987 sheet: -3.31 (0.17), residues: 664 loop : -1.71 (0.10), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 112 HIS 0.009 0.001 HIS C 272 PHE 0.031 0.002 PHE B 81 TYR 0.021 0.002 TYR g 302 ARG 0.008 0.001 ARG U 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1133 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6709 (tp-100) REVERT: A 156 TYR cc_start: 0.7955 (m-80) cc_final: 0.7488 (m-80) REVERT: A 181 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 59 SER cc_start: 0.8229 (p) cc_final: 0.7874 (m) REVERT: B 88 THR cc_start: 0.8220 (t) cc_final: 0.6533 (t) REVERT: B 229 MET cc_start: 0.6286 (mmp) cc_final: 0.5896 (tpp) REVERT: C 90 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6210 (mt-10) REVERT: C 93 ILE cc_start: 0.8882 (mt) cc_final: 0.8611 (mt) REVERT: E 194 VAL cc_start: 0.9431 (t) cc_final: 0.9063 (m) REVERT: G 59 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7420 (mp10) REVERT: G 217 MET cc_start: 0.6567 (mmp) cc_final: 0.6069 (ptt) REVERT: G 227 GLN cc_start: 0.5449 (mt0) cc_final: 0.4953 (tp40) REVERT: H 138 GLU cc_start: 0.4456 (mt-10) cc_final: 0.2986 (pm20) REVERT: I 150 ASP cc_start: 0.7474 (t0) cc_final: 0.7230 (p0) REVERT: I 154 LYS cc_start: 0.7184 (mttt) cc_final: 0.6692 (mtpt) REVERT: I 189 VAL cc_start: 0.7679 (t) cc_final: 0.7410 (p) REVERT: J 13 TYR cc_start: 0.8829 (p90) cc_final: 0.8447 (p90) REVERT: J 35 TYR cc_start: 0.8037 (m-10) cc_final: 0.7783 (m-80) REVERT: N 25 TRP cc_start: 0.8296 (p90) cc_final: 0.7825 (p90) REVERT: N 138 ASN cc_start: 0.8433 (p0) cc_final: 0.8228 (p0) REVERT: O 62 VAL cc_start: 0.8888 (t) cc_final: 0.8463 (m) REVERT: O 119 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7795 (mt) REVERT: O 124 MET cc_start: 0.8401 (mmm) cc_final: 0.7922 (mmm) REVERT: W 13 SER cc_start: 0.8612 (m) cc_final: 0.8398 (p) REVERT: Y 44 LEU cc_start: 0.8739 (tp) cc_final: 0.8244 (tp) REVERT: d 3 HIS cc_start: 0.4662 (p90) cc_final: 0.4429 (p90) REVERT: e 24 LYS cc_start: 0.6605 (ptpt) cc_final: 0.6349 (tptt) REVERT: h 4 LYS cc_start: 0.7519 (ttmt) cc_final: 0.6868 (tttm) REVERT: D 11 PHE cc_start: 0.7635 (m-80) cc_final: 0.7420 (m-10) REVERT: D 59 LEU cc_start: 0.7926 (mt) cc_final: 0.7634 (tp) REVERT: D 101 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7639 (tp40) REVERT: D 162 ASP cc_start: 0.7773 (t0) cc_final: 0.7525 (t0) REVERT: F 34 SER cc_start: 0.7363 (p) cc_final: 0.7100 (t) REVERT: F 76 MET cc_start: 0.7174 (mmm) cc_final: 0.6959 (tpp) REVERT: K 15 LEU cc_start: 0.7420 (tp) cc_final: 0.7188 (tp) REVERT: K 46 MET cc_start: 0.8118 (tpp) cc_final: 0.7870 (mmt) REVERT: K 89 ILE cc_start: 0.5930 (mm) cc_final: 0.5689 (mt) REVERT: M 60 MET cc_start: 0.7363 (tpp) cc_final: 0.7148 (tpp) REVERT: M 93 LYS cc_start: 0.6116 (mttt) cc_final: 0.5758 (mtmt) REVERT: P 85 ILE cc_start: 0.8312 (mt) cc_final: 0.8011 (mt) REVERT: P 88 GLU cc_start: 0.7814 (mp0) cc_final: 0.7369 (pt0) REVERT: P 127 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7168 (mmtm) REVERT: Q 84 ILE cc_start: 0.8248 (pt) cc_final: 0.7754 (mt) REVERT: R 104 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7458 (tm-30) REVERT: S 34 LYS cc_start: 0.7680 (mttt) cc_final: 0.7139 (mttt) REVERT: S 54 LYS cc_start: 0.6990 (mttt) cc_final: 0.6499 (mmtt) REVERT: S 106 LYS cc_start: 0.7308 (mttt) cc_final: 0.6677 (mtpt) REVERT: T 39 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5473 (mp) REVERT: T 49 ASP cc_start: 0.4659 (t70) cc_final: 0.4221 (t70) REVERT: U 48 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5871 (mp) REVERT: U 72 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6753 (tm-30) REVERT: U 99 LYS cc_start: 0.8213 (tttt) cc_final: 0.7953 (mptt) REVERT: Z 54 THR cc_start: 0.5568 (OUTLIER) cc_final: 0.5138 (m) REVERT: Z 66 LYS cc_start: 0.5333 (mmtt) cc_final: 0.5115 (tttt) REVERT: Z 103 HIS cc_start: 0.6712 (t-90) cc_final: 0.6472 (t70) REVERT: Z 104 ARG cc_start: 0.7387 (mtm180) cc_final: 0.7097 (mtm180) REVERT: c 16 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7475 (mmtt) REVERT: f 83 LYS cc_start: 0.4456 (tptt) cc_final: 0.3836 (pttm) REVERT: g 18 VAL cc_start: 0.7781 (t) cc_final: 0.7476 (t) REVERT: g 90 TRP cc_start: 0.6859 (m100) cc_final: 0.6546 (m100) REVERT: g 128 THR cc_start: 0.6387 (m) cc_final: 0.5417 (m) outliers start: 152 outliers final: 83 residues processed: 1223 average time/residue: 0.7353 time to fit residues: 1495.0012 Evaluate side-chains 1011 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 924 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 MET Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 222 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 322 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 482 optimal weight: 9.9990 chunk 395 optimal weight: 0.0010 chunk 160 optimal weight: 20.0000 chunk 581 optimal weight: 0.2980 chunk 627 optimal weight: 20.0000 chunk 517 optimal weight: 0.0770 chunk 576 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 466 optimal weight: 0.0870 overall best weight: 0.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 GLN B 186 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN G 65 GLN H 168 HIS I 7 ASN I 116 HIS I 146 GLN I 181 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 GLN d 5 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN F 65 GLN F 83 ASN F 95 HIS K 39 ASN S 85 ASN U 81 GLN Z 64 ASN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 GLN g 64 HIS ** g 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 79200 Z= 0.148 Angle : 0.622 12.450 114868 Z= 0.318 Chirality : 0.038 0.318 14185 Planarity : 0.004 0.066 8389 Dihedral : 24.221 179.390 31391 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 3.27 % Allowed : 16.46 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.11), residues: 4790 helix: -3.68 (0.11), residues: 1023 sheet: -2.81 (0.17), residues: 707 loop : -1.39 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 52 HIS 0.012 0.001 HIS K 28 PHE 0.023 0.002 PHE P 119 TYR 0.020 0.001 TYR g 302 ARG 0.009 0.000 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1044 time to evaluate : 4.