Starting phenix.real_space_refine on Sun Mar 17 03:10:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5i_4353/03_2024/6g5i_4353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5i_4353/03_2024/6g5i_4353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5i_4353/03_2024/6g5i_4353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5i_4353/03_2024/6g5i_4353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5i_4353/03_2024/6g5i_4353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g5i_4353/03_2024/6g5i_4353.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 1657 5.49 5 S 186 5.16 5 C 42233 2.51 5 N 14184 2.21 5 O 18922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 149": "NH1" <-> "NH2" Residue "Q PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 76": "NH1" <-> "NH2" Residue "x ARG 84": "NH1" <-> "NH2" Residue "x ARG 114": "NH1" <-> "NH2" Residue "x ARG 178": "NH1" <-> "NH2" Residue "x ARG 182": "NH1" <-> "NH2" Residue "x ARG 199": "NH1" <-> "NH2" Residue "x ARG 201": "NH1" <-> "NH2" Residue "x ARG 222": "NH1" <-> "NH2" Residue "x ARG 242": "NH1" <-> "NH2" Residue "x ARG 247": "NH1" <-> "NH2" Residue "y ARG 16": "NH1" <-> "NH2" Residue "y ARG 31": "NH1" <-> "NH2" Residue "y ARG 38": "NH1" <-> "NH2" Residue "y ARG 43": "NH1" <-> "NH2" Residue "y ARG 44": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y ARG 54": "NH1" <-> "NH2" Residue "y ARG 64": "NH1" <-> "NH2" Residue "y ARG 264": "NH1" <-> "NH2" Residue "z ARG 546": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77185 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 35380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1657, 35380 Classifications: {'RNA': 1657} Modifications used: {'rna2p_pur': 129, 'rna2p_pyr': 110, 'rna3p_pur': 750, 'rna3p_pyr': 668} Link IDs: {'rna2p': 238, 'rna3p': 1418} Chain breaks: 12 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} 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: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} 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: "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: "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: "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: "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: "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: "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: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} 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: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 990 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} 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: "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: "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: "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: "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: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} 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: "f" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} 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: "x" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1365 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "y" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "z" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 257 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} 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} Chain: "y" 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 69386 SG CYS d 21 152.331 159.316 69.620 1.00 45.37 S ATOM 69410 SG CYS d 24 149.574 156.628 68.815 1.00 48.64 S ATOM 69531 SG CYS d 39 149.085 160.361 70.691 1.00 47.03 S ATOM 69557 SG CYS d 42 149.674 157.206 72.378 1.00 48.50 S ATOM 70418 SG CYS f 121 176.211 150.710 27.192 1.00 87.72 S ATOM 70572 SG CYS f 141 172.744 149.600 27.181 1.00 94.15 S ATOM 70591 SG CYS f 144 174.234 151.010 30.171 1.00 89.78 S ATOM 75819 SG CYS y 270 109.905 167.562 152.597 1.00 61.38 S ATOM 75839 SG CYS y 273 111.022 164.684 154.776 1.00 53.93 S ATOM 75936 SG CYS y 285 109.231 165.379 149.901 1.00 53.64 S ATOM 75958 SG CYS y 288 110.753 162.638 151.809 1.00 49.23 S Time building chain proxies: 29.72, per 1000 atoms: 0.39 Number of scatterers: 77185 At special positions: 0 Unit cell: (205.96, 252.572, 202.708, 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 186 16.00 P 1657 15.00 O 18922 8.00 N 14184 7.00 C 42233 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: 30.73 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 144 " pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " Number of angles added : 12 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9732 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 73 sheets defined 27.1% alpha, 8.1% beta 525 base pairs and 885 stacking pairs defined. Time for finding SS restraints: 22.68 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.529A pdb=" N VAL A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 removed outlier: 4.519A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.858A pdb=" N VAL A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 93' Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.934A pdb=" N GLU A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 167 through 175 removed outlier: 3.952A pdb=" N GLY A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.856A pdb=" N ARG A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.881A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'B' and resid 23 through 26 removed outlier: 3.767A pdb=" N SER B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.980A pdb=" N CYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.829A pdb=" N ARG B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.804A pdb=" N ILE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 172 " --> pdb=" O MET B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.909A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 177' Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.911A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 189' Processing helix chain 'B' and resid 193 through 200 removed outlier: 3.918A pdb=" N ILE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 193 through 200' Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.029A pdb=" N GLU B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.920A 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: 3.875A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 72' Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.984A pdb=" N ASP C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 removed outlier: 3.946A pdb=" N ILE C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.622A pdb=" N ILE C 162 " --> pdb=" O LYS C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 218 removed outlier: 4.024A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 238 removed outlier: 3.845A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.968A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 257 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.929A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 3.928A pdb=" N PHE D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.760A pdb=" N GLU D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 21' Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.923A pdb=" N ARG D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 28 " --> pdb=" O PHE D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 28' Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.971A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.851A pdb=" N SER D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 105 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 106' Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.596A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 123 " --> pdb=" O CYS D 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 114 through 128' Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.632A pdb=" N TRP E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.951A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.925A pdb=" N PHE E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.862A pdb=" N CYS E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.680A pdb=" N LYS E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR E 121 " --> pdb=" O GLU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'E' and resid 247 through 262 removed outlier: 3.865A pdb=" N ARG E 252 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 258 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.883A pdb=" N THR F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN F 74 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 75' Processing helix chain 'F' and resid 76 through 83 removed outlier: 4.595A pdb=" N HIS F 79 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY F 80 " --> pdb=" O MET F 77 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG F 81 " --> pdb=" O MET F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 removed outlier: 3.850A pdb=" N PHE F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 102' Processing helix chain 'F' and resid 108 through 118 removed outlier: 3.969A pdb=" N LEU F 112 " --> pdb=" O PRO F 108 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 118' Processing helix chain 'F' and resid 146 through 151 removed outlier: 3.872A pdb=" N ALA F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 146 through 151' Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 171 through 181 removed outlier: 3.968A pdb=" N ASP F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 176 " --> pdb=" O CYS F 172 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 180 " --> pdb=" O GLU F 176 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 171 through 181' Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.899A pdb=" N LYS F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER F 202 " --> pdb=" O ARG F 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 28 removed outlier: 4.000A pdb=" N PHE G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 142 removed outlier: 3.968A pdb=" N ARG G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 216 Processing helix chain 'G' and resid 217 through 230 removed outlier: 3.918A pdb=" N LYS G 221 " --> pdb=" O MET G 217 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 30 removed outlier: 3.991A pdb=" N GLY H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU H 27 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU H 28 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H 29 " --> pdb=" O GLN H 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 18 through 30' Processing helix chain 'H' and resid 38 through 43 removed outlier: 4.021A pdb=" N GLU H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU H 43 " --> pdb=" O GLN H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 38 through 43' Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 70 through 75 removed outlier: 3.985A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.021A 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 82 removed outlier: 3.848A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 75 through 82' Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.911A pdb=" N HIS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE H 129 " --> pdb=" O