Starting phenix.real_space_refine on Tue Sep 24 09:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/09_2024/7lxt_23574.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/09_2024/7lxt_23574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/09_2024/7lxt_23574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/09_2024/7lxt_23574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/09_2024/7lxt_23574.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/09_2024/7lxt_23574.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 272 5.16 5 B 6 2.79 5 C 32182 2.51 5 N 8432 2.21 5 O 9644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 188 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50536 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2001 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1805 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "C" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1934 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "D" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1802 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "F" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1866 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1968 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "H" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1772 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 1, 'TRANS': 218} Chain breaks: 1 Chain: "I" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1664 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "J" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1698 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "K" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1647 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 1, 'TRANS': 207} Chain: "M" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1696 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "N" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1872 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "O" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2001 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain: "P" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1805 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "Q" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1934 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "R" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "S" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1802 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "T" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1866 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "U" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1968 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "V" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1772 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 1, 'TRANS': 218} Chain breaks: 1 Chain: "W" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1664 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "X" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1698 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "Y" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1647 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 1, 'TRANS': 207} Chain: "a" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1696 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "b" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1872 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.91, per 1000 atoms: 0.39 Number of scatterers: 50536 At special positions: 0 Unit cell: (179.47, 145.41, 136.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 272 16.00 O 9644 8.00 N 8432 7.00 C 32182 6.00 B 6 5.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.47 Conformation dependent library (CDL) restraints added in 4.7 seconds 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11856 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 76 sheets defined 37.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.732A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.658A pdb=" N SER A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 134 removed outlier: 3.609A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.646A pdb=" N ILE A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.810A pdb=" N THR A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.899A pdb=" N ILE A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 4.249A pdb=" N ASN A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.537A pdb=" N ARG B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.607A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.900A pdb=" N LYS B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.677A pdb=" N LYS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.641A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.793A pdb=" N LYS B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 229' Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.986A pdb=" N ASN C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 102 removed outlier: 3.878A pdb=" N LEU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.735A pdb=" N VAL C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.750A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 removed outlier: 3.935A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.958A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.697A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 99 removed outlier: 