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8153 (mm) REVERT: A 84 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6830 (tp-100) REVERT: A 156 TYR cc_start: 0.7855 (m-80) cc_final: 0.7572 (m-80) REVERT: A 174 MET cc_start: 0.7746 (mmm) cc_final: 0.7485 (mmt) REVERT: B 59 SER cc_start: 0.8156 (p) cc_final: 0.7902 (m) REVERT: C 93 ILE cc_start: 0.8742 (mt) cc_final: 0.8478 (mt) REVERT: E 97 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6101 (mm-30) REVERT: G 45 TRP cc_start: 0.7654 (m-90) cc_final: 0.7325 (m100) REVERT: G 59 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7400 (mp10) REVERT: G 217 MET cc_start: 0.6757 (mmp) cc_final: 0.6268 (ptt) REVERT: G 227 GLN cc_start: 0.5437 (mt0) cc_final: 0.4859 (tp40) REVERT: H 138 GLU cc_start: 0.4021 (mt-10) cc_final: 0.2723 (pm20) REVERT: I 189 VAL cc_start: 0.7634 (t) cc_final: 0.7347 (p) REVERT: J 35 TYR cc_start: 0.7933 (m-80) cc_final: 0.7671 (m-80) REVERT: N 20 ARG cc_start: 0.7452 (mtt90) cc_final: 0.6695 (mtm-85) REVERT: O 119 LEU cc_start: 0.8088 (pp) cc_final: 0.7869 (mt) REVERT: O 124 MET cc_start: 0.8365 (mmm) cc_final: 0.7876 (mmm) REVERT: W 46 TYR cc_start: 0.8605 (m-80) cc_final: 0.8389 (m-80) REVERT: X 64 SER cc_start: 0.8333 (m) cc_final: 0.8017 (t) REVERT: d 3 HIS cc_start: 0.4625 (p90) cc_final: 0.4416 (p90) REVERT: e 24 LYS cc_start: 0.6597 (ptpt) cc_final: 0.6262 (tptt) REVERT: h 4 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7189 (tttp) REVERT: D 10 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7378 (tmmt) REVERT: D 11 PHE cc_start: 0.7596 (m-80) cc_final: 0.7392 (m-80) REVERT: D 113 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7517 (tp) REVERT: F 70 GLU cc_start: 0.6662 (tt0) cc_final: 0.6280 (tt0) REVERT: K 24 LYS cc_start: 0.8188 (tptt) cc_final: 0.7657 (tptt) REVERT: M 83 LYS cc_start: 0.6365 (tptt) cc_final: 0.6142 (tppt) REVERT: Q 87 SER cc_start: 0.6299 (p) cc_final: 0.5911 (t) REVERT: S 34 LYS cc_start: 0.7769 (mttt) cc_final: 0.7241 (mttt) REVERT: S 54 LYS cc_start: 0.7043 (mttt) cc_final: 0.6708 (mmtt) REVERT: S 68 ILE cc_start: 0.6559 (pt) cc_final: 0.5987 (tp) REVERT: S 106 LYS cc_start: 0.7239 (mttt) cc_final: 0.6766 (mmtp) REVERT: S 117 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5666 (mm) REVERT: T 39 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5718 (mp) REVERT: T 56 ARG cc_start: 0.7234 (ttt-90) cc_final: 0.6668 (ttt180) REVERT: T 112 MET cc_start: 0.7686 (mtp) cc_final: 0.7475 (mtp) REVERT: U 48 LEU cc_start: 0.6180 (tp) cc_final: 0.5888 (mp) REVERT: U 72 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6774 (tm-30) REVERT: U 99 LYS cc_start: 0.8176 (tttt) cc_final: 0.7877 (mmtt) REVERT: Z 104 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6879 (mtm-85) REVERT: c 16 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7526 (mmtt) REVERT: c 46 VAL cc_start: 0.7784 (p) cc_final: 0.7536 (t) REVERT: f 83 LYS cc_start: 0.4625 (tptt) cc_final: 0.4121 (pttm) REVERT: g 18 VAL cc_start: 0.7603 (t) cc_final: 0.7236 (t) REVERT: g 90 TRP cc_start: 0.6928 (m100) cc_final: 0.4859 (m100) REVERT: g 289 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7005 (tp) outliers start: 137 outliers final: 79 residues processed: 1124 average time/residue: 0.7498 time to fit residues: 1401.8098 Evaluate side-chains 995 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 911 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 MET Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 164 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 574 optimal weight: 6.9990 chunk 437 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 chunk 583 optimal weight: 10.0000 chunk 617 optimal weight: 6.9990 chunk 304 optimal weight: 0.7980 chunk 552 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS E 179 ASN E 209 HIS G 70 HIS H 91 HIS H 162 GLN I 7 ASN I 165 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 ASN L 39 ASN N 62 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 GLN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 HIS ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN F 203 ASN M 19 GLN Q 97 GLN R 93 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 GLN ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 GLN U 81 GLN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 ASN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 79200 Z= 0.319 Angle : 0.718 13.652 114868 Z= 0.364 Chirality : 0.042 0.399 14185 Planarity : 0.005 0.054 8389 Dihedral : 24.182 179.482 31386 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 5.09 % Allowed : 17.22 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.11), residues: 4790 helix: -3.38 (0.11), residues: 1153 sheet: -2.66 (0.16), residues: 809 loop : -1.28 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 235 HIS 0.012 0.001 HIS X 31 PHE 0.022 0.002 PHE E 175 TYR 0.019 0.002 TYR Q 95 ARG 0.009 0.001 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 964 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (mm) REVERT: A 84 GLN cc_start: 0.7629 (mm-40) cc_final: 0.6990 (tp-100) REVERT: A 156 TYR cc_start: 0.8284 (m-80) cc_final: 0.7972 (m-80) REVERT: A 174 MET cc_start: 0.7842 (mmm) cc_final: 0.7517 (mmt) REVERT: B 59 SER cc_start: 0.8245 (p) cc_final: 0.8010 (m) REVERT: G 59 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7583 (mp10) REVERT: G 217 MET cc_start: 0.7278 (mmp) cc_final: 0.6652 (ptt) REVERT: H 58 LYS cc_start: 0.5446 (mttt) cc_final: 0.5108 (mtpt) REVERT: H 106 ARG cc_start: 0.5916 (mtt-85) cc_final: 0.5370 (ttm110) REVERT: I 27 TYR cc_start: 0.8860 (p90) cc_final: 0.8582 (p90) REVERT: I 64 ASN cc_start: 0.7395 (p0) cc_final: 0.6819 (p0) REVERT: I 73 THR cc_start: 0.7882 (m) cc_final: 0.7526 (p) REVERT: I 154 LYS cc_start: 0.7264 (mttt) cc_final: 0.6806 (tttt) REVERT: I 189 VAL cc_start: 0.8221 (t) cc_final: 0.7857 (p) REVERT: N 36 GLN cc_start: 0.8540 (tp40) cc_final: 0.8330 (tp40) REVERT: O 116 LEU cc_start: 0.9109 (tt) cc_final: 0.8787 (tt) REVERT: O 119 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8235 (mt) REVERT: O 124 MET cc_start: 0.8480 (mmm) cc_final: 0.7945 (mmm) REVERT: V 49 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7965 (mm-40) REVERT: W 92 ASN cc_start: 0.8574 (m-40) cc_final: 0.8340 (m-40) REVERT: Y 86 GLU cc_start: 0.8336 (tp30) cc_final: 0.8079 (mm-30) REVERT: Y 107 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8228 (ptt90) REVERT: a 42 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6615 (ptt90) REVERT: h 4 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7784 (ttpp) REVERT: D 73 VAL cc_start: 0.7383 (m) cc_final: 0.6820 (m) REVERT: D 169 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7041 (p0) REVERT: F 70 GLU cc_start: 0.6790 (tt0) cc_final: 0.6329 (tt0) REVERT: F 142 SER cc_start: 0.7892 (m) cc_final: 0.7485 (m) REVERT: F 192 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7855 (mmmm) REVERT: K 24 LYS cc_start: 0.8030 (tptt) cc_final: 0.7536 (tppt) REVERT: K 53 LYS cc_start: 0.8359 (ptmm) cc_final: 0.7923 (pttm) REVERT: Q 92 LEU cc_start: 0.8732 (mp) cc_final: 0.8299 (tt) REVERT: S 34 LYS cc_start: 0.7560 (mttt) cc_final: 0.7002 (mttt) REVERT: S 54 LYS cc_start: 0.7165 (mttt) cc_final: 0.6843 (mmtt) REVERT: S 106 LYS cc_start: 0.7426 (mttt) cc_final: 0.6876 (mmtt) REVERT: T 12 GLN cc_start: 0.6845 (tt0) cc_final: 0.6635 (tt0) REVERT: T 13 GLU cc_start: 0.7547 (tt0) cc_final: 0.7322 (tt0) REVERT: T 39 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5797 (mp) REVERT: T 49 ASP cc_start: 0.5043 (OUTLIER) cc_final: 0.4713 (t70) REVERT: U 48 LEU cc_start: 0.6230 (tp) cc_final: 0.5879 (mp) REVERT: U 72 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6650 (tm-30) REVERT: U 99 LYS cc_start: 0.8252 (tttt) cc_final: 0.7977 (mptt) REVERT: Z 103 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.5648 (t-90) REVERT: Z 104 ARG cc_start: 0.7275 (mtm180) cc_final: 0.6864 (mtm-85) REVERT: c 16 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7535 (mmtt) REVERT: f 83 LYS cc_start: 0.4791 (tptt) cc_final: 0.4219 (pttm) REVERT: f 119 ARG cc_start: 0.4008 (mmp-170) cc_final: 0.3238 (mtm-85) REVERT: g 18 VAL cc_start: 0.7784 (t) cc_final: 0.7415 (t) REVERT: g 90 TRP cc_start: 0.7030 (m100) cc_final: 0.4942 (m100) outliers start: 213 outliers final: 147 residues processed: 1081 average time/residue: 0.7449 time to fit residues: 1344.3063 Evaluate side-chains 1053 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 898 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 34 ILE Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 15 GLN Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 70 CYS Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain g residue 303 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 514 optimal weight: 9.9990 chunk 350 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 459 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 527 optimal weight: 5.9990 chunk 426 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 554 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 overall best weight: 6.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 91 HIS I 7 ASN I 84 ASN I 165 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 GLN d 45 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN F 29 GLN P 54 HIS ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 222 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 79200 Z= 0.382 Angle : 0.767 12.779 114868 Z= 0.389 Chirality : 0.044 0.446 14185 Planarity : 0.006 0.061 8389 Dihedral : 24.266 178.524 31386 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 5.78 % Allowed : 18.39 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.11), residues: 4790 helix: -3.05 (0.12), residues: 1211 sheet: -2.34 (0.17), residues: 810 loop : -1.32 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP E 235 HIS 0.013 0.002 HIS X 31 PHE 0.025 0.002 PHE E 175 TYR 0.034 0.002 TYR K 68 ARG 0.010 0.001 ARG S 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 921 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7109 (tp-100) REVERT: A 156 TYR cc_start: 0.8494 (m-80) cc_final: 0.8153 (m-80) REVERT: A 174 MET cc_start: 0.7807 (mmm) cc_final: 0.7568 (mmt) REVERT: B 169 MET cc_start: 0.7322 (mpp) cc_final: 0.6578 (mpp) REVERT: B 217 MET cc_start: 0.8281 (tmm) cc_final: 0.7406 (tmm) REVERT: E 255 ARG cc_start: 0.7476 (ptp-170) cc_final: 0.7272 (ptp90) REVERT: G 59 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7550 (mp10) REVERT: G 217 MET cc_start: 0.7240 (mmp) cc_final: 0.6593 (ptt) REVERT: H 106 ARG cc_start: 0.5776 (mtt-85) cc_final: 0.5314 (ttm110) REVERT: I 73 THR cc_start: 0.8078 (m) cc_final: 0.7810 (p) REVERT: I 150 ASP cc_start: 0.7503 (t0) cc_final: 0.6952 (m-30) REVERT: I 154 LYS cc_start: 0.7278 (mttt) cc_final: 0.6763 (tttt) REVERT: N 25 TRP cc_start: 0.8605 (p90) cc_final: 0.8132 (p90) REVERT: N 36 GLN cc_start: 0.8714 (tp40) cc_final: 0.8476 (tp40) REVERT: O 67 ASP cc_start: 0.8386 (p0) cc_final: 0.8145 (p0) REVERT: O 70 SER cc_start: 0.8727 (m) cc_final: 0.8522 (t) REVERT: O 116 LEU cc_start: 0.9201 (tt) cc_final: 0.8879 (tt) REVERT: O 119 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8500 (mt) REVERT: O 124 MET cc_start: 0.8555 (mmm) cc_final: 0.7995 (mmp) REVERT: V 21 ASN cc_start: 0.8871 (t0) cc_final: 0.8601 (t0) REVERT: V 49 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8111 (mm-40) REVERT: Y 22 GLN cc_start: 0.8306 (tt0) cc_final: 0.8082 (tt0) REVERT: Y 83 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: Y 98 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: a 42 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6775 (ptt90) REVERT: b 72 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5759 (ptt180) REVERT: h 14 LYS cc_start: 0.8249 (tttt) cc_final: 0.8043 (ttmm) REVERT: D 73 VAL cc_start: 0.7504 (m) cc_final: 0.7114 (m) REVERT: D 162 ASP cc_start: 0.7818 (t0) cc_final: 0.7606 (t0) REVERT: D 169 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7428 (p0) REVERT: F 70 GLU cc_start: 0.6608 (tt0) cc_final: 0.6112 (tt0) REVERT: F 192 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7792 (mmmm) REVERT: K 9 ILE cc_start: 0.8259 (mt) cc_final: 0.8048 (mp) REVERT: K 24 LYS cc_start: 0.8175 (tptt) cc_final: 0.7880 (tppt) REVERT: K 53 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7973 (pttm) REVERT: P 58 LYS cc_start: 0.7626 (mtpt) cc_final: 0.7379 (pptt) REVERT: Q 92 LEU cc_start: 0.8764 (mp) cc_final: 0.8340 (tt) REVERT: R 96 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5846 (tp) REVERT: S 34 LYS cc_start: 0.7565 (mttt) cc_final: 0.6974 (mttt) REVERT: S 106 LYS cc_start: 0.7567 (mttt) cc_final: 0.7079 (mmtt) REVERT: T 13 GLU cc_start: 0.7577 (tt0) cc_final: 0.7329 (tt0) REVERT: T 39 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5816 (mp) REVERT: T 49 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4777 (t70) REVERT: U 48 LEU cc_start: 0.6289 (tp) cc_final: 0.6029 (mp) REVERT: U 99 LYS cc_start: 0.8295 (tttt) cc_final: 0.7966 (mptt) REVERT: Z 103 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5217 (t-170) REVERT: Z 104 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6934 (mtm-85) REVERT: c 16 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7497 (mmtt) REVERT: g 18 VAL cc_start: 0.7953 (t) cc_final: 0.7648 (t) REVERT: g 90 TRP cc_start: 0.7134 (m100) cc_final: 0.5043 (m100) REVERT: g 139 LYS cc_start: 0.7662 (mttt) cc_final: 0.7175 (tptp) outliers start: 242 outliers final: 178 residues processed: 1064 average time/residue: 0.7334 time to fit residues: 1308.8058 Evaluate side-chains 1042 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 854 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 188 TYR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 34 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 83 LYS Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 51 GLN Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 15 GLN Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 127 TRP Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 221 LEU Chi-restraints excluded: chain g residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 207 optimal weight: 7.9990 chunk 556 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 362 optimal weight: 0.0370 chunk 152 optimal weight: 20.0000 chunk 618 optimal weight: 7.9990 chunk 513 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 208 HIS ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN I 7 ASN I 165 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN J 134 HIS J 177 ASN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 GLN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 GLN b 51 GLN ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 79200 Z= 0.204 Angle : 0.645 14.400 114868 Z= 0.328 Chirality : 0.039 0.370 14185 Planarity : 0.004 0.052 8389 Dihedral : 24.175 178.990 31386 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.72 % Favored : 94.24 % Rotamer: Outliers : 4.52 % Allowed : 20.40 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.11), residues: 4790 helix: -2.65 (0.12), residues: 1220 sheet: -2.17 (0.17), residues: 826 loop : -1.15 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 235 HIS 0.008 0.001 HIS K 28 PHE 0.023 0.002 PHE J 159 TYR 0.037 0.001 TYR K 68 ARG 0.007 0.000 ARG J 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 912 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.7788 (mm-40) cc_final: 0.6991 (tp-100) REVERT: A 130 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7517 (p0) REVERT: A 156 TYR cc_start: 0.8393 (m-80) cc_final: 0.8073 (m-80) REVERT: B 169 MET cc_start: 0.7285 (mpp) cc_final: 0.6431 (mpp) REVERT: B 217 MET cc_start: 0.8219 (tmm) cc_final: 0.7287 (tmm) REVERT: C 102 LEU cc_start: 0.8959 (tp) cc_final: 0.8725 (tt) REVERT: E 16 LYS cc_start: 0.8373 (tptp) cc_final: 0.8124 (ttmt) REVERT: E 235 TRP cc_start: 0.8028 (m-10) cc_final: 0.7439 (m-10) REVERT: G 59 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7537 (mp10) REVERT: G 217 MET cc_start: 0.7037 (mmp) cc_final: 0.6541 (ptp) REVERT: H 106 ARG cc_start: 0.5898 (mtt-85) cc_final: 0.5507 (ttm110) REVERT: H 188 GLU cc_start: 0.6326 (mt-10) cc_final: 0.6041 (mt-10) REVERT: I 27 TYR cc_start: 0.8813 (p90) cc_final: 0.8561 (p90) REVERT: I 73 THR cc_start: 0.8196 (m) cc_final: 0.7854 (p) REVERT: I 154 LYS cc_start: 0.7257 (mttt) cc_final: 0.6744 (tttt) REVERT: L 99 TYR cc_start: 0.9226 (m-10) cc_final: 0.9009 (m-80) REVERT: N 25 TRP cc_start: 0.8506 (p90) cc_final: 0.8205 (p90) REVERT: N 36 GLN cc_start: 0.8638 (tp40) cc_final: 0.8310 (tp40) REVERT: O 66 ARG cc_start: 0.7888 (ptp90) cc_final: 0.7626 (ptp-110) REVERT: O 67 ASP cc_start: 0.8371 (p0) cc_final: 0.8143 (p0) REVERT: O 116 LEU cc_start: 0.9146 (tt) cc_final: 0.8824 (tt) REVERT: O 124 MET cc_start: 0.8626 (mmm) cc_final: 0.7740 (mmm) REVERT: V 21 ASN cc_start: 0.8726 (t0) cc_final: 0.8444 (t0) REVERT: V 61 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7751 (mtp180) REVERT: X 64 SER cc_start: 0.8534 (m) cc_final: 0.8308 (t) REVERT: Y 106 GLN cc_start: 0.8116 (tp40) cc_final: 0.7899 (tm-30) REVERT: a 42 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6509 (ptt90) REVERT: h 14 LYS cc_start: 0.8051 (tttt) cc_final: 0.7794 (tttm) REVERT: D 73 VAL cc_start: 0.7446 (m) cc_final: 0.7170 (m) REVERT: D 87 TYR cc_start: 0.6707 (m-80) cc_final: 0.6369 (m-80) REVERT: D 162 ASP cc_start: 0.7836 (t70) cc_final: 0.7583 (t0) REVERT: D 169 ASP cc_start: 0.7730 (m-30) cc_final: 0.7472 (p0) REVERT: F 78 MET cc_start: 0.6934 (mtp) cc_final: 0.6649 (mmp) REVERT: F 192 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7741 (mmmm) REVERT: K 24 LYS cc_start: 0.8182 (tptt) cc_final: 0.7885 (tptt) REVERT: K 53 LYS cc_start: 0.8174 (ptmm) cc_final: 0.7952 (pttm) REVERT: P 58 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7391 (pptt) REVERT: P 101 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6182 (p) REVERT: Q 92 LEU cc_start: 0.8761 (mp) cc_final: 0.8230 (tt) REVERT: R 96 