VAL H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 removed outlier: 3.632A pdb=" N PHE H 135 " --> pdb=" O ASP H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.594A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 171 removed outlier: 4.234A pdb=" N GLU H 171 " --> pdb=" O HIS H 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 168 through 171' Processing helix chain 'H' and resid 175 through 181 removed outlier: 3.910A pdb=" N LEU H 180 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR H 181 " --> pdb=" O TYR H 177 " (cutoff:3.500A) 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 88 through 93 removed outlier: 3.982A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 removed outlier: 3.913A pdb=" N GLN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP I 112 " --> pdb=" O PRO I 108 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER I 115 " --> pdb=" O GLN I 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR I 117 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 135 removed outlier: 3.760A pdb=" N GLU I 135 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 153 removed outlier: 3.968A pdb=" N LYS I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR I 149 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS I 153 " --> pdb=" O TYR I 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 153' Processing helix chain 'I' and resid 154 through 156 No H-bonds generated for 'chain 'I' and resid 154 through 156' Processing helix chain 'I' and resid 159 through 164 removed outlier: 3.956A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 169 removed outlier: 3.913A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 204 removed outlier: 3.941A pdb=" N PHE I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR I 198 " --> pdb=" O GLU I 194 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU I 199 " --> pdb=" O LEU I 195 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS I 201 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE I 202 " --> pdb=" O TYR I 198 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS I 203 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 193 through 204' Processing helix chain 'J' and resid 29 through 34 removed outlier: 3.922A pdb=" N GLY J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.878A 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 39 through 44 removed outlier: 3.652A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 44' Processing helix chain 'J' and resid 67 through 73 removed outlier: 3.970A pdb=" N PHE J 72 " --> pdb=" O PRO J 68 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 78 removed outlier: 3.778A pdb=" N LEU J 77 " --> pdb=" O GLU J 73 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU J 78 " --> pdb=" O GLY J 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 73 through 78' Processing helix chain 'J' and resid 93 through 97 removed outlier: 3.745A pdb=" N TYR J 96 " --> pdb=" O LYS J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 115 removed outlier: 3.832A pdb=" N VAL J 114 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 110 through 115' Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.917A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL J 128 " --> pdb=" O HIS J 124 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU J 129 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.634A pdb=" N GLN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 179 removed outlier: 3.935A pdb=" N ARG J 175 " --> pdb=" O GLY J 171 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS J 176 " --> pdb=" O ARG J 172 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN J 177 " --> pdb=" O VAL J 173 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA J 178 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 171 through 179' Processing helix chain 'K' and resid 6 through 15 removed outlier: 3.959A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU K 13 " --> pdb=" O ILE K 9 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU K 15 " --> pdb=" O ILE K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 15' Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.921A pdb=" N LYS K 53 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 54' Processing helix chain 'K' and resid 72 through 78 removed outlier: 3.939A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 81 No H-bonds generated for 'chain 'K' and resid 79 through 81' Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.887A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 18 removed outlier: 3.842A pdb=" N LEU M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 28 removed outlier: 3.846A pdb=" N THR M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE M 27 " --> pdb=" O LYS M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 removed outlier: 3.975A pdb=" N ALA M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 35 through 41' Processing helix chain 'M' and resid 58 through 69 removed outlier: 3.545A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS M 69 " --> pdb=" O VAL M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 119 through 130 removed outlier: 4.011A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU M 126 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 4.009A 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 'N' and resid 29 through 39 removed outlier: 3.973A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE N 37 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.951A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU N 54 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP N 56 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER N 57 " --> pdb=" O ILE N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.890A pdb=" N THR N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 76 removed outlier: 3.795A pdb=" N ILE N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU N 75 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 70 through 76' Processing helix chain 'N' and resid 85 through 93 removed outlier: 3.947A pdb=" N HIS N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE N 92 " --> pdb=" O LEU N 88 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS N 93 " --> pdb=" O TYR N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 130 removed outlier: 3.845A pdb=" N TYR N 129 " --> pdb=" O LEU N 125 " (cutoff:3.500A) removed outlier: 3.837A 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 145 through 149 removed outlier: 3.513A pdb=" N ALA N 148 " --> pdb=" O THR N 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 removed outlier: 4.112A pdb=" N LYS O 61 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 57 through 62' Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 72 through 85 removed outlier: 3.870A pdb=" N LEU O 76 " --> pdb=" O TYR O 72 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN O 79 " --> pdb=" O MET O 75 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN O 83 " --> pdb=" O GLN O 79 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS O 85 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 72 through 85' Processing helix chain 'O' and resid 110 through 119 removed outlier: 3.885A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA O 115 " --> pdb=" O GLY O 111 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA O 118 " --> pdb=" O SER O 114 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 119' Processing helix chain 'P' and resid 21 through 26 removed outlier: 4.004A pdb=" N LEU P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.267A pdb=" N LEU P 33 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 34' Processing helix chain 'P' and resid 38 through 47 removed outlier: 3.985A pdb=" N ARG P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN P 46 " --> pdb=" O ARG P 42 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG P 47 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 64 removed outlier: 3.887A pdb=" N ARG P 59 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU P 60 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 3.894A 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: 3.655A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) 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 53 removed outlier: 3.615A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 82 removed outlier: 3.900A pdb=" N ILE Q 81 " --> pdb=" O HIS Q 77 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 90 removed outlier: 3.823A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS Q 90 " --> pdb=" O GLN Q 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 85 through 90' Processing helix chain 'Q' and resid 90 through 99 removed outlier: 3.838A pdb=" N ALA Q 94 " --> pdb=" O LYS Q 90 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN Q 97 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.620A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS Q 109 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU Q 112 " --> pdb=" O ILE Q 108 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE Q 113 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN Q 114 " --> pdb=" O ASP Q 110 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 removed outlier: 3.819A pdb=" N LEU Q 120 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 117 through 120' Processing helix chain 'R' and resid 14 through 19 removed outlier: 3.839A pdb=" N GLU R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 14 through 19' Processing helix chain 'R' and resid 29 through 37 removed outlier: 3.991A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS R 35 " --> pdb=" O ASN R 31 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 37' Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.913A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 80 removed outlier: 3.978A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG R 78 " --> pdb=" O GLN R 74 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU R 79 " --> pdb=" O GLU R 75 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 73 through 80' Processing helix chain 'R' and resid 101 through 108 removed outlier: 3.867A pdb=" N MET R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU R 108 " --> pdb=" O GLU R 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 101 through 108' Processing helix chain 'S' and resid 37 through 45 removed outlier: 3.943A pdb=" N HIS S 42 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL S 44 " --> pdb=" O TYR S 40 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 71 removed outlier: 4.434A pdb=" N VAL S 64 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG S 66 " --> pdb=" O ASP S 62 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL S 67 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE S 68 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE S 70 " --> pdb=" O ARG S 66 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET S 71 " --> pdb=" O VAL S 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 60 through 71' Processing helix chain 'S' and resid 99 through 109 removed outlier: 3.997A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS S 106 " --> pdb=" O GLY S 102 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU S 107 " --> pdb=" O LEU S 103 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG S 108 " --> pdb=" O