3.712A pdb=" N ARG D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 92 " --> pdb=" O ARG D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.670A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.805A pdb=" N VAL D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.947A pdb=" N ILE D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 234 removed outlier: 3.573A pdb=" N ILE D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 28 removed outlier: 3.699A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 81 through 103 removed outlier: 4.033A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.549A pdb=" N LEU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.609A pdb=" N LEU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.676A pdb=" N ILE E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.800A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 removed outlier: 3.506A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 122 removed outlier: 4.280A pdb=" N LYS F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.700A pdb=" N SER F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 174 " --> pdb=" O TYR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.529A pdb=" N SER F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 removed outlier: 4.578A pdb=" N GLU F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 Processing helix chain 'G' and resid 52 through 56 removed outlier: 4.080A pdb=" N ASP G 56 " --> pdb=" O SER G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 removed outlier: 3.737A pdb=" N ARG G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 125 removed outlier: 4.749A pdb=" N ASN G 116 " --> pdb=" O HIS G 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 180 removed outlier: 3.744A pdb=" N PHE G 175 " --> pdb=" O ASN G 171 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 204 removed outlier: 4.164A pdb=" N ASP G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 226 Processing helix chain 'G' and resid 233 through 241 removed outlier: 3.501A pdb=" N LEU G 237 " --> pdb=" O HIS G 233 " (cutoff:3.500A) Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 48 through 68 removed outlier: 3.520A pdb=" N LYS H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.849A pdb=" N ILE H 135 " --> pdb=" O ASN H 131 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 188 removed outlier: 3.630A pdb=" N TYR H 188 " --> pdb=" O GLY H 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 188' Processing helix chain 'H' and resid 189 through 197 Processing helix chain 'H' and resid 202 through 220 Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.722A pdb=" N GLU I 64 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.746A pdb=" N SER I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.520A pdb=" N VAL I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS I 141 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 165 removed outlier: 3.741A pdb=" N ASN I 153 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE I 164 " --> pdb=" O CYS I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 81 removed outlier: 3.656A pdb=" N GLN J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.982A pdb=" N TYR J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 removed outlier: 4.394A pdb=" N GLY J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET J 162 " --> pdb=" O GLN J 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 189 removed outlier: 4.263A pdb=" N GLU J 178 " --> pdb=" O ASN J 174 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER J 186 " --> pdb=" O GLN J 182 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA J 187 " --> pdb=" O CYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.878A pdb=" N GLN K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 92 removed outlier: 3.536A pdb=" N LYS K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.341A pdb=" N ALA K 141 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 removed outlier: 3.572A pdb=" N GLU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 70 removed outlier: 4.971A pdb=" N TRP L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'L' and resid 131 through 141 removed outlier: 3.662A pdb=" N SER L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.638A pdb=" N TYR L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS L 199 " --> pdb=" O ASP L 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 194 through 199' Processing helix chain 'M' and resid 85 through 108 removed outlier: 3.603A pdb=" N LEU M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 126 Processing helix chain 'M' and resid 169 through 178 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 194 through 213 removed outlier: 4.117A pdb=" N ASN M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR M 210 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU M 211 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 4.028A pdb=" N ALA N 61 " --> pdb=" O GLU N 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN N 62 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE N 73 " --> pdb=" O THR N 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU N 78 " --> pdb=" O ASN N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.776A pdb=" N MET N 85 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 105 removed outlier: 3.685A pdb=" N ARG N 97 " --> pdb=" O SER N 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG N 105 " --> pdb=" O VAL N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 193 