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5739 (tp) REVERT: S 34 LYS cc_start: 0.7557 (mttt) cc_final: 0.7004 (mttt) REVERT: S 106 LYS cc_start: 0.7544 (mttt) cc_final: 0.7053 (mmtt) REVERT: T 13 GLU cc_start: 0.7544 (tt0) cc_final: 0.7336 (tt0) REVERT: T 39 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5921 (mp) REVERT: T 114 GLU cc_start: 0.7201 (pm20) cc_final: 0.6856 (pm20) REVERT: U 48 LEU cc_start: 0.6313 (tp) cc_final: 0.5996 (mp) REVERT: U 54 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7716 (t) REVERT: U 62 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7519 (mtt180) REVERT: U 72 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6879 (tm-30) REVERT: U 99 LYS cc_start: 0.8286 (tttt) cc_final: 0.7978 (mptt) REVERT: Z 103 HIS cc_start: 0.6199 (OUTLIER) cc_final: 0.5048 (t-170) REVERT: Z 104 ARG cc_start: 0.7244 (mtm180) cc_final: 0.6439 (mtm180) REVERT: c 16 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7408 (mmtt) REVERT: g 18 VAL cc_start: 0.7864 (t) cc_final: 0.7550 (t) REVERT: g 90 TRP cc_start: 0.7074 (m100) cc_final: 0.5004 (m100) outliers start: 189 outliers final: 143 residues processed: 1030 average time/residue: 0.7267 time to fit residues: 1258.0136 Evaluate side-chains 1011 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 861 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 55 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 34 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain f residue 139 HIS Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 221 LEU Chi-restraints excluded: chain g residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 596 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 352 optimal weight: 0.0020 chunk 451 optimal weight: 20.0000 chunk 349 optimal weight: 7.9990 chunk 520 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 615 optimal weight: 7.9990 chunk 385 optimal weight: 3.9990 chunk 375 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 227 GLN I 7 ASN I 165 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN Y 15 ASN ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 HIS ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 74 GLN ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 79200 Z= 0.253 Angle : 0.668 15.473 114868 Z= 0.338 Chirality : 0.040 0.388 14185 Planarity : 0.005 0.052 8389 Dihedral : 24.120 179.942 31386 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.70 % Favored : 93.26 % Rotamer: Outliers : 5.16 % Allowed : 20.62 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 4790 helix: -2.39 (0.13), residues: 1242 sheet: -2.07 (0.17), residues: 821 loop : -1.17 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 235 HIS 0.007 0.001 HIS X 31 PHE 0.021 0.002 PHE N 65 TYR 0.039 0.002 TYR K 68 ARG 0.008 0.001 ARG O 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 887 time to evaluate : 5.130 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: A 52 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7735 (tmtt) REVERT: A 69 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6843 (tm-30) REVERT: A 84 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7087 (tp-100) REVERT: A 130 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 156 TYR cc_start: 0.8430 (m-80) cc_final: 0.8108 (m-80) REVERT: B 169 MET cc_start: 0.7423 (mpp) cc_final: 0.6504 (mpp) REVERT: B 217 MET cc_start: 0.8286 (tmm) cc_final: 0.7440 (tmm) REVERT: C 216 MET cc_start: 0.7683 (mtm) cc_final: 0.7476 (mtm) REVERT: E 16 LYS cc_start: 0.8376 (tptp) cc_final: 0.8121 (ttmt) REVERT: E 235 TRP cc_start: 0.8056 (m-10) cc_final: 0.7582 (m-10) REVERT: G 59 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7529 (mp10) REVERT: G 217 MET cc_start: 0.7062 (mmp) cc_final: 0.6616 (ptt) REVERT: H 106 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5523 (ttm110) REVERT: H 188 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6055 (mt-10) REVERT: I 27 TYR cc_start: 0.8829 (p90) cc_final: 0.8601 (p90) REVERT: I 64 ASN cc_start: 0.7268 (p0) cc_final: 0.6559 (p0) REVERT: I 73 THR cc_start: 0.8243 (m) cc_final: 0.7936 (p) REVERT: I 154 LYS cc_start: 0.7259 (mttt) cc_final: 0.6715 (tttt) REVERT: N 25 TRP cc_start: 0.8446 (p90) cc_final: 0.8098 (p90) REVERT: N 36 GLN cc_start: 0.8698 (tp40) cc_final: 0.8379 (tp40) REVERT: O 116 LEU cc_start: 0.9142 (tt) cc_final: 0.8941 (tt) REVERT: O 124 MET cc_start: 0.8609 (mmm) cc_final: 0.7946 (mmm) REVERT: Y 22 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: Y 106 GLN cc_start: 0.8156 (tp40) cc_final: 0.7934 (tm-30) REVERT: a 42 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6686 (ptt90) REVERT: b 33 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7176 (mtt) REVERT: b 72 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.5788 (ptt180) REVERT: h 14 LYS cc_start: 0.7866 (tttt) cc_final: 0.7660 (tttm) REVERT: D 73 VAL cc_start: 0.7517 (m) cc_final: 0.7282 (m) REVERT: D 162 ASP cc_start: 0.7821 (t70) cc_final: 0.7566 (t0) REVERT: D 169 ASP cc_start: 0.7792 (m-30) cc_final: 0.7536 (p0) REVERT: F 45 TYR cc_start: 0.8336 (m-80) cc_final: 0.8088 (m-80) REVERT: F 78 MET cc_start: 0.6986 (mtp) cc_final: 0.6746 (mmp) REVERT: F 142 SER cc_start: 0.8327 (m) cc_final: 0.7676 (p) REVERT: F 192 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7694 (mmmm) REVERT: K 24 LYS cc_start: 0.8035 (tptt) cc_final: 0.7790 (tptt) REVERT: P 32 GLN cc_start: 0.8427 (mp10) cc_final: 0.8143 (mp10) REVERT: P 61 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6848 (tpp-160) REVERT: P 101 THR cc_start: 0.6418 (OUTLIER) cc_final: 0.6104 (p) REVERT: Q 92 LEU cc_start: 0.8772 (mp) cc_final: 0.8249 (tt) REVERT: R 96 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5744 (tp) REVERT: S 34 LYS cc_start: 0.7507 (mttt) cc_final: 0.6947 (mttt) REVERT: S 106 LYS cc_start: 0.7542 (mttt) cc_final: 0.7034 (mmtt) REVERT: T 39 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5706 (mp) REVERT: T 62 ARG cc_start: 0.6824 (tmm-80) cc_final: 0.6600 (tmm-80) REVERT: U 31 SER cc_start: 0.8412 (m) cc_final: 0.8143 (p) REVERT: U 48 LEU cc_start: 0.6312 (tp) cc_final: 0.5981 (mp) REVERT: U 72 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6942 (tm-30) REVERT: U 99 LYS cc_start: 0.8260 (tttt) cc_final: 0.7912 (mptt) REVERT: Z 103 HIS cc_start: 0.6204 (OUTLIER) cc_final: 0.5012 (t-170) REVERT: Z 104 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6335 (mtm180) REVERT: c 16 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7394 (mmtt) REVERT: g 18 VAL cc_start: 0.7809 (t) cc_final: 0.7493 (t) outliers start: 216 outliers final: 174 residues processed: 1021 average time/residue: 0.7250 time to fit residues: 1250.0500 Evaluate side-chains 1040 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 856 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 34 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 70 CYS Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 78 LYS Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 29 GLN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain f residue 139 HIS Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 381 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 367 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 391 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 484 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN I 7 ASN I 165 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN g 64 HIS ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 79200 Z= 0.310 Angle : 0.705 15.770 114868 Z= 0.357 Chirality : 0.042 0.408 14185 Planarity : 0.005 0.052 8389 Dihedral : 24.143 179.277 31386 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.27 % Favored : 92.69 % Rotamer: Outliers : 5.57 % Allowed : 20.74 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 4790 helix: -2.23 (0.13), residues: 1274 sheet: -2.02 (0.17), residues: 839 loop : -1.20 (0.12), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 235 HIS 0.008 0.001 HIS X 31 PHE 0.021 0.002 PHE d 43 TYR 0.048 0.002 TYR K 68 ARG 0.010 0.001 ARG c 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 874 time to evaluate : 4.525 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: A 52 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7762 (tmtt) REVERT: A 69 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6990 (tm-30) REVERT: A 84 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7132 (tp-100) REVERT: A 156 TYR cc_start: 0.8428 (m-80) cc_final: 0.8018 (m-80) REVERT: B 44 ILE cc_start: 0.8850 (pt) cc_final: 0.8493 (mt) REVERT: B 78 GLU cc_start: 0.5899 (mm-30) cc_final: 0.5625 (mm-30) REVERT: B 169 MET cc_start: 0.7539 (mpp) cc_final: 0.6881 (mpp) REVERT: B 217 MET cc_start: 0.8359 (tmm) cc_final: 0.7562 (tmm) REVERT: E 16 LYS cc_start: 0.8383 (tptp) cc_final: 0.8114 (ttmt) REVERT: E 211 LYS cc_start: 0.8390 (tttt) cc_final: 0.7916 (tptp) REVERT: E 235 TRP cc_start: 0.8253 (m-10) cc_final: 0.7911 (m-10) REVERT: G 217 MET cc_start: 0.7052 (mmp) cc_final: 0.6637 (ptt) REVERT: H 106 ARG cc_start: 0.5849 (mtt-85) cc_final: 0.5406 (ttm110) REVERT: I 27 TYR cc_start: 0.8884 (p90) cc_final: 0.8665 (p90) REVERT: I 73 THR cc_start: 0.8299 (m) cc_final: 0.7967 (p) REVERT: I 150 ASP cc_start: 0.7622 (t70) cc_final: 0.6977 (m-30) REVERT: L 55 TYR cc_start: 0.8157 (p90) cc_final: 0.7906 (p90) REVERT: N 25 TRP cc_start: 0.8459 (p90) cc_final: 0.8248 (p90) REVERT: N 36 GLN cc_start: 0.8740 (tp40) cc_final: 0.8376 (tp40) REVERT: O 116 LEU cc_start: 0.9171 (tt) cc_final: 0.8964 (tt) REVERT: O 124 MET cc_start: 0.8518 (mmm) cc_final: 0.7980 (mmm) REVERT: Y 22 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: a 33 ASP cc_start: 0.7761 (p0) cc_final: 0.7499 (p0) REVERT: a 42 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6708 (ptt90) REVERT: b 14 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: b 72 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5731 (ptt180) REVERT: h 14 LYS cc_start: 0.7928 (tttt) cc_final: 0.7656 (tttm) REVERT: h 18 ARG cc_start: 0.6984 (ttm110) cc_final: 0.6655 (mtm180) REVERT: D 87 TYR cc_start: 0.6802 (m-80) cc_final: 0.6445 (m-80) REVERT: D 169 ASP cc_start: 0.7833 (m-30) cc_final: 0.7552 (p0) REVERT: F 45 TYR cc_start: 0.8470 (m-80) cc_final: 0.8253 (m-80) REVERT: F 142 SER cc_start: 0.8460 (m) cc_final: 0.7846 (p) REVERT: F 192 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7680 (mmtm) REVERT: K 24 LYS cc_start: 0.8095 (tptt) cc_final: 0.7618 (tppt) REVERT: P 32 GLN cc_start: 0.8498 (mp10) cc_final: 0.8264 (mp10) REVERT: P 60 LEU cc_start: 0.8558 (mt) cc_final: 0.8012 (pp) REVERT: P 61 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6918 (tpp-160) REVERT: Q 41 MET cc_start: 0.6739 (mmm) cc_final: 0.6424 (mmm) REVERT: Q 92 LEU cc_start: 0.8813 (mp) cc_final: 0.8199 (tt) REVERT: Q 96 TYR cc_start: 0.7682 (m-80) cc_final: 0.6868 (m-80) REVERT: Q 97 GLN cc_start: 0.7955 (tt0) cc_final: 0.7651 (tt0) REVERT: R 96 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5782 (tp) REVERT: S 34 LYS cc_start: 0.7467 (mttt) cc_final: 0.6918 (mttt) REVERT: S 106 LYS cc_start: 0.7582 (mttt) cc_final: 0.7136 (mmtt) REVERT: S 109 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6227 (tm-30) REVERT: S 113 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7402 (ptm160) REVERT: T 39 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5744 (mp) REVERT: U 31 SER cc_start: 0.8341 (m) cc_final: 0.8091 (p) REVERT: U 48 LEU cc_start: 0.6263 (tp) cc_final: 0.5965 (mp) REVERT: U 72 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6974 (tm-30) REVERT: U 99 LYS cc_start: 0.8294 (tttt) cc_final: 0.7923 (mptt) REVERT: Z 103 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.5279 (t-170) REVERT: Z 104 ARG cc_start: 0.7240 (mtm180) cc_final: 0.6430 (mtm180) REVERT: c 16 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7421 (mmtt) REVERT: f 83 LYS cc_start: 0.3787 (tppt) cc_final: 0.3164 (pptt) REVERT: g 90 TRP cc_start: 0.7184 (m100) cc_final: 0.6853 (m100) outliers start: 233 outliers final: 190 residues processed: 1015 average time/residue: 0.7351 time to fit