ASP S 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU S 109 " --> pdb=" O ASN S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 117 removed outlier: 3.943A pdb=" N LYS S 116 " --> pdb=" O GLU S 112 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE S 117 " --> pdb=" O ARG S 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 112 through 117' Processing helix chain 'S' and resid 121 through 126 removed outlier: 3.994A pdb=" N HIS S 125 " --> pdb=" O ARG S 121 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE S 126 " --> pdb=" O GLY S 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 121 through 126' Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.922A pdb=" N VAL T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU T 18 " --> pdb=" O PHE T 14 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA T 19 " --> pdb=" O VAL T 15 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE T 21 " --> pdb=" O ALA T 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU T 22 " --> pdb=" O LEU T 18 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER T 25 " --> pdb=" O PHE T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 36 removed outlier: 4.548A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR T 36 " --> pdb=" O TRP T 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 32 through 36' Processing helix chain 'T' and resid 51 through 65 removed outlier: 3.893A pdb=" N ARG T 56 " --> pdb=" O TRP T 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA T 57 " --> pdb=" O PHE T 53 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA T 58 " --> pdb=" O TYR T 54 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER T 59 " --> pdb=" O THR T 55 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR T 60 " --> pdb=" O ARG T 56 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA T 61 " --> pdb=" O ALA T 57 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG T 62 " --> pdb=" O ALA T 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS T 63 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR T 65 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 77 removed outlier: 3.590A pdb=" N MET T 75 " --> pdb=" O GLY T 71 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR T 76 " --> pdb=" O VAL T 72 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 71 through 77' Processing helix chain 'T' and resid 100 through 108 removed outlier: 3.948A pdb=" N LEU T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN T 105 " --> pdb=" O ARG T 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU T 107 " --> pdb=" O VAL T 103 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU T 108 " --> pdb=" O LEU T 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 100 through 108' Processing helix chain 'T' and resid 126 through 139 removed outlier: 3.924A pdb=" N ASP T 130 " --> pdb=" O GLN T 126 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU T 131 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP T 132 " --> pdb=" O GLN T 128 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG T 133 " --> pdb=" O ARG T 129 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA T 135 " --> pdb=" O LEU T 131 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY T 136 " --> pdb=" O ASP T 132 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL T 138 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA T 139 " --> pdb=" O ALA T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 126 through 139' Processing helix chain 'U' and resid 30 through 42 removed outlier: 3.933A pdb=" N LYS U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL U 35 " --> pdb=" O SER U 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS U 36 " --> pdb=" O LEU U 32 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA U 37 " --> pdb=" O GLU U 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP U 38 " --> pdb=" O LYS U 34 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU U 39 " --> pdb=" O VAL U 35 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE U 40 " --> pdb=" O CYS U 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY U 42 " --> pdb=" O ASP U 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 30 through 42' Processing helix chain 'U' and resid 95 through 105 removed outlier: 3.988A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 4.083A 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: 4.067A pdb=" N THR U 102 " --> pdb=" O VAL U 98 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 95 through 105' Processing helix chain 'V' and resid 56 through 61 removed outlier: 3.874A pdb=" N ARG V 60 " --> pdb=" O CYS V 56 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG V 61 " --> pdb=" O GLY V 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 56 through 61' Processing helix chain 'V' and resid 65 through 75 removed outlier: 3.909A pdb=" N ILE V 69 " --> pdb=" O SER V 65 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU V 70 " --> pdb=" O ASP V 66 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG V 71 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA V 73 " --> pdb=" O ILE V 69 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS V 74 " --> pdb=" O LEU V 70 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 65 through 75' Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.799A pdb=" N ALA W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 44 removed outlier: 3.899A pdb=" N LYS W 43 " --> pdb=" O THR W 39 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 39 through 44' Processing helix chain 'W' and resid 88 through 93 removed outlier: 3.961A pdb=" N ASN W 92 " --> pdb=" O LYS W 88 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU W 93 " --> pdb=" O TRP W 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 88 through 93' Processing helix chain 'W' and resid 114 through 119 removed outlier: 3.964A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS W 119 " --> pdb=" O GLU W 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 114 through 119' Processing helix chain 'X' and resid 26 through 31 removed outlier: 3.987A pdb=" N ALA X 30 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 3.831A 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 'Y' and resid 38 through 43 removed outlier: 3.959A pdb=" N GLU Y 42 " --> pdb=" O THR Y 38 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 38 through 43' Processing helix chain 'Y' and resid 44 through 49 removed outlier: 3.828A pdb=" N TYR Y 48 " --> pdb=" O LEU Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 55 removed outlier: 3.567A pdb=" N VAL Y 54 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 84 removed outlier: 3.971A pdb=" N LYS Y 83 " --> pdb=" O LEU Y 79 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS Y 84 " --> pdb=" O ASP Y 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 79 through 84' Processing helix chain 'Y' and resid 87 through 93 removed outlier: 3.598A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG Y 93 " --> pdb=" O HIS Y 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 87 through 93' Processing helix chain 'Y' and resid 108 through 114 removed outlier: 3.905A pdb=" N ASN Y 112 " --> pdb=" O LYS Y 108 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET Y 114 " --> pdb=" O ARG Y 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 108 through 114' Processing helix chain 'Y' and resid 120 through 124 removed outlier: 4.018A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN Y 124 " --> pdb=" O ALA Y 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 120 through 124' Processing helix chain 'Z' and resid 51 through 56 removed outlier: 3.952A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 65 removed outlier: 3.766A pdb=" N ASN Z 64 " --> pdb=" O GLU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 74 removed outlier: 3.600A pdb=" N VAL Z 73 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER Z 74 " --> pdb=" O PRO Z 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 69 through 74' Processing helix chain 'Z' and resid 80 through 95 removed outlier: 3.978A pdb=" N ARG Z 85 " --> pdb=" O GLY Z 81 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA Z 86 " --> pdb=" O SER Z 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU Z 88 " --> pdb=" O ALA Z 84 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU Z 90 " --> pdb=" O ALA Z 86 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU Z 91 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU Z 92 " --> pdb=" O LEU Z 88 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.918A pdb=" N LYS b 16 " --> pdb=" O PRO b 12 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 46 removed outlier: 3.941A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR d 46 " --> pdb=" O CYS d 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 40 through 46' Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 32 through 42 removed outlier: 3.906A pdb=" N MET e 36 " --> pdb=" O ALA e 32 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN e 37 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN e 39 " --> pdb=" O ARG e 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 105 Processing helix chain 'x' and resid 84 through 90 removed outlier: 3.622A pdb=" N LEU x 88 " --> pdb=" O ARG x 84 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS x 89 " --> pdb=" O TYR x 85 " (cutoff:3.500A) Processing helix chain 'x' and resid 95 through 101 removed outlier: 4.307A pdb=" N ILE x 99 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL x 100 " --> pdb=" O PHE x 96 " (cutoff:3.500A) Processing helix chain 'x' and resid 126 through 129 Processing helix chain 'x' and resid 130 through 135 removed outlier: 3.886A pdb=" N ALA x 134 " --> pdb=" O LEU x 130 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP x 135 " --> pdb=" O THR x 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 130 through 135' Processing helix chain 'x' and resid 135 through 140 removed outlier: 3.788A pdb=" N ALA x 139 " --> pdb=" O ASP x 135 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE x 140 " --> pdb=" O PHE x 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 135 through 140' Processing helix chain 'x' and resid 145 through 150 removed outlier: 3.885A pdb=" N LEU x 150 " --> pdb=" O VAL x 146 " (cutoff:3.500A) Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.869A pdb=" N ARG x 154 " --> pdb=" O LEU x 150 " (cutoff:3.500A) Processing helix chain 'x' and resid 178 through 185 removed outlier: 3.573A pdb=" N ARG x 182 " --> pdb=" O ARG x 178 " (cutoff:3.500A) Processing helix chain 'x' and resid 190 through 198 removed outlier: 3.885A pdb=" N GLU x 195 " --> pdb=" O LYS x 191 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN x 196 " --> pdb=" O PHE x 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL x 197 " --> pdb=" O THR x 193 " (cutoff:3.500A) Processing helix chain 'x' and resid 214 through 220 removed outlier: 3.837A pdb=" N LYS x 219 " --> pdb=" O PHE x 215 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET x 220 " --> pdb=" O GLN x 216 " (cutoff:3.500A) Processing helix chain 'x' and resid 222 through 230 removed outlier: 3.770A pdb=" N CYS x 226 " --> pdb=" O ARG x 222 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN x 227 " --> pdb=" O THR x 223 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU x 228 " --> pdb=" O