removed outlier: 3.816A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 217 removed outlier: 4.049A pdb=" N ILE N 212 " --> pdb=" O GLU N 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE N 215 " --> pdb=" O ARG N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.731A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 72 Processing helix chain 'O' and resid 89 through 112 removed outlier: 3.657A pdb=" N SER O 105 " --> pdb=" O ARG O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 134 removed outlier: 3.609A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 195 removed outlier: 3.646A pdb=" N ILE O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER O 183 " --> pdb=" O GLN O 179 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU O 186 " --> pdb=" O ILE O 182 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU O 190 " --> pdb=" O GLU O 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG O 192 " --> pdb=" O LEU O 188 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 220 removed outlier: 3.809A pdb=" N THR O 218 " --> pdb=" O GLU O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.898A pdb=" N ILE O 229 " --> pdb=" O ALA O 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 254 removed outlier: 4.249A pdb=" N ASN O 251 " --> pdb=" O LYS O 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR O 252 " --> pdb=" O GLU O 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 30 removed outlier: 3.536A pdb=" N ARG P 28 " --> pdb=" O TYR P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.607A pdb=" N VAL P 85 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.901A pdb=" N LYS P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU P 120 " --> pdb=" O SER P 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 3.677A pdb=" N LYS P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 removed outlier: 3.642A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 199 Processing helix chain 'P' and resid 224 through 229 removed outlier: 3.794A pdb=" N LYS P 228 " --> pdb=" O GLN P 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP P 229 " --> pdb=" O ASN P 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 224 through 229' Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 79 through 84 removed outlier: 3.987A pdb=" N ASN Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 102 removed outlier: 3.876A pdb=" N LEU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 121 removed outlier: 3.735A pdb=" N VAL Q 112 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN Q 113 " --> pdb=" O GLN Q 109 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 3.749A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Q 178 " --> pdb=" O VAL Q 174 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP Q 179 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 200 removed outlier: 3.934A pdb=" N LEU Q 190 " --> pdb=" O GLU Q 186 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 242 removed outlier: 3.959A pdb=" N GLU Q 233 " --> pdb=" O GLU Q 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Q 237 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Q 240 " --> pdb=" O ILE Q 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 28 removed outlier: 3.696A pdb=" N ALA R 22 " --> pdb=" O GLN R 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.711A pdb=" N ARG R 81 " --> pdb=" O ASN R 77 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.670A pdb=" N THR R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 173 removed outlier: 3.805A pdb=" N VAL R 168 " --> pdb=" O ASN R 164 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE R 171 " --> pdb=" O ILE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 removed outlier: 3.946A pdb=" N ILE R 186 " --> pdb=" O GLN R 182 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 234 removed outlier: 3.573A pdb=" N ILE R 222 " --> pdb=" O GLU R 218 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 28 removed outlier: 3.698A pdb=" N GLU S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 33 Processing helix chain 'S' and resid 81 through 103 removed outlier: 4.034A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 3.547A pdb=" N LEU S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 187 removed outlier: 3.608A pdb=" N LEU S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 206 removed outlier: 3.676A pdb=" N ILE S 198 " --> pdb=" O GLU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 239 Processing helix chain 'S' and resid 240 through 243 Processing helix chain 'T' and resid 19 through 25 Processing helix chain 'T' and resid 28 through 32 Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.800A pdb=" N LEU T 84 " --> pdb=" O ASP T 80 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER T 94 " --> pdb=" O ASN T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 114 removed outlier: 3.507A pdb=" N SER T 111 " --> pdb=" O SER T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 122 removed outlier: 4.280A pdb=" N LYS T 122 " --> pdb=" O LYS T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 174 removed outlier: 3.699A pdb=" N SER T 167 " --> pdb=" O ARG T 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN T 174 " --> pdb=" O TYR T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 198 removed outlier: 3.529A pdb=" N SER T 197 " --> pdb=" O ALA T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 224 through 237 removed outlier: 4.579A pdb=" N GLU T 230 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR T 