residues: 1249.4066 Evaluate side-chains 1052 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 853 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 34 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 15 GLN Chi-restraints excluded: chain e residue 44 ASN Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 113 ARG Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 70 CYS Chi-restraints excluded: chain U residue 101 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain f residue 139 HIS Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain g residue 303 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 560 optimal weight: 3.9990 chunk 590 optimal weight: 0.3980 chunk 538 optimal weight: 0.9980 chunk 573 optimal weight: 0.8980 chunk 589 optimal weight: 0.9990 chunk 345 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 450 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 518 optimal weight: 20.0000 chunk 542 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN I 7 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN e 15 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN R 93 GLN S 85 ASN Z 112 ASN c 26 GLN g 14 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 79200 Z= 0.142 Angle : 0.612 15.234 114868 Z= 0.310 Chirality : 0.037 0.303 14185 Planarity : 0.004 0.051 8389 Dihedral : 24.029 179.958 31386 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 3.30 % Allowed : 23.29 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4790 helix: -1.80 (0.14), residues: 1241 sheet: -1.84 (0.18), residues: 801 loop : -1.00 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 235 HIS 0.006 0.001 HIS J 124 PHE 0.026 0.001 PHE d 43 TYR 0.024 0.001 TYR R 21 ARG 0.014 0.001 ARG R 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 960 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8234 (mt) cc_final: 0.8029 (mt) REVERT: A 52 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7674 (tmtt) REVERT: A 84 GLN cc_start: 0.7662 (mm-40) cc_final: 0.6971 (tp-100) REVERT: A 156 TYR cc_start: 0.8239 (m-80) cc_final: 0.7904 (m-80) REVERT: B 169 MET cc_start: 0.7523 (mpp) cc_final: 0.6826 (mpp) REVERT: E 16 LYS cc_start: 0.8188 (tptp) cc_final: 0.7987 (ttmm) REVERT: E 211 LYS cc_start: 0.8245 (tttt) cc_final: 0.7843 (tptp) REVERT: E 235 TRP cc_start: 0.7718 (m-10) cc_final: 0.7492 (m-10) REVERT: G 7 PHE cc_start: 0.8307 (t80) cc_final: 0.8090 (t80) REVERT: G 217 MET cc_start: 0.7057 (mmp) cc_final: 0.6701 (ptt) REVERT: G 219 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6451 (mm-30) REVERT: H 106 ARG cc_start: 0.5724 (mtt-85) cc_final: 0.5415 (ttm110) REVERT: I 27 TYR cc_start: 0.8741 (p90) cc_final: 0.8502 (p90) REVERT: I 73 THR cc_start: 0.8274 (m) cc_final: 0.7880 (p) REVERT: I 165 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7890 (mt0) REVERT: L 55 TYR cc_start: 0.8059 (p90) cc_final: 0.7752 (p90) REVERT: L 118 ARG cc_start: 0.6630 (mtm110) cc_final: 0.6377 (ptt90) REVERT: N 9 LYS cc_start: 0.7654 (tttm) cc_final: 0.7320 (tttm) REVERT: N 62 GLN cc_start: 0.6358 (tt0) cc_final: 0.6003 (mt0) REVERT: V 61 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7637 (mtp180) REVERT: W 32 LYS cc_start: 0.8818 (ptpt) cc_final: 0.8426 (ptpt) REVERT: Y 22 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: b 33 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: b 72 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5729 (ptt180) REVERT: d 14 PHE cc_start: 0.6209 (p90) cc_final: 0.5977 (p90) REVERT: D 87 TYR cc_start: 0.6705 (m-80) cc_final: 0.6443 (m-80) REVERT: D 103 GLU cc_start: 0.8171 (mm-30) cc_final: 0.6920 (mt-10) REVERT: D 162 ASP cc_start: 0.8021 (t0) cc_final: 0.7644 (t0) REVERT: F 78 MET cc_start: 0.6650 (mtp) cc_final: 0.6389 (mmp) REVERT: F 142 SER cc_start: 0.8117 (m) cc_final: 0.7568 (p) REVERT: F 192 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7640 (mmtm) REVERT: K 24 LYS cc_start: 0.7987 (tptt) cc_final: 0.7589 (tppt) REVERT: K 52 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7404 (mm) REVERT: P 60 LEU cc_start: 0.8390 (mt) cc_final: 0.7904 (pp) REVERT: Q 92 LEU cc_start: 0.8721 (mp) cc_final: 0.8147 (tt) REVERT: Q 97 GLN cc_start: 0.7862 (tt0) cc_final: 0.7559 (tt0) REVERT: R 44 LYS cc_start: 0.7619 (mttp) cc_final: 0.7392 (mttm) REVERT: R 96 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5700 (tp) REVERT: S 34 LYS cc_start: 0.7483 (mttt) cc_final: 0.6934 (mttt) REVERT: S 68 ILE cc_start: 0.7156 (pt) cc_final: 0.6565 (tp) REVERT: S 106 LYS cc_start: 0.7506 (mttt) cc_final: 0.7016 (mmtt) REVERT: T 39 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5419 (mp) REVERT: U 48 LEU cc_start: 0.6318 (tp) cc_final: 0.5898 (mp) REVERT: U 72 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7005 (tm-30) REVERT: U 83 ARG cc_start: 0.7516 (ttm170) cc_final: 0.6912 (tpp-160) REVERT: U 99 LYS cc_start: 0.8215 (tttt) cc_final: 0.7878 (mptt) REVERT: Z 103 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.5677 (t-170) REVERT: Z 104 ARG cc_start: 0.7199 (mtm180) cc_final: 0.6838 (mtm-85) REVERT: c 16 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7366 (mmtt) REVERT: c 20 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7272 (ttm-80) REVERT: c 24 GLN cc_start: 0.8217 (mp10) cc_final: 0.7850 (mp10) REVERT: g 18 VAL cc_start: 0.7623 (t) cc_final: 0.7198 (t) REVERT: g 302 TYR cc_start: 0.8197 (m-10) cc_final: 0.7920 (m-10) outliers start: 138 outliers final: 96 residues processed: 1046 average time/residue: 0.7275 time to fit residues: 1289.0770 Evaluate side-chains 991 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 887 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 113 ARG Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain U residue 70 CYS Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain f residue 139 HIS Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 571 optimal weight: 6.9990 chunk 376 optimal weight: 6.9990 chunk 606 optimal weight: 40.0000 chunk 370 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 421 optimal weight: 9.9990 chunk 636 optimal weight: 20.0000 chunk 585 optimal weight: 7.9990 chunk 506 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 chunk 391 optimal weight: 4.