ALA x 224 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE x 229 " --> pdb=" O ILE x 225 " (cutoff:3.500A) Processing helix chain 'x' and resid 235 through 245 removed outlier: 3.977A pdb=" N GLY x 239 " --> pdb=" O SER x 235 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN x 240 " --> pdb=" O LYS x 236 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE x 241 " --> pdb=" O VAL x 237 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG x 242 " --> pdb=" O TYR x 238 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA x 243 " --> pdb=" O GLY x 239 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL x 244 " --> pdb=" O ASN x 240 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA x 245 " --> pdb=" O ILE x 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 235 through 245' Processing helix chain 'y' and resid 10 through 16 removed outlier: 3.802A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG y 16 " --> pdb=" O GLY y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 10 through 16' Processing helix chain 'y' and resid 31 through 36 removed outlier: 4.024A pdb=" N THR y 35 " --> pdb=" O ARG y 31 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 31 through 36' Processing helix chain 'y' and resid 39 through 44 Processing helix chain 'y' and resid 44 through 49 removed outlier: 3.942A pdb=" N VAL y 48 " --> pdb=" O ARG y 44 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU y 49 " --> pdb=" O ARG y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 44 through 49' Processing helix chain 'y' and resid 50 through 53 Processing helix chain 'y' and resid 59 through 67 removed outlier: 3.957A pdb=" N ARG y 64 " --> pdb=" O PRO y 60 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU y 65 " --> pdb=" O GLU y 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL y 66 " --> pdb=" O TYR y 62 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR y 67 " --> pdb=" O VAL y 63 " (cutoff:3.500A) Processing helix chain 'y' and resid 67 through 72 removed outlier: 3.881A pdb=" N LYS y 71 " --> pdb=" O THR y 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS y 72 " --> pdb=" O GLU y 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 67 through 72' Processing helix chain 'y' and resid 80 through 97 removed outlier: 4.028A pdb=" N GLN y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL y 86 " --> pdb=" O THR y 82 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU y 87 " --> pdb=" O ASP y 83 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA y 88 " --> pdb=" O ILE y 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU y 89 " --> pdb=" O GLN y 85 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR y 90 " --> pdb=" O VAL y 86 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR y 91 " --> pdb=" O LEU y 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN y 92 " --> pdb=" O ALA y 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU y 93 " --> pdb=" O LEU y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 99 through 103 removed outlier: 4.108A pdb=" N HIS y 102 " --> pdb=" O GLY y 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 213 through 217 removed outlier: 3.907A pdb=" N ILE y 217 " --> pdb=" O ILE y 214 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 246 removed outlier: 3.868A pdb=" N ASN y 243 " --> pdb=" O PHE y 239 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL y 244 " --> pdb=" O ALA y 240 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU y 245 " --> pdb=" O MET y 241 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU y 246 " --> pdb=" O GLN y 242 " (cutoff:3.500A) Processing helix chain 'y' and resid 319 through 323 removed outlier: 3.889A pdb=" N LEU y 322 " --> pdb=" O PRO y 319 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG y 323 " --> pdb=" O ARG y 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 319 through 323' Processing helix chain 'y' and resid 352 through 357 removed outlier: 3.775A pdb=" N GLN y 357 " --> pdb=" O GLN y 353 " (cutoff:3.500A) Processing helix chain 'y' and resid 382 through 386 removed outlier: 3.606A pdb=" N LEU y 385 " --> pdb=" O SER y 382 " (cutoff:3.500A) Processing helix chain 'y' and resid 393 through 399 removed outlier: 3.902A pdb=" N ARG y 397 " --> pdb=" O GLY y 393 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG y 398 " --> pdb=" O ALA y 394 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU y 399 " --> pdb=" O GLY y 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 393 through 399' Processing helix chain 'z' and resid 532 through 547 removed outlier: 4.221A pdb=" N VAL z 538 " --> pdb=" O ARG z 534 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS z 539 " --> pdb=" O LYS z 535 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA z 541 " --> pdb=" O MET z 537 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG z 546 " --> pdb=" O GLN z 542 " (cutoff:3.500A) Processing helix chain 'z' and resid 554 through 559 removed outlier: 4.171A pdb=" N GLU z 559 " --> pdb=" O LYS z 555 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 4.015A pdb=" N LYS A 40 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.192A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 75 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 147 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 34 removed outlier: 7.220A pdb=" N ASP B 29 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 48 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 31 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS B 46 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 33 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.889A pdb=" N LYS B 83 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 104 " --> pdb=" O LYS B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.873A pdb=" N ILE B 121 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 141 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 123 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS B 139 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 125 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 137 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 127 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 135 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 114 removed outlier: 6.979A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG C 121 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 128 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 140 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.643A pdb=" N VAL C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 205 Processing sheet with id=AB1, first strand: chain 'D' and resid 34 through 41 removed outlier: 7.203A pdb=" N LEU D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.962A pdb=" N SER D 139 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 183 " --> pdb=" O SER D 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.796A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.930A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'E' and resid 126 through 132 removed outlier: 7.317A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 195 through 198 removed outlier: 3.826A pdb=" N THR E 196 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL E 210 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 218 " --> pdb=" O VAL E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 123 through 124 removed outlier: 3.903A pdb=" N ASP F 124 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL F 139 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 49 through 52 removed outlier: 6.881A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL G 114 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG G 51 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL G 112 " --> pdb=" O ARG G 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 56 through 57 removed outlier: 6.906A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 73 through 76 removed outlier: 3.895A pdb=" N VAL G 73 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 97 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 75 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS G 95 " --> pdb=" O LEU G 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.957A pdb=" N LYS G 160 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS G 172 " --> pdb=" O LYS G 160 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU G 162 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG G 170 " --> pdb=" O LEU G 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 47 through 49 removed outlier: 3.931A pdb=" N ALA H 47 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE H 63 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS H 49 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE H 61 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN H 97 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL H 64 " --> pdb=" O GLN H 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 139 through 141 removed outlier: 6.532A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 145 through 146 removed outlier: 3.881A pdb=" N ARG H 145 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU H 153 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.789A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 62 through 64 removed outlier: 3.891A pdb=" N GLY I 63 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR I 76 " --> pdb=" O GLY I 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 83 through 84 removed outlier: 3.515A pdb=" N TYR I 83 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 173 through 175 removed outlier: 3.826A pdb=" N CYS I 174 " --> pdb=" O TYR I 188 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR I 188 " --> pdb=" O CYS I 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AD3, first strand: chain 'L' and resid 76 through 82 removed outlier: 7.079A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N MET L 80 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N THR L 85 " --> pdb=" O MET L 80 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 91 through 92 removed outlier: 3.975A pdb=" N TYR L 92 " --> pdb=" O ARG L 105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG L 105 " --> pdb=" O TYR L 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'L' and resid 128 through 130 Processing sheet with id=AD6, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.927A pdb=" N ALA M 32 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL M 110 " --> pdb=" O ALA M 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'M' and resid 49 through 53 removed outlier: 3.919A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU M 52 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL M 79 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 93 through 94 removed outlier: 6.613A pdb=" N LYS M 93 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 92 through 93 Processing sheet with id=AE1, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.965A pdb=" N VAL P 76 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY P 95 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR P 78 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER P 92 " --> pdb=" O ILE P 107 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL P 94 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL P 105 " --> pdb=" O VAL P 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.902A pdb=" N VAL Q 10 " --> pdb=" O CYS Q 25 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS Q 25 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'Q' and resid 20 through 21 removed outlier: 3.867A pdb=" N THR Q 20 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS Q 73 " --> pdb=" O THR Q 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'Q' and resid 37 through 38 removed outlier: 3.846A pdb=" N LYS Q 33 " --> pdb=" O ILE Q 68 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 97 through 98 removed outlier: 3.913A pdb=" N VAL R 98 " --> pdb=" O GLN R 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'S' and resid 13 through 15 removed outlier: 3.946A pdb=" N LEU S 13 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE S 20 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL S 15 " --> pdb=" O THR S 18 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR S 18 " --> pdb=" O VAL S 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'T' and resid 82 through 83 removed outlier: 3.976A pdb=" N GLN T 83 " --> pdb=" O HIS T 91 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS T 91 " --> pdb=" O GLN T 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'T' and resid 113 through 115 removed outlier: 3.974A pdb=" N GLU T 114 " --> pdb=" O LYS T 122 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS T 122 " --> pdb=" O GLU T 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'U' and resid 54 through 60 removed outlier: 4.140A pdb=" N LYS U 86 " --> pdb=" O MET U 56 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR U 58 " --> pdb=" O ILE U 84 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE U 84 " --> pdb=" O THR U 58 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 63 through 66 removed outlier: 3.958A pdb=" N ILE U 63 " --> pdb=" O PHE U 80 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE U 80 " --> pdb=" O ILE U 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR U 65 " --> pdb=" O ASP U 78 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP U 78 " --> pdb=" O THR U 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'W' and resid 24 through 26 removed outlier: 3.828A 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=AF2 Processing sheet with id=AF3, first strand: chain 'W' and resid 104 through 106 removed outlier: 3.782A pdb=" N LEU W 104 " --> pdb=" O MET W 111 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET W 111 " --> pdb=" O LEU W 104 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR W 106 " --> pdb=" O GLY W 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 49 through 51 Processing sheet with id=AF5, first strand: chain 'X' and resid 56 through 58 removed outlier: 4.003A pdb=" N VAL X 57 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG X 67 " --> pdb=" O VAL X 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'X' and resid 124 through 125 Processing sheet with id=AF7, first strand: chain 'Y' and resid 23 through 25 removed outlier: 3.876A pdb=" N MET Y 23 " --> pdb=" O GLY Y 73 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY Y 73 " --> pdb=" O MET Y 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE Y 25 " --> pdb=" O GLY Y 71 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY Y 71 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE Y 72 " --> pdb=" O GLY Y 59 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLY Y 59 " --> pdb=" O PHE Y 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 98 through 101 removed outlier: 6.231A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER Z 101 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AG1, first strand: chain 'c' and resid 17 through 21 removed outlier: 3.931A pdb=" N THR c 28 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL c 46 " --> pdb=" O THR c 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL c 30 " --> pdb=" O ARG c 44 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG c 44 " --> pdb=" O VAL c 30 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.774A pdb=" N MET d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'f' and resid 106 through 108 removed outlier: 4.020A pdb=" N LYS f 107 " --> pdb=" O SER f 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER f 115 " --> pdb=" O LYS f 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'f' and resid 133 through 134 removed outlier: 3.853A pdb=" N ALA f 133 " --> pdb=" O TYR f 140 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR f 140 " --> pdb=" O ALA f 133 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 4 through 11 removed outlier: 5.941A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA g 300 " --> pdb=" O ARG g 308 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP g 310 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU g 298 " --> pdb=" O TRP g 310 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE g 299 " --> pdb=" O LEU g 289 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU g 289 " --> pdb=" O PHE g 299 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY g 301 " --> pdb=" O THR g 287 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 18 through 22 removed outlier: 3.692A pdb=" N THR g 19 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER g 33 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE g 41 " --> pdb=" O SER g 33 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 70 through 71 Processing sheet with id=AG8, first strand: chain 'g' and resid 88 through 91 removed outlier: 7.301A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 108 through 110 removed outlier: 4.011A pdb=" N SER g 110 " --> pdb=" O GLY g 123 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY g 123 " --> pdb=" O SER g 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'g' and resid 129 through 130 Processing sheet with id=AH2, first strand: chain 'g' and resid 154 through 156 Processing sheet with id=AH3, first strand: chain 'g' and resid 173 through 177 removed outlier: 7.142A pdb=" N VAL g 174 " --> pdb=" O ASN g 187 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASN g 187 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS g 185 " --> pdb=" O VAL g 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'g' and resid 206 through 207 removed outlier: 4.005A pdb=" N CYS g 207 " --> pdb=" O TRP g 219 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP g 219 " --> pdb=" O CYS g 207 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'g' and resid 238 through 239 removed outlier: 4.074A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA g 251 " --> pdb=" O ALA g 238 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA g 250 " --> pdb=" O LYS g 257 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS g 257 " --> pdb=" O ALA g 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'x' and resid 78 through 79 removed outlier: 4.082A pdb=" N ASN x 115 " --> pdb=" O ASN x 110 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN x 110 " --> pdb=" O ASN x 115 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'x' and resid 202 through 204 removed outlier: 3.876A pdb=" N VAL x 203 " --> pdb=" O HIS x 210 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS x 210 " --> pdb=" O VAL x 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'y' and resid 8 through 9 removed outlier: 6.948A pdb=" N VAL y 8 " --> pdb=" O LEU y 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'y' and resid 28 through 29 removed outlier: 3.637A pdb=" N THR y 29 " --> pdb=" O ARG y 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'y' and resid 264 through 269 removed outlier: 3.822A pdb=" N SER y 265 " --> pdb=" O VAL y 298 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL y 298 " --> pdb=" O SER y 265 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE y 267 " --> pdb=" O VAL y 296 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL y 296 " --> pdb=" O ILE y 267 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG y 269 " --> pdb=" O LYS y 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS y 294 " --> pdb=" O ARG y 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 250 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1302 hydrogen bonds 2050 hydrogen bond angles 0 basepair planarities 525 basepair parallelities 885 stacking parallelities Total time for adding SS restraints: 48.45 Time building geometry restraints manager: 33.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 9754 1.32 - 1.45: 31287 1.45 - 1.57: 37452 1.57 - 1.70: 3298 1.70 - 1.83: 284 Bond restraints: 82075 Sorted by residual: bond pdb=" C ALA A 96 " pdb=" N THR A 97 " ideal model delta sigma weight residual 1.327 1.280 0.048 1.32e-02 5.74e+03 1.30e+01 bond pdb=" C THR Y 50 " pdb=" N THR Y 51 " ideal model delta sigma weight residual 1.333 1.252 0.081 2.74e-02 1.33e+03 8.74e+00 bond pdb=" CG ARG L 101 " pdb=" CD ARG L 101 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.97e+00 bond pdb=" C LEU y 49 " pdb=" N PRO y 50 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.41e+00 bond pdb=" CG LEU N 117 " pdb=" CD2 LEU N 117 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.98e+00 ... (remaining 82070 not shown) Histogram of bond angle deviations from ideal: 96.50 - 104.69: 7836 104.69 - 112.88: 47049 112.88 - 121.07: 40821 121.07 - 129.26: 21511 129.26 - 137.45: 1500 Bond angle restraints: 118717 Sorted by residual: angle pdb=" N LYS R 44 " pdb=" CA LYS R 44 " pdb=" C LYS R 44 " ideal model delta sigma weight residual 111.33 124.72 -13.39 1.21e+00 6.83e-01 1.22e+02 angle pdb=" N GLY Y 119 " pdb=" CA GLY Y 119 " pdb=" C GLY Y 119 " ideal model delta sigma weight residual 112.73 122.54 -9.81 1.20e+00 6.94e-01 6.68e+01 angle pdb=" C ARG R 60 " pdb=" N ILE R 61 " pdb=" CA ILE R 61 " ideal model delta sigma weight residual 120.46 131.42 -10.96 1.37e+00 5.33e-01 6.40e+01 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 134.26 -12.72 1.91e+00 2.74e-01 4.44e+01 angle pdb=" C ARG A 184 " pdb=" N MET A 185 " pdb=" CA MET A 185 " ideal model delta sigma weight residual 120.28 128.85 -8.57 1.34e+00 5.57e-01 4.09e+01 ... (remaining 118712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 47434 35.97 - 71.94: 4185 71.94 - 107.91: 483 107.91 - 143.88: 26 143.88 - 179.85: 36 Dihedral angle restraints: 52164 sinusoidal: 37082 harmonic: 15082 Sorted by residual: 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 -133.43 -46.57 0 5.00e+00 4.00e-02 8.67e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 15.63 -175.63 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 21551 " pdb=" C1' U 21551 " pdb=" N1 U 21551 " pdb=" C2 U 21551 " ideal model delta sinusoidal sigma weight residual -160.00 14.94 -174.94 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 52161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 14044 0.129 - 0.259: 550 0.259 - 0.388: 39 0.388 - 0.518: 4 0.518 - 0.647: 1 Chirality restraints: 14638 Sorted by residual: 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 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CB ILE x 225 " pdb=" CA ILE x 225 " pdb=" CG1 ILE x 225 " pdb=" CG2 ILE x 225 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE x 107 " pdb=" CA ILE x 107 " pdb=" CG1 ILE x 107 " pdb=" CG2 ILE x 107 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 14635 not