231 " --> pdb=" O GLN T 227 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER T 233 " --> pdb=" O GLU T 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS T 236 " --> pdb=" O LEU T 232 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET T 237 " --> pdb=" O SER T 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 32 Processing helix chain 'U' and resid 52 through 56 removed outlier: 4.081A pdb=" N ASP U 56 " --> pdb=" O SER U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 106 removed outlier: 3.736A pdb=" N ARG U 88 " --> pdb=" O ASP U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 125 removed outlier: 4.749A pdb=" N ASN U 116 " --> pdb=" O HIS U 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR U 121 " --> pdb=" O ARG U 117 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 180 removed outlier: 3.744A pdb=" N PHE U 175 " --> pdb=" O ASN U 171 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 204 removed outlier: 4.164A pdb=" N ASP U 195 " --> pdb=" O ASP U 191 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR U 202 " --> pdb=" O LYS U 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP U 204 " --> pdb=" O ILE U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 226 Processing helix chain 'U' and resid 233 through 241 removed outlier: 3.501A pdb=" N LEU U 237 " --> pdb=" O HIS U 233 " (cutoff:3.500A) Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 48 through 68 removed outlier: 3.520A pdb=" N LYS V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN V 68 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 144 removed outlier: 3.848A pdb=" N ILE V 135 " --> pdb=" O ASN V 131 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE V 140 " --> pdb=" O THR V 136 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR V 141 " --> pdb=" O LYS V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 188 removed outlier: 3.629A pdb=" N TYR V 188 " --> pdb=" O GLY V 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 185 through 188' Processing helix chain 'V' and resid 189 through 197 Processing helix chain 'V' and resid 202 through 220 Processing helix chain 'W' and resid 48 through 70 removed outlier: 3.723A pdb=" N GLU W 64 " --> pdb=" O GLN W 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.746A pdb=" N SER W 81 " --> pdb=" O SER W 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS W 89 " --> pdb=" O GLN W 85 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR W 90 " --> pdb=" O GLU W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.519A pdb=" N VAL W 137 " --> pdb=" O ASN W 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS W 141 " --> pdb=" O VAL W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 165 removed outlier: 3.742A pdb=" N ASN W 153 " --> pdb=" O GLU W 149 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE W 164 " --> pdb=" O CYS W 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 81 removed outlier: 3.657A pdb=" N GLN X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 100 removed outlier: 3.981A pdb=" N TYR X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 167 removed outlier: 4.395A pdb=" N GLY X 161 " --> pdb=" O GLU X 157 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET X 162 " --> pdb=" O GLN X 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 189 removed outlier: 4.263A pdb=" N GLU X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS X 183 " --> pdb=" O THR X 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER X 186 " --> pdb=" O GLN X 182 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA X 187 " --> pdb=" O CYS X 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 72 removed outlier: 3.878A pdb=" N GLN Y 56 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU Y 59 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 92 removed outlier: 3.536A pdb=" N LYS Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 5.341A pdb=" N ALA Y 141 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 removed outlier: 3.571A pdb=" N GLU Y 166 " --> pdb=" O LEU Y 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 removed outlier: 4.970A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 89 Processing helix chain 'Z' and resid 131 through 141 removed outlier: 3.661A pdb=" N SER Z 141 " --> pdb=" O SER Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 194 through 199 removed outlier: 3.638A pdb=" N TYR Z 198 " --> pdb=" O PHE Z 194 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS Z 199 " --> pdb=" O ASP Z 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 194 through 199' Processing helix chain 'a' and resid 85 through 108 removed outlier: 3.603A pdb=" N LEU a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 126 Processing helix chain 'a' and resid 169 through 178 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 194 through 213 removed outlier: 4.117A pdb=" N ASN a 200 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a 210 " --> pdb=" O ILE a 206 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG a 212 " --> pdb=" O SER a 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 4.029A pdb=" N ALA b 61 " --> pdb=" O GLU b 57 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN b 62 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU b 66 " --> pdb=" O GLN b 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU b 78 " --> pdb=" O ASN b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 85 removed outlier: 3.775A pdb=" N MET b 85 " --> pdb=" O LYS b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 105 removed outlier: 3.685A pdb=" N ARG b 97 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG b 105 " --> pdb=" O VAL b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 193 removed outlier: 3.816A pdb=" N LEU b 188 " --> pdb=" O PHE b 184 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP b 191 " --> pdb=" O THR b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 198 through 217 removed outlier: 4.050A pdb=" N ILE b 212 " --> pdb=" O GLU b 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE b 215 " --> pdb=" O ARG b 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.747A pdb=" N CYS A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 52 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.548A pdb=" N GLY A 148 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 78 removed outlier: 3.679A pdb=" N SER C 133 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AA9, first strand: chain 'D' and resid 132 through 136 removed outlier: 3.894A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 154 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB2, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'F' and resid 35 through 39 removed outlier: 5.552A pdb=" N GLY F 215 " --> pdb=" O PRO F 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.575A pdb=" N GLY F 131 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.565A pdb=" N LEU F 132 " --> pdb=" O THR F 146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 146 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 165 through 168 removed outlier: 3.580A pdb=" N THR G 36 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER G 219 " --> pdb=" O CYS G 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 70 through 72 removed outlier: 3.571A pdb=" N SER G 81 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER G 137 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 119 through 121 removed outlier: 4.030A pdb=" N PHE H 237 " --> pdb=" O THR H 234 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 239 " --> pdb=" O ASN H 232 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE H 3 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.795A pdb=" N THR H 20 " --> pdb=" O SER H 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 44 removed outlier: 3.521A pdb=" N GLN H 163 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 21 removed outlier: 6.776A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.610A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL I 99 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 176 through 177 removed outlier: 3.969A pdb=" N VAL I 177 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 212 through 217 removed outlier: 3.820A pdb=" N ILE I 212 " --> pdb=" O LYS J 212 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.145A pdb=" N VAL J 51 " --> pdb=" O MET J 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.502A pdb=" N GLY K 6 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR K 184 " --> pdb=" O LYS K 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 43 through 44 removed outlier: 4.026A pdb=" N CYS K 44 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA K 105 " --> pdb=" O CYS K 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'L' and resid 15 through 16 removed outlier: 6.967A pdb=" N HIS L 178 " --> pdb=" O LYS L 186 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.260A pdb=" N ALA L 20 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 98 through 100 Processing sheet with id=AD4, first strand: chain 'L' and resid 103 through 105 removed outlier: 3.676A pdb=" N GLY L 103 " --> pdb=" O ASN L 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 163 through 167 removed outlier: 3.531A pdb=" N VAL M 166 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 163 through 167 removed outlier: 3.531A pdb=" N VAL M 166 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 57 through 58 removed outlier: 7.012A pdb=" N LEU M 57 " --> pdb=" O TYR M 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 71 through 75 removed outlier: 6.611A pdb=" N CYS M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN M 151 " --> pdb=" O CYS M 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS M 159 " --> pdb=" O ASN M 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AE1, first strand: chain 'N' and resid 175 through 176 Processing sheet with id=AE2, first strand: chain 'N' and resid 44 through 45 removed outlier: 3.505A pdb=" N PHE N 44 " --> pdb=" O MET N 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 171 through 174 removed outlier: 3.747A pdb=" N CYS O 47 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER O 52 " --> pdb=" O GLU O 230 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 76 through 77 removed outlier: 3.549A pdb=" N GLY O 148 " --> pdb=" O GLU O 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 160 through 162 Processing sheet with id=AE6, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AE7, first strand: chain 'Q' and resid 161 through 162 Processing sheet with id=AE8, first strand: chain 'Q' and resid 72 through 78 removed outlier: 3.679A pdb=" N SER Q 133 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 160 through 161 Processing sheet with id=AF1, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AF2, first strand: chain 'R' and resid 132 through 136 removed outlier: 3.893A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA R 154 " --> pdb=" O GLN R 146 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF4, first strand: chain 'S' and resid 74 through 75 Processing sheet with id=AF5, first strand: chain 'T' and resid 35 through 39 removed outlier: 5.553A pdb=" N GLY T 215 " --> pdb=" O PRO T 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 64 through 65 removed outlier: 3.575A pdb=" N GLY T 131 " --> pdb=" O SER T 75 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 64 through 65 removed outlier: 3.565A pdb=" N LEU T 132 " --> pdb=" O THR T 146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR T 146 " --> pdb=" O LEU T 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 165 through 168 removed outlier: 3.580A pdb=" N THR U 36 " --> pdb=" O ILE U 51 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER U 219 " --> pdb=" O CYS U 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 70 through 72 removed outlier: 3.570A pdb=" N SER U 81 " --> pdb=" O SER U 137 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER U 137 " --> pdb=" O SER U 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE U 151 " --> pdb=" O TYR U 163 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 119 through 121 removed outlier: 4.031A pdb=" N PHE V 237 " --> pdb=" O THR V 234 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU V 239 " --> pdb=" O ASN V 232 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY V 11 " --> pdb=" O TYR V 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE V 3 " --> pdb=" O SER V 182 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 19 through 21 removed outlier: 6.796A pdb=" N THR V 20 " --> pdb=" O SER V 27 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 41 through 44 removed outlier: 3.520A pdb=" N GLN V 163 " --> pdb=" O GLY V 155 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 12 through 13 Processing sheet with id=AG5, first strand: chain 'W' and resid 20 through 21 removed outlier: 6.776A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.611A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL W 99 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 176 through 177 removed outlier: 3.970A pdb=" N VAL W 177 " --> pdb=" O GLN W 184 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 212 through 217 removed outlier: 3.752A pdb=" N ILE W 212 " --> pdb=" O LYS X 212 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 44 through 48 removed outlier: 6.145A pdb=" N VAL X 51 " --> pdb=" O MET X 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.503A pdb=" N GLY Y 6 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR Y 184 " --> pdb=" O LYS Y 187 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 43 through 44 removed outlier: 4.025A pdb=" N CYS Y 44 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Y 105 " --> pdb=" O CYS Y 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'Z' and resid 15 through 16 removed outlier: 6.967A pdb=" N HIS Z 178 " --> pdb=" O LYS Z 186 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.260A pdb=" N ALA Z 20 " --> pdb=" O SER Z 27 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 98 through 100 Processing sheet with id=AH6, first strand: chain 'Z' and resid 103 through 105 removed outlier: 3.676A pdb=" N GLY Z 103 " --> pdb=" O ASN Z 110 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 163 through 167 removed outlier: 3.531A pdb=" N VAL a 166 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 163 through 167 removed outlier: 3.531A pdb=" N VAL a 166 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 57 through 58 Processing sheet with id=AI1, first strand: chain 'a' and resid 71 through 75 removed outlier: 6.611A pdb=" N CYS a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN a 151 " --> pdb=" O CYS a 159 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS a 159 " --> pdb=" O ASN a 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 7 through 8 Processing sheet with id=AI3, first strand: chain 'b' and resid 175 through 176 Processing sheet with id=AI4, first strand: chain 'b' and resid 44 through 45 removed outlier: 3.506A pdb=" N PHE b 44 " --> pdb=" O MET b 52 " (cutoff:3.500A) 2081 hydrogen bonds defined for protein. 5880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.74 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 8482 1.30 - 1.43: 13279 1.43 - 1.55: 29305 1.55 - 1.68: 12 1.68 - 1.81: 386 Bond restraints: 51464 Sorted by residual: bond pdb=" C18 BO2 W 301 " pdb=" N20 BO2 W 301 " ideal model delta sigma weight residual 1.342 1.445 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C18 BO2 I 301 " pdb=" N20 BO2 I 301 " ideal model delta sigma weight residual 1.342 1.445 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C7 BO2 H 301 " pdb=" N9 BO2 H 301 " ideal model delta sigma weight residual 1.339 1.441 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C7 BO2 W 301 " pdb=" N9 BO2 W 301 " ideal model delta sigma weight residual 1.339 1.441 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C7 BO2 V 301 " pdb=" N9 BO2 V 301 " ideal model delta sigma weight residual 1.339 1.441 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 51459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 68911 3.42 - 6.85: 519 6.85 - 10.27: 38 10.27 - 13.69: 10 13.69 - 17.11: 6 Bond angle restraints: 69484 Sorted by residual: angle pdb=" CG ARG C 8 " pdb=" CD ARG C 8 " pdb=" NE ARG C 8 " ideal model delta sigma weight residual 112.00 126.83 -14.83 2.20e+00 2.07e-01 4.54e+01 angle pdb=" CG ARG Q 8 " pdb=" CD ARG Q 8 " pdb=" NE ARG Q 8 " ideal model delta sigma weight residual 112.00 126.76 -14.76 2.20e+00 2.07e-01 4.50e+01 angle pdb=" CA LEU N 109 " pdb=" CB LEU N 109 " pdb=" CG LEU N 109 " ideal model delta sigma weight residual 116.30 133.41 -17.11 3.50e+00 8.16e-02 2.39e+01 angle pdb=" CA LEU b 109 " pdb=" CB LEU b 109 " pdb=" CG LEU b 109 " ideal model delta sigma weight residual 116.30 133.41 -17.11 3.50e+00 8.16e-02 2.39e+01 angle pdb=" CD ARG Q 8 " pdb=" NE ARG Q 8 " pdb=" CZ ARG Q 8 " ideal model delta sigma weight residual 124.40 131.01 -6.61 1.40e+00 5.10e-01 2.23e+01 ... (remaining 69479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27586 17.99 - 35.97: 2780 35.97 - 53.96: 466 53.96 - 71.95: 104 71.95 - 89.93: 46 Dihedral angle restraints: 30982 sinusoidal: 12446 harmonic: 18536 Sorted by residual: dihedral pdb=" CA ILE Y 22 " pdb=" C ILE Y 22 " pdb=" N ASN Y 23 " pdb=" CA ASN Y 23 " ideal model delta harmonic sigma weight residual -180.00 -149.96 -30.04 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ILE K 22 " pdb=" C ILE K 22 " pdb=" N ASN K 23 " pdb=" CA ASN K 23 " ideal model delta harmonic sigma weight residual -180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA PHE T 160 " pdb=" C PHE T 160 " pdb=" N GLY T 161 " pdb=" CA GLY T 161 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 30979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5935 0.058 - 0.117: 1639 0.117 - 0.175: 173 0.175 - 0.234: 7 0.234 - 0.292: 10 Chirality restraints: 7764 Sorted by residual: chirality pdb=" C21 BO2 L 301 " pdb=" B26 BO2 L 301 " pdb=" C22 BO2 L 301 " pdb=" N20 BO2 L 301 " both_signs ideal model delta sigma weight residual False 2.49 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C21 BO2 Z 301 " pdb=" B26 BO2 Z 301 " pdb=" C22 BO2 Z 301 " pdb=" N20 BO2 Z 301 " both_signs ideal model delta sigma weight residual False 2.49 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU T 158 " pdb=" CB LEU T 158 " pdb=" CD1 LEU T 158 " pdb=" CD2 LEU T 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 7761 not shown) Planarity restraints: 8864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 187 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO I 188 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO I 188 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO I 188 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG W 187 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO W 188 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO W 188 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO W 188 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 156 " -0.010 2.00e-02 2.50e+03 2.48e-02 1.23e+01 pdb=" CG TYR H 156 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR H 156 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 156 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR H 156 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 156 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 156 " 0.007 2.00e-02 2.50e+03 ... (remaining 8861 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 561 2.56 - 3.14: 44428 3.14 - 3.73: 75604 3.73 - 4.31: 111264 4.31 - 4.90: 187275 Nonbonded interactions: 419132 Sorted by model distance: nonbonded pdb=" OD1 ASP a 153 " pdb=" OG SER a 157 " model vdw 1.972 3.040 nonbonded pdb=" OD1 ASP M 153 " pdb=" OG SER M 157 " model vdw 1.972 3.040 nonbonded pdb=" OG1 THR E 36 " pdb=" OE2 GLU E 51 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR S 36 " pdb=" OE2 GLU S 51 " model vdw 2.051 3.040 nonbonded pdb=" O THR X 60 " pdb=" NH2 ARG Y 86 " model vdw 2.088 3.120 ... (remaining 419127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.410 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 81.590 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.103 51464 Z= 0.594 Angle : 0.854 17.114 69484 Z= 0.456 Chirality : 0.051 0.292 7764 Planarity : 0.005 0.119 8864 Dihedral : 14.932 89.934 19126 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.70 % Favored : 89.26 % Rotamer: Outliers : 0.79 % Allowed : 0.65 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 6250 helix: -1.36 (0.11), residues: 2066 sheet: -1.88 (0.14), residues: 1346 loop : -2.29 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G 220 HIS 0.014 0.002 HIS N 167 PHE 0.041 0.003 PHE T 178 TYR 0.057 0.002 TYR H 156 ARG 0.013 0.001 ARG a 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 914 time to evaluate : 4.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 GLN cc_start: 0.8112 (tt0) cc_final: 0.7794 (tt0) REVERT: B 159 MET cc_start: 0.8135 (mmt) cc_final: 0.7719 (mmt) REVERT: C 41 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0) REVERT: D 37 SER cc_start: 0.8779 (t) cc_final: 0.8565 (t) REVERT: D 98 MET cc_start: 0.7936 (tpp) cc_final: 0.7446 (mpp) REVERT: E 205 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7991 (ttm170) REVERT: F 159 SER cc_start: 0.8946 (p) cc_final: 0.8728 (p) REVERT: F 223 ILE cc_start: 0.8423 (mm) cc_final: 0.7704 (mm) REVERT: F 227 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8356 (tm-30) REVERT: H 130 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: H 190 GLN cc_start: 0.8606 (tp40) cc_final: 0.8372 (tp40) REVERT: I 141 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8265 (mtpp) REVERT: I 157 GLU cc_start: 0.8154 (tt0) cc_final: 0.7916 (tt0) REVERT: J 201 LEU cc_start: 0.8744 (tt) cc_final: 0.8491 (tt) REVERT: K 20 TYR cc_start: 0.8295 (m-10) cc_final: 0.7692 (m-10) REVERT: K 53 ASP cc_start: 0.8182 (m-30) cc_final: 0.7971 (m-30) REVERT: K 99 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7269 (tm-30) REVERT: K 173 LEU cc_start: 0.8635 (pp) cc_final: 0.8420 (pp) REVERT: L 116 ASP cc_start: 0.7791 (p0) cc_final: 0.7501 (p0) REVERT: L 197 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7927 (t-170) REVERT: M 29 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7519 (tpm170) REVERT: M 56 ARG cc_start: 0.8954 (ttm170) cc_final: 0.8699 (ttm170) REVERT: M 59 LEU cc_start: 0.8392 (tp) cc_final: 0.8190 (tp) REVERT: Q 41 ASP cc_start: 0.7768 (t0) cc_final: 0.7544 (t0) REVERT: R 37 SER cc_start: 0.8758 (t) cc_final: 0.8525 (t) REVERT: R 153 TYR cc_start: 0.8625 (p90) cc_final: 0.8259 (p90) REVERT: S 205 ARG cc_start: 0.8439 (ttm110) cc_final: 0.7855 (ttm170) REVERT: T 7 ASP cc_start: 0.8944 (t70) cc_final: 0.8740 (t0) REVERT: T 223 ILE cc_start: 0.8425 (mm) cc_final: 0.7712 (mm) REVERT: T 227 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8356 (tm-30) REVERT: V 36 ARG cc_start: 0.8733 (ttt-90) cc_final: 0.8527 (ttt-90) REVERT: V 130 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: V 190 GLN cc_start: 0.8628 (tp40) cc_final: 0.8421 (tp40) REVERT: W 104 ASP cc_start: 0.7661 (p0) cc_final: 0.6952 (p0) REVERT: Y 20 TYR cc_start: 0.8318 (m-10) cc_final: 0.7729 (m-10) REVERT: Y 53 ASP cc_start: 0.8201 (m-30) cc_final: 0.7960 (m-30) REVERT: Y 59 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8131 (mm-30) REVERT: Y 69 GLN cc_start: 0.8122 (mt0) cc_final: 0.7847 (mt0) REVERT: Y 99 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7326 (tm-30) REVERT: Z 116 ASP cc_start: 0.7509 (p0) cc_final: 0.7176 (p0) REVERT: Z 192 ASP cc_start: 0.6606 (t0) cc_final: 0.6401 (t0) REVERT: Z 197 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7961 (t-170) REVERT: a 29 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7584 (tpm170) REVERT: a 56 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8664 (ttm170) outliers start: 44 outliers final: 8 residues processed: 934 average time/residue: 0.5015 time to fit residues: 778.6809 Evaluate side-chains 745 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 733 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain K residue 23 ASN Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain b residue 110 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 523 optimal weight: 0.6980 chunk 469 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 160 optimal weight: 0.4980 chunk 316 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 485 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 295 optimal weight: 2.9990 chunk 361 optimal weight: 0.9990 chunk 563 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 74 ASN G 108 ASN G 116 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN K 69 GLN L 89 GLN M 136 ASN M 179 ASN M 186 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 ASN N 192 HIS ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 ASN U 116 ASN U 230 GLN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN Y 69 GLN Z 89 GLN a 136 ASN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 192 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51464 Z= 0.213 Angle : 0.648 17.120 69484 Z= 0.347 Chirality : 0.046 0.176 7764 Planarity : 0.004 0.077 8864 Dihedral : 7.586 94.068 7052 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.26 % Allowed : 8.68 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.10), residues: 6250 helix: -0.25 (0.11), residues: 2124 sheet: -1.66 (0.14), residues: 1372 loop : -2.14 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 220 HIS 0.010 0.001 HIS H 134 PHE 0.021 0.002 PHE H 76 TYR 0.024 0.001 TYR Z 161 ARG 0.012 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 924 time to evaluate : 4.468 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 158 TRP cc_start: 0.8652 (m100) cc_final: 0.8286 (m100) REVERT: B 159 MET cc_start: 0.8308 (mmt) cc_final: 0.7949 (mmt) REVERT: B 184 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6049 (mt) REVERT: D 37 SER cc_start: 0.8821 (t) cc_final: 0.8605 (t) REVERT: D 66 ASP cc_start: 0.8393 (m-30) cc_final: 0.8095 (m-30) REVERT: D 96 LEU cc_start: 0.8661 (tt) cc_final: 0.8388 (tp) REVERT: D 99 ASP cc_start: 0.8425 (t0) cc_final: 0.8179 (t0) REVERT: D 153 TYR cc_start: 0.8677 (p90) cc_final: 0.8465 (p90) REVERT: E 114 GLU cc_start: 0.8270 (tp30) cc_final: 0.7979 (tt0) REVERT: E 121 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8368 (tt) REVERT: E 205 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7841 (ttm170) REVERT: E 230 TYR cc_start: 0.8276 (t80) cc_final: 0.8007 (t80) REVERT: F 68 ASP cc_start: 0.7790 (m-30) cc_final: 0.7421 (m-30) REVERT: F 116 TYR cc_start: 0.8720 (m-80) cc_final: 0.8495 (m-10) REVERT: F 159 SER cc_start: 0.8747 (p) cc_final: 0.8526 (p) REVERT: F 223 ILE cc_start: 0.8432 (mm) cc_final: 0.7720 (mm) REVERT: F 227 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8365 (tm-30) REVERT: G 57 LYS cc_start: 0.6344 (tmtt) cc_final: 0.5983 (tptp) REVERT: G 118 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8570 (tp) REVERT: H 32 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7532 (mmt180) REVERT: H 156 TYR cc_start: 0.8163 (t80) cc_final: 0.7959 (t80) REVERT: I 53 GLU cc_start: 0.7907 (tt0) cc_final: 0.7441 (mt-10) REVERT: I 96 CYS cc_start: 0.8706 (p) cc_final: 0.8103 (p) REVERT: I 104 ASP cc_start: 0.7905 (p0) cc_final: 0.6901 (p0) REVERT: I 174 ASP cc_start: 0.8947 (p0) cc_final: 0.8673 (p0) REVERT: J 25 CYS cc_start: 0.8959 (p) cc_final: 0.8661 (p) REVERT: J 134 LEU cc_start: 0.8619 (mt) cc_final: 0.8367 (