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 7 ASN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN S 85 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 79200 Z= 0.310 Angle : 0.709 15.461 114868 Z= 0.357 Chirality : 0.041 0.391 14185 Planarity : 0.005 0.073 8389 Dihedral : 24.037 179.128 31384 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 3.42 % Allowed : 23.63 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.12), residues: 4790 helix: -1.88 (0.13), residues: 1291 sheet: -1.83 (0.18), residues: 810 loop : -1.08 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 235 HIS 0.008 0.001 HIS K 66 PHE 0.027 0.002 PHE H 94 TYR 0.037 0.002 TYR K 68 ARG 0.010 0.001 ARG W 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9580 Ramachandran restraints generated. 4790 Oldfield, 0 Emsley, 4790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 881 time to evaluate : 4.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7088 (tp-100) REVERT: A 156 TYR cc_start: 0.8447 (m-80) cc_final: 0.8057 (m-80) REVERT: B 44 ILE cc_start: 0.8842 (pt) cc_final: 0.8514 (mt) REVERT: B 169 MET cc_start: 0.7679 (mpp) cc_final: 0.6965 (mpp) REVERT: B 217 MET cc_start: 0.8291 (tmm) cc_final: 0.7736 (tmm) REVERT: C 187 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6631 (mmm-85) REVERT: E 16 LYS cc_start: 0.8332 (tptp) cc_final: 0.8069 (ttmm) REVERT: E 211 LYS cc_start: 0.8384 (tttt) cc_final: 0.7937 (tptp) REVERT: E 235 TRP cc_start: 0.8195 (m-10) cc_final: 0.7916 (m-10) REVERT: G 217 MET cc_start: 0.7106 (mmp) cc_final: 0.6649 (ptt) REVERT: H 106 ARG cc_start: 0.5995 (mtt-85) cc_final: 0.5618 (ttm110) REVERT: I 27 TYR cc_start: 0.8870 (p90) cc_final: 0.8665 (p90) REVERT: I 73 THR cc_start: 0.8320 (m) cc_final: 0.7938 (p) REVERT: I 150 ASP cc_start: 0.7682 (t70) cc_final: 0.7047 (m-30) REVERT: O 116 LEU cc_start: 0.9190 (tt) cc_final: 0.8982 (tt) REVERT: Y 22 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: a 33 ASP cc_start: 0.7712 (p0) cc_final: 0.7443 (p0) REVERT: a 42 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6856 (ptt90) REVERT: b 72 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.5695 (ptt180) REVERT: d 14 PHE cc_start: 0.6301 (p90) cc_final: 0.6034 (p90) REVERT: h 10 MET cc_start: 0.7597 (ttt) cc_final: 0.7101 (ttm) REVERT: h 18 ARG cc_start: 0.7086 (ttm110) cc_final: 0.6854 (mtm180) REVERT: D 87 TYR cc_start: 0.6847 (m-80) cc_final: 0.6531 (m-80) REVERT: D 162 ASP cc_start: 0.8157 (t0) cc_final: 0.7772 (t0) REVERT: F 78 MET cc_start: 0.7002 (mtp) cc_final: 0.6714 (mmp) REVERT: F 88 MET cc_start: 0.8717 (tmm) cc_final: 0.8078 (tpp) REVERT: F 192 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7683 (mmtm) REVERT: K 24 LYS cc_start: 0.8045 (tptt) cc_final: 0.7607 (tppt) REVERT: K 52 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7502 (mm) REVERT: P 60 LEU cc_start: 0.8427 (mt) cc_final: 0.7950 (pp) REVERT: Q 92 LEU cc_start: 0.8759 (mp) cc_final: 0.8147 (tt) REVERT: Q 96 TYR cc_start: 0.7630 (m-80) cc_final: 0.7216 (m-80) REVERT: R 96 ILE cc_start: 0.6175 (OUTLIER) cc_final: 0.5771 (tp) REVERT: S 34 LYS cc_start: 0.7514 (mttt) cc_final: 0.6907 (mttt) REVERT: S 106 LYS cc_start: 0.7630 (mttt) cc_final: 0.7238 (mmtt) REVERT: T 39 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5783 (mp) REVERT: U 48 LEU cc_start: 0.6321 (tp) cc_final: 0.6079 (mp) REVERT: U 72 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7017 (tm-30) REVERT: U 99 LYS cc_start: 0.8254 (tttt) cc_final: 0.7855 (mptt) REVERT: Z 103 HIS cc_start: 0.6422 (OUTLIER) cc_final: 0.5532 (t-170) REVERT: Z 104 ARG cc_start: 0.7123 (mtm180) cc_final: 0.6699 (mtm180) REVERT: c 16 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7470 (mmtt) REVERT: c 20 ARG cc_start: 0.8462 (ttm170) cc_final: 0.7437 (ttm-80) REVERT: g 18 VAL cc_start: 0.7725 (t) cc_final: 0.7291 (t) REVERT: g 90 TRP cc_start: 0.7166 (m100) cc_final: 0.6816 (m100) outliers start: 143 outliers final: 118 residues processed: 967 average time/residue: 0.7482 time to fit residues: 1211.6971 Evaluate side-chains 966 residues out of total 4191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 840 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 103 HIS Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain f residue 139 HIS Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 310 optimal weight: 0.9990 chunk 402 optimal weight: 0.8980 chunk 540 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 467 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 507 optimal weight: 0.5980 chunk 212 optimal weight: 10.0000 chunk 521 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN G 65 GLN G 70 HIS I 7 ASN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 ASN ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS S 85 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.122708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102386 restraints weight = 190811.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102602 restraints weight = 122195.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103505 restraints weight = 90939.698| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 79200 Z= 0.247 Angle : 0.673 15.523 114868 Z= 0.340 Chirality : 0.040 0.368 14185 Planarity : 0.005 0.107 8389 Dihedral : 24.042 179.219 31382 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.80 % Rotamer: Outliers : 3.54 % Allowed : 23.67 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4790 helix: -1.75 (0.13), residues: 1281 sheet: -1.78 (0.18), residues: 826 loop : -1.03 (0.12), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 235 HIS 0.007 0.001 HIS g 191 PHE 0.031 0.002 PHE D 24 TYR 0.035 0.002 TYR K 68 ARG 0.014 0.001 ARG W 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19140.81 seconds wall clock time: 337 minutes 7.18 seconds (20227.18 seconds total)