shown) Planarity restraints: 8911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 601 " 0.050 2.00e-02 2.50e+03 2.59e-02 2.01e+01 pdb=" N9 G 2 601 " -0.042 2.00e-02 2.50e+03 pdb=" C8 G 2 601 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G 2 601 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G 2 601 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 601 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G 2 601 " 0.032 2.00e-02 2.50e+03 pdb=" N1 G 2 601 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 2 601 " -0.045 2.00e-02 2.50e+03 pdb=" N2 G 2 601 " 0.022 2.00e-02 2.50e+03 pdb=" N3 G 2 601 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G 2 601 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 162 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO D 163 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 21853 " -0.028 2.00e-02 2.50e+03 2.80e-02 1.77e+01 pdb=" N1 C 21853 " 0.019 2.00e-02 2.50e+03 pdb=" C2 C 21853 " 0.064 2.00e-02 2.50e+03 pdb=" O2 C 21853 " -0.030 2.00e-02 2.50e+03 pdb=" N3 C 21853 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C 21853 " 0.015 2.00e-02 2.50e+03 pdb=" N4 C 21853 " -0.022 2.00e-02 2.50e+03 pdb=" C5 C 21853 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C 21853 " -0.003 2.00e-02 2.50e+03 ... (remaining 8908 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 395 2.44 - 3.05: 42383 3.05 - 3.67: 129579 3.67 - 4.28: 195098 4.28 - 4.90: 286231 Nonbonded interactions: 653686 Sorted by model distance: nonbonded pdb=" OP1 U 21867 " pdb=" N GLY y 393 " model vdw 1.824 2.520 nonbonded pdb=" CG1 VAL R 66 " pdb=" CG1 ILE R 69 " model vdw 1.859 3.860 nonbonded pdb=" O2' A 21869 " pdb=" NE2 HIS y 118 " model vdw 1.945 2.520 nonbonded pdb=" NZ LYS y 72 " pdb=" OE2 GLU y 106 " model vdw 2.039 2.520 nonbonded pdb=" N2 G 21606 " pdb=" N7 A 21633 " model vdw 2.127 2.600 ... (remaining 653681 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 12.560 Check model and map are aligned: 0.880 Set scattering table: 0.520 Process input model: 198.620 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.190 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.009 0.106 82075 Z= 0.546 Angle : 1.250 15.164 118717 Z= 0.654 Chirality : 0.061 0.647 14638 Planarity : 0.008 0.108 8911 Dihedral : 22.060 179.851 42432 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.11 % Favored : 89.75 % Rotamer: Outliers : 0.69 % Allowed : 3.58 % Favored : 95.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 1.42 % 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: -4.49 (0.09), residues: 5172 helix: -4.93 (0.08), residues: 842 sheet: -3.77 (0.18), residues: 556 loop : -2.56 (0.09), residues: 3774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP K 64 HIS 0.015 0.003 HIS L 106 PHE 0.045 0.005 PHE C 236 TYR 0.044 0.004 TYR y 366 ARG 0.022 0.002 ARG O 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1341 time to evaluate : 4.499 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: 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 34 MET cc_start: 0.7026 (mmm) cc_final: 0.5718 (mmm) REVERT: A 99 ILE cc_start: 0.8017 (mt) cc_final: 0.7599 (mt) REVERT: A 130 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6871 (p0) REVERT: B 48 LEU cc_start: 0.6879 (tp) cc_final: 0.6630 (tp) REVERT: B 88 THR cc_start: 0.5975 (t) cc_final: 0.5674 (p) REVERT: C 104 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.6125 (p0) REVERT: J 115 PHE cc_start: 0.6924 (t80) cc_final: 0.6723 (t80) REVERT: L 27 GLU cc_start: 0.3680 (tt0) cc_final: 0.2241 (mm-30) REVERT: M 99 LYS cc_start: 0.8014 (mttt) cc_final: 0.7777 (tmtt) REVERT: M 132 LYS cc_start: 0.2166 (mttt) cc_final: 0.1331 (mtpt) REVERT: O 67 ASP cc_start: 0.6857 (m-30) cc_final: 0.6149 (m-30) REVERT: O 90 ILE cc_start: 0.8075 (mp) cc_final: 0.7860 (mt) REVERT: P 53 GLN cc_start: 0.7131 (mt0) cc_final: 0.6647 (mt0) REVERT: P 96 VAL cc_start: 0.7983 (t) cc_final: 0.7745 (p) REVERT: Q 53 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6385 (mt-10) REVERT: R 58 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7355 (mmm) REVERT: V 66 ASP cc_start: 0.5701 (t0) cc_final: 0.5271 (t0) REVERT: W 4 MET cc_start: 0.8639 (mpp) cc_final: 0.8417 (mpp) REVERT: W 5 ASN cc_start: 0.7941 (t0) cc_final: 0.7693 (t0) REVERT: d 41 GLN cc_start: 0.6303 (mp10) cc_final: 0.6076 (mp10) REVERT: f 94 LYS cc_start: 0.5668 (pttt) cc_final: 0.4811 (mmtt) REVERT: y 241 MET cc_start: 0.6556 (mmm) cc_final: 0.6188 (mmm) outliers start: 31 outliers final: 9 residues processed: 1363 average time/residue: 0.8195 time to fit residues: 1812.9603 Evaluate side-chains 750 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 738 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 227 ASN Chi-restraints excluded: chain y residue 400 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 569 optimal weight: 9.9990 chunk 511 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 345 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 529 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 321 optimal weight: 0.4980 chunk 393 optimal weight: 6.9990 chunk 612 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 113 GLN A 131 HIS A 141 ASN B 92 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS D 57 ASN D 101 GLN E 8 HIS E 17 HIS E 50 ASN F 36 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 225 GLN H 25 GLN H 68 GLN H 76 GLN H 97 GLN H 165 ASN I 87 ASN I 99 ASN I 111 GLN ** I 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN K 28 HIS K 32 HIS K 77 GLN L 65 ASN N 58 HIS N 69 ASN N 105 ASN N 123 HIS O 26 ASN P 41 GLN P 46 ASN P 53 GLN P 54 HIS P 79 HIS ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 ASN ** S 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS S 120 HIS ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS U 92 HIS U 100 GLN V 47 ASN X 31 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 HIS Y 112 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 HIS d 26 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS g 76 GLN g 311 GLN x 102 HIS x 106 GLN ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS y 307 HIS y 344 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 82075 Z= 0.175 Angle : 0.697 12.963 118717 Z= 0.355 Chirality : 0.040 0.315 14638 Planarity : 0.005 0.069 8911 Dihedral : 24.252 177.849 31685 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.41 % Allowed : 12.28 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.95 (0.10), residues: 5172 helix: -4.59 (0.08), residues: 993 sheet: -2.95 (0.19), residues: 628 loop : -2.05 (0.09), residues: 3551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP S 127 HIS 0.014 0.001 HIS y 129 PHE 0.022 0.002 PHE T 14 TYR 0.043 0.002 TYR P 37 ARG 0.010 0.001 ARG y 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 918 time to evaluate : 4.496 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.8184 (m) cc_final: 0.7750 (p) REVERT: A 113 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5359 (mm-40) REVERT: A 130 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7023 (p0) REVERT: C 269 PHE cc_start: 0.7454 (m-80) cc_final: 0.7112 (m-80) REVERT: E 172 PHE cc_start: 0.6791 (p90) cc_final: 0.6397 (p90) REVERT: F 81 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7704 (ptt180) REVERT: I 95 THR cc_start: 0.7780 (m) cc_final: 0.7554 (p) REVERT: K 24 LYS cc_start: 0.6936 (mtpt) cc_final: 0.6409 (mtmt) REVERT: L 102 PHE cc_start: 0.8454 (m-80) cc_final: 0.8235 (m-80) REVERT: M 19 GLN cc_start: 0.5271 (pt0) cc_final: 0.4086 (tp40) REVERT: M 132 LYS cc_start: 0.2086 (mttt) cc_final: 0.1234 (mtpt) REVERT: O 106 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5820 (mptt) REVERT: P 53 GLN cc_start: 0.7177 (mt0) cc_final: 0.6877 (mt0) REVERT: Q 41 MET cc_start: 0.6461 (mmt) cc_final: 0.5907 (mmt) REVERT: V 66 ASP cc_start: 0.5492 (t0) cc_final: 0.5265 (t0) REVERT: W 5 ASN cc_start: 0.7544 (t0) cc_final: 0.7296 (t0) REVERT: W 115 GLU cc_start: 0.6280 (tp30) cc_final: 0.5826 (tp30) REVERT: b 35 VAL cc_start: 0.7532 (p) cc_final: 0.7153 (p) REVERT: f 94 LYS cc_start: 0.5466 (pttt) cc_final: 0.4822 (mptt) outliers start: 154 outliers final: 66 residues processed: 1006 average time/residue: 0.8357 time to fit residues: 1433.0278 Evaluate side-chains 810 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 740 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 24 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 68 SER 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 106 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 13 MET Chi-restraints excluded: chain Y residue 114 MET Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain d residue 53 ILE Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 195 GLU Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 374 VAL Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain z residue 547 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 340 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 510 optimal weight: 0.5980 chunk 417 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 614 optimal weight: 0.0370 chunk 663 optimal weight: 20.0000 chunk 546 optimal weight: 0.0170 chunk 608 optimal weight: 0.0010 chunk 209 optimal weight: 5.9990 chunk 492 optimal weight: 20.0000 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN I 111 GLN I 116 HIS J 140 GLN S 10 GLN ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN X 31 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 ASN Y 106 GLN Z 64 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 GLN g 20 GLN g 188 HIS x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS y 290 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 82075 Z= 0.138 Angle : 0.631 10.589 118717 Z= 0.319 Chirality : 0.038 0.300 14638 Planarity : 0.004 0.063 8911 Dihedral : 24.035 178.782 31667 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.36 % Allowed : 14.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.52 (0.10), residues: 5172 helix: -4.18 (0.10), residues: 1015 sheet: -2.74 (0.18), residues: 671 loop : -1.72 (0.10), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP g 170 HIS 0.008 0.001 HIS P 54 PHE 0.037 0.001 PHE A 32 TYR 0.024 0.001 TYR y 366 ARG 0.009 0.000 ARG F 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 846 time to evaluate : 4.588 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: A 28 THR cc_start: 0.8087 (m) cc_final: 0.7598 (p) REVERT: A 130 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7105 (p0) REVERT: A 206 ASP cc_start: 0.7053 (t0) cc_final: 0.6762 (t0) REVERT: C 123 ARG cc_start: 0.5427 (ptm160) cc_final: 0.5161 (ptm160) REVERT: C 187 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.7086 (tpp80) REVERT: C 269 PHE cc_start: 0.7535 (m-80) cc_final: 0.7084 (m-80) REVERT: F 81 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7891 (ptt180) REVERT: K 3 MET cc_start: 0.1454 (pmm) cc_final: 0.1209 (pmm) REVERT: K 24 LYS cc_start: 0.6810 (mtpt) cc_final: 0.6315 (mtmt) REVERT: K 71 LEU cc_start: 0.3712 (OUTLIER) cc_final: 0.3330 (pt) REVERT: K 84 HIS cc_start: 0.4054 (m-70) cc_final: 0.3691 (m-70) REVERT: L 76 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8710 (m) REVERT: M 19 GLN cc_start: 0.4914 (pt0) cc_final: 0.4062 (tp40) REVERT: M 132 LYS cc_start: 0.1968 (mttt) cc_final: 0.1130 (mtpt) REVERT: N 103 GLU cc_start: 0.5465 (pm20) cc_final: 0.4947 (pm20) REVERT: O 106 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5820 (mptt) REVERT: R 74 GLN cc_start: 0.5228 (mm-40) cc_final: 0.4109 (pp30) REVERT: f 94 LYS cc_start: 0.5538 (pttt) cc_final: 0.4908 (mmtt) REVERT: g 145 GLU cc_start: 0.6695 (tp30) cc_final: 0.5549 (mt-10) REVERT: g 236 ILE cc_start: 0.6343 (mt) cc_final: 0.6132 (mm) outliers start: 152 outliers final: 80 residues processed: 939 average time/residue: 0.7475 time to fit residues: 1190.9744 Evaluate side-chains 776 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 691 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 24 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 GLN Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 42 VAL 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 X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 195 GLU Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain z residue 547 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 606 optimal weight: 9.9990 chunk 461 optimal weight: 0.0070 chunk 318 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 616 optimal weight: 0.0770 chunk 652 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 584 optimal weight: 0.1980 chunk 175 optimal weight: 6.9990 overall best weight: 2.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 159 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 HIS I 111 GLN N 69 ASN O 38 ASN ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 217 ASN y 92 GLN y 271 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 82075 Z= 0.177 Angle : 0.620 9.859 118717 Z= 0.313 Chirality : 0.038 0.293 14638 Planarity : 0.004 0.066 8911 Dihedral : 23.950 178.010 31667 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.81 % Allowed : 15.16 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.23 (0.11), residues: 5172 helix: -3.76 (0.11), residues: 1065 sheet: -2.44 (0.18), residues: 711 loop : -1.55 (0.10), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP g 170 HIS 0.008 0.001 HIS P 54 PHE 0.034 0.001 PHE A 32 TYR 0.032 0.001 TYR P 37 ARG 0.008 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 739 time to evaluate : 4.619 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: A 130 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7022 (p0) REVERT: D 166 TYR cc_start: 0.6423 (p90) cc_final: 0.6169 (p90) REVERT: F 88 MET cc_start: 0.7148 (tpt) cc_final: 0.6840 (tpt) REVERT: I 161 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7795 (tp) REVERT: K 24 LYS cc_start: 0.6883 (mtpt) cc_final: 0.6302 (mtmt) REVERT: L 76 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8659 (m) REVERT: M 19 GLN cc_start: 0.5050 (pt0) cc_final: 0.4081 (tp-100) REVERT: M 132 LYS cc_start: 0.1875 (mttt) cc_final: 0.1095 (mtpt) REVERT: O 106 LYS cc_start: 0.6340 (OUTLIER) cc_final: 0.5922 (mptt) REVERT: Z 111 ARG cc_start: 0.5734 (mtp-110) cc_final: 0.5361 (mtp-110) REVERT: f 94 LYS cc_start: 0.5531 (pttt) cc_final: 0.4830 (mptt) REVERT: g 30 MET cc_start: 0.5750 (tmm) cc_final: 0.5537 (tmm) REVERT: g 145 GLU cc_start: 0.6821 (tp30) cc_final: 0.5807 (mt-10) REVERT: g 236 ILE cc_start: 0.6503 (mt) cc_final: 0.6282 (mm) outliers start: 172 outliers final: 108 residues processed: 851 average time/residue: 0.7353 time to fit residues: 1077.2997 Evaluate side-chains 784 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 672 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 24 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 88 TRP Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 195 GLU Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 238 ASP Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Chi-restraints excluded: chain z residue 547 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 543 optimal weight: 2.9990 chunk 370 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 485 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 556 optimal weight: 6.9990 chunk 451 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 585 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN I 88 ASN I 111 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 GLN S 97 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 82075 Z= 0.168 Angle : 0.607 11.269 118717 Z= 0.306 Chirality : 0.037 0.285 14638 Planarity : 0.004 0.078 8911 Dihedral : 23.899 177.948 31665 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.87 % Allowed : 15.51 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.89 (0.11), residues: 5172 helix: -3.37 (0.12), residues: 1090 sheet: -2.17 (0.18), residues: 755 loop : -1.33 (0.11), residues: 3327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP g 170 HIS 0.008 0.001 HIS P 54 PHE 0.033 0.001 PHE A 32 TYR 0.024 0.001 TYR g 194 ARG 0.014 0.000 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 724 time to evaluate : 4.773 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: C 73 MET cc_start: 0.6035 (mmm) cc_final: 0.5405 (ttm) REVERT: C 80 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: C 215 MET cc_start: 0.5895 (mmm) cc_final: 0.5588 (mmm) REVERT: D 166 TYR cc_start: 0.6445 (p90) cc_final: 0.6217 (p90) REVERT: F 88 MET cc_start: 0.7090 (tpt) cc_final: 0.6828 (tpt) REVERT: I 62 VAL cc_start: 0.8089 (t) cc_final: 0.7830 (m) REVERT: J 156 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6398 (p-80) REVERT: K 3 MET cc_start: 0.1817 (pmm) cc_final: 0.1522 (pmm) REVERT: K 24 LYS cc_start: 0.6827 (mtpt) cc_final: 0.6298 (mtmt) REVERT: K 84 HIS cc_start: 0.4333 (m-70) cc_final: 0.4017 (m-70) REVERT: L 76 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (m) REVERT: M 19 GLN cc_start: 0.5022 (pt0) cc_final: 0.4050 (tp40) REVERT: M 132 LYS cc_start: 0.1895 (mttt) cc_final: 0.1187 (mtpt) REVERT: P 76 VAL cc_start: 0.3717 (OUTLIER) cc_final: 0.3505 (m) REVERT: R 58 MET cc_start: 0.7431 (tpp) cc_final: 0.7196 (tpp) REVERT: T 112 MET cc_start: 0.6556 (mmp) cc_final: 0.6338 (mmt) REVERT: c 59 LEU cc_start: 0.4567 (mm) cc_final: 0.4178 (mm) REVERT: e 44 ASN cc_start: 0.5952 (p0) cc_final: 0.5587 (p0) REVERT: f 94 LYS cc_start: 0.5538 (pttt) cc_final: 0.4896 (mptt) REVERT: g 145 GLU cc_start: 0.6878 (tp30) cc_final: 0.6013 (mt-10) outliers start: 175 outliers final: 135 residues processed: 842 average time/residue: 0.7040 time to fit residues: 1023.2131 Evaluate side-chains 803 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 664 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 24 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 GLN Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 112 ASN Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 203 VAL Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Chi-restraints excluded: chain z residue 547 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 219 optimal weight: 8.9990 chunk 587 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 chunk 161 optimal weight: 40.0000 chunk 653 optimal weight: 0.6980 chunk 542 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN I 111 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN Q 29 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 213 ASN y 271 HIS z 548 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 82075 Z= 0.233 Angle : 0.644 11.114 118717 Z= 0.324 Chirality : 0.038 0.290 14638 Planarity : 0.005 0.080 8911 Dihedral : 23.920 179.127 31665 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.05 % Allowed : 16.13 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: -2.66 (0.11), residues: 5172 helix: -2.70 (0.13), residues: 1154 sheet: -2.09 (0.17), residues: 812 loop : -1.28 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 192 HIS 0.011 0.001 HIS S 11 PHE 0.031 0.002 PHE A 32 TYR 0.025 0.002 TYR R 20 ARG 0.012 0.001 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 700 time to evaluate : 4.518 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: A 6 ASP cc_start: 0.6537 (t0) cc_final: 0.6324 (t0) REVERT: C 73 MET cc_start: 0.6040 (mmm) cc_final: 0.5481 (ttm) REVERT: C 80 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: D 166 TYR cc_start: 0.6706 (p90) cc_final: 0.6490 (p90) REVERT: F 88 MET cc_start: 0.7274 (tpt) cc_final: 0.7018 (tpt) REVERT: F 176 GLU cc_start: 0.5696 (mm-30) cc_final: 0.5307 (mt-10) REVERT: J 156 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6582 (p-80) REVERT: K 24 LYS cc_start: 0.6900 (mtpt) cc_final: 0.6354 (mtmt) REVERT: L 15 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7676 (t) REVERT: M 19 GLN cc_start: 0.5183 (pt0) cc_final: 0.3915 (tp40) REVERT: M 132 LYS cc_start: 0.1785 (mttt) cc_final: 0.1043 (mtpt) REVERT: P 37 TYR cc_start: 0.5263 (m-80) cc_final: 0.4948 (m-80) REVERT: V 66 ASP cc_start: 0.6225 (t0) cc_final: 0.5884 (t0) REVERT: W 51 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7617 (tp30) REVERT: Z 111 ARG cc_start: 0.5779 (mtp-110) cc_final: 0.5326 (mtp-110) REVERT: c 59 LEU cc_start: 0.4483 (mm) cc_final: 0.4086 (mm) REVERT: e 44 ASN cc_start: 0.5946 (p0) cc_final: 0.5652 (p0) REVERT: f 94 LYS cc_start: 0.5655 (pttt) cc_final: 0.4986 (mptt) REVERT: g 100 ARG cc_start: 0.6741 (mmm-85) cc_final: 0.6325 (mmm-85) REVERT: g 145 GLU cc_start: 0.6982 (tp30) cc_final: 0.6054 (mt-10) REVERT: g 217 MET cc_start: 0.4271 (tmm) cc_final: 0.3807 (tmm) outliers start: 183 outliers final: 142 residues processed: 815 average time/residue: 0.7137 time to fit residues: 1003.8899 Evaluate side-chains 811 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 666 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 24 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 93 MET Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 153 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 195 GLU Chi-restraints excluded: chain x residue 203 VAL Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 238 ASP Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 629 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 372 optimal weight: 1.9990 chunk 476 optimal weight: 0.3980 chunk 369 optimal weight: 3.9990 chunk 549 optimal weight: 7.9990 chunk 364 optimal weight: 0.8980 chunk 650 optimal weight: 0.9980 chunk 407 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 118 GLN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 213 ASN y 271 HIS z 548 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 82075 Z= 0.151 Angle : 0.598 9.826 118717 Z= 0.301 Chirality : 0.037 0.280 14638 Planarity : 0.004 0.060 8911 Dihedral : 23.857 178.844 31665 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.58 % Allowed : 17.33 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.11), residues: 5172 helix: -2.38 (0.13), residues: 1177 sheet: -1.99 (0.17), residues: 821 loop : -1.17 (0.11), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 192 HIS 0.009 0.001 HIS J 156 PHE 0.030 0.001 PHE J 115 TYR 0.036 0.001 TYR P 37 ARG 0.009 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 699 time to evaluate : 4.514 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: A 6 ASP cc_start: 0.6581 (t0) cc_final: 0.6360 (t0) REVERT: C 73 MET cc_start: 0.5954 (mmm) cc_final: 0.5397 (ttm) REVERT: C 80 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6756 (tt0) REVERT: D 166 TYR cc_start: 0.6552 (p90) cc_final: 0.6317 (p90) REVERT: E 114 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8213 (mt) REVERT: F 88 MET cc_start: 0.7195 (tpt) cc_final: 0.6895 (tpt) REVERT: F 176 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5590 (mt-10) REVERT: I 62 VAL cc_start: 0.8208 (t) cc_final: 0.7999 (m) REVERT: J 156 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6438 (p-80) REVERT: K 3 MET cc_start: 0.2315 (pmm) cc_final: 0.2008 (pmm) REVERT: K 24 LYS cc_start: 0.6842 (mtpt) cc_final: 0.6545 (mtmt) REVERT: M 132 LYS cc_start: 0.1738 (mttt) cc_final: 0.0998 (mtpt) REVERT: U 56 MET cc_start: 0.6095 (mmm) cc_final: 0.5722 (mmm) REVERT: Z 111 ARG cc_start: 0.5661 (mtp-110) cc_final: 0.5248 (mtp-110) REVERT: c 59 LEU cc_start: 0.4423 (mm) cc_final: 0.4065 (mm) REVERT: e 44 ASN cc_start: 0.5857 (p0) cc_final: 0.5325 (p0) REVERT: f 94 LYS cc_start: 0.5595 (pttt) cc_final: 0.4970 (mptt) REVERT: f 116 ARG cc_start: 0.2349 (mmt90) cc_final: 0.1680 (mtp180) REVERT: g 145 GLU cc_start: 0.6956 (tp30) cc_final: 0.6090 (mt-10) REVERT: g 217 MET cc_start: 0.4291 (tmm) cc_final: 0.3854 (tmm) outliers start: 162 outliers final: 130 residues processed: 804 average time/residue: 0.7418 time to fit residues: 1032.6481 Evaluate side-chains 785 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 652 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 238 ASP Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 402 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 388 optimal weight: 0.6980 chunk 195 optimal weight: 0.3980 chunk 127 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 413 optimal weight: 0.8980 chunk 443 optimal weight: 7.9990 chunk 321 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 511 optimal weight: 7.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 82075 Z= 0.183 Angle : 0.606 10.542 118717 Z= 0.304 Chirality : 0.037 0.278 14638 Planarity : 0.004 0.061 8911 Dihedral : 23.816 179.232 31663 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.76 % Allowed : 17.19 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.11), residues: 5172 helix: -2.08 (0.14), residues: 1198 sheet: -1.91 (0.18), residues: 822 loop : -1.16 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 192 HIS 0.009 0.001 HIS J 156 PHE 0.023 0.001 PHE A 32 TYR 0.032 0.001 TYR P 37 ARG 0.007 0.000 ARG b 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 679 time to evaluate : 4.593 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: C 73 MET cc_start: 0.5854 (mmm) cc_final: 0.5329 (ttm) REVERT: C 80 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: D 166 TYR cc_start: 0.6609 (p90) cc_final: 0.6370 (p90) REVERT: F 88 MET cc_start: 0.7241 (tpt) cc_final: 0.6967 (tpt) REVERT: F 137 GLN cc_start: 0.2263 (tm-30) cc_final: 0.2056 (tm-30) REVERT: F 176 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5766 (mt-10) REVERT: G 91 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6139 (pp20) REVERT: J 156 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6486 (p-80) REVERT: K 3 MET cc_start: 0.2625 (pmm) cc_final: 0.2259 (pmm) REVERT: K 24 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6554 (mtmt) REVERT: L 130 GLU cc_start: 0.5815 (tt0) cc_final: 0.5594 (tt0) REVERT: M 132 LYS cc_start: 0.1670 (mttt) cc_final: 0.1030 (mtpt) REVERT: V 66 ASP cc_start: 0.6224 (t0) cc_final: 0.6009 (t0) REVERT: Z 111 ARG cc_start: 0.5730 (mtp-110) cc_final: 0.5474 (mtp-110) REVERT: c 59 LEU cc_start: 0.4449 (mm) cc_final: 0.4084 (mm) REVERT: e 44 ASN cc_start: 0.5868 (p0) cc_final: 0.5544 (p0) REVERT: f 94 LYS cc_start: 0.5690 (pttt) cc_final: 0.5035 (mptt) REVERT: g 145 GLU cc_start: 0.6936 (tp30) cc_final: 0.6101 (mt-10) REVERT: g 217 MET cc_start: 0.4277 (tmm) cc_final: 0.3859 (tmm) outliers start: 170 outliers final: 139 residues processed: 788 average time/residue: 0.7244 time to fit residues: 982.8587 Evaluate side-chains 796 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 654 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 93 MET Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 83 PHE Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 238 ASP Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 591 optimal weight: 0.5980 chunk 623 optimal weight: 6.9990 chunk 568 optimal weight: 7.9990 chunk 606 optimal weight: 0.9980 chunk 364 optimal weight: 0.6980 chunk 264 optimal weight: 0.0980 chunk 476 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 547 optimal weight: 1.9990 chunk 573 optimal weight: 6.9990 chunk 604 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 HIS ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 HIS g 196 ASN x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 82075 Z= 0.135 Angle : 0.589 11.502 118717 Z= 0.294 Chirality : 0.036 0.278 14638 Planarity : 0.004 0.061 8911 Dihedral : 23.729 179.430 31663 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.83 % Allowed : 18.52 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 5172 helix: -1.77 (0.14), residues: 1200 sheet: -1.75 (0.18), residues: 832 loop : -1.09 (0.11), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 192 HIS 0.008 0.001 HIS J 156 PHE 0.036 0.001 PHE J 115 TYR 0.026 0.001 TYR P 37 ARG 0.009 0.000 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 706 time to evaluate : 4.653 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: C 73 MET cc_start: 0.5935 (mmm) cc_final: 0.5466 (ttm) REVERT: C 80 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: D 166 TYR cc_start: 0.6353 (p90) cc_final: 0.6107 (p90) REVERT: E 114 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8255 (mt) REVERT: F 77 MET cc_start: 0.6060 (ptp) cc_final: 0.5841 (ptp) REVERT: F 88 MET cc_start: 0.7279 (tpt) cc_final: 0.7056 (tpt) REVERT: F 137 GLN cc_start: 0.2339 (tm-30) cc_final: 0.1974 (tm-30) REVERT: G 63 MET cc_start: 0.6342 (ppp) cc_final: 0.5850 (ptt) REVERT: G 91 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6077 (pp20) REVERT: J 156 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6551 (p-80) REVERT: K 3 MET cc_start: 0.2601 (pmm) cc_final: 0.2235 (pmm) REVERT: K 24 LYS cc_start: 0.6754 (mtpt) cc_final: 0.6436 (mtmt) REVERT: L 130 GLU cc_start: 0.5725 (tt0) cc_final: 0.5509 (tt0) REVERT: M 132 LYS cc_start: 0.1636 (mttt) cc_final: 0.0969 (mtpt) REVERT: N 86 GLU cc_start: 0.6639 (pp20) cc_final: 0.6364 (pp20) REVERT: O 124 MET cc_start: 0.6086 (mmm) cc_final: 0.5809 (tpt) REVERT: V 66 ASP cc_start: 0.6196 (t0) cc_final: 0.5934 (t0) REVERT: X 95 GLU cc_start: 0.7371 (pt0) cc_final: 0.7113 (mt-10) REVERT: c 35 MET cc_start: 0.5853 (ptp) cc_final: 0.5645 (ptp) REVERT: c 47 LYS cc_start: 0.6197 (mttt) cc_final: 0.5798 (mptt) REVERT: c 59 LEU cc_start: 0.4531 (mm) cc_final: 0.4210 (mm) REVERT: d 36 LEU cc_start: 0.7673 (mm) cc_final: 0.7460 (mt) REVERT: e 44 ASN cc_start: 0.5824 (p0) cc_final: 0.5360 (p0) REVERT: f 94 LYS cc_start: 0.5551 (pttt) cc_final: 0.4919 (mptt) REVERT: f 116 ARG cc_start: 0.2351 (mmt90) cc_final: 0.1684 (mtp180) REVERT: g 145 GLU cc_start: 0.6915 (tp30) cc_final: 0.6028 (mt-10) REVERT: g 217 MET cc_start: 0.4384 (tmm) cc_final: 0.3924 (tmm) outliers start: 128 outliers final: 103 residues processed: 795 average time/residue: 0.7302 time to fit residues: 996.1267 Evaluate side-chains 763 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 656 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 42 VAL 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 47 ILE Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 398 optimal weight: 0.0670 chunk 641 optimal weight: 0.0980 chunk 391 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 445 optimal weight: 0.9990 chunk 672 optimal weight: 20.0000 chunk 618 optimal weight: 6.9990 chunk 535 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 413 optimal weight: 2.9990 chunk 328 optimal weight: 0.9980 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 ASN x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 82075 Z= 0.140 Angle : 0.588 11.808 118717 Z= 0.292 Chirality : 0.036 0.272 14638 Planarity : 0.004 0.070 8911 Dihedral : 23.655 179.584 31663 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.37 % Allowed : 19.03 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.12), residues: 5172 helix: -1.56 (0.14), residues: 1200 sheet: -1.70 (0.18), residues: 825 loop : -1.04 (0.11), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 192 HIS 0.008 0.001 HIS C 272 PHE 0.022 0.001 PHE W 101 TYR 0.027 0.001 TYR P 37 ARG 0.010 0.000 ARG I 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 696 time to evaluate : 4.600 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: C 73 MET cc_start: 0.5860 (mmm) cc_final: 0.5304 (ttm) REVERT: C 80 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: D 166 TYR cc_start: 0.6287 (p90) cc_final: 0.6063 (p90) REVERT: F 88 MET cc_start: 0.7198 (tpt) cc_final: 0.6981 (tpt) REVERT: G 91 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6044 (pp20) REVERT: K 24 LYS cc_start: 0.6798 (mtpt) cc_final: 0.6429 (mtmt) REVERT: M 132 LYS cc_start: 0.1620 (mttt) cc_final: 0.0945 (mtpt) REVERT: N 86 GLU cc_start: 0.6618 (pp20) cc_final: 0.6321 (pp20) REVERT: P 28 MET cc_start: 0.4234 (mtp) cc_final: 0.3995 (mtt) REVERT: Z 111 ARG cc_start: 0.5547 (mtp180) cc_final: 0.5129 (mtp-110) REVERT: b 15 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6531 (mm-30) REVERT: c 59 LEU cc_start: 0.4430 (mm) cc_final: 0.4151 (mm) REVERT: e 44 ASN cc_start: 0.5890 (p0) cc_final: 0.5552 (p0) REVERT: f 94 LYS cc_start: 0.5506 (pttt) cc_final: 0.4900 (mptt) REVERT: f 116 ARG cc_start: 0.2305 (mmt90) cc_final: 0.1508 (mtp180) REVERT: g 145 GLU cc_start: 0.6881 (tp30) cc_final: 0.6047 (mt-10) REVERT: g 217 MET cc_start: 0.4494 (tmm) cc_final: 0.4059 (tmm) outliers start: 107 outliers final: 95 residues processed: 767 average time/residue: 0.7325 time to fit residues: 968.0745 Evaluate side-chains 748 residues out of total 4528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 651 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain U residue 22 ILE Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 112 ASN Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain y residue 61 GLU Chi-restraints excluded: chain y residue 242 GLN Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 425 optimal weight: 9.9990 chunk 570 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 493 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 536 optimal weight: 30.0000 chunk 224 optimal weight: 0.8980 chunk 550 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS ** x 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.085152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065597 restraints weight = 365034.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.067015 restraints weight = 157192.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067835 restraints weight = 100137.132| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 82075 Z= 0.213 Angle : 0.638 59.194 118717 Z= 0.331 Chirality : 0.038 0.935 14638 Planarity : 0.004 0.068 8911 Dihedral : 23.651 179.532 31663 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.30 % Allowed : 19.45 % Favored : 78.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 5172 helix: -1.55 (0.14), residues: 1204 sheet: -1.69 (0.18), residues: 827 loop : -1.06 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 67 HIS 0.011 0.001 HIS J 156 PHE 0.018 0.001 PHE W 101 TYR 0.030 0.001 TYR A 39 ARG 0.013 0.000 ARG I 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17626.14 seconds wall clock time: 312 minutes 4.13 seconds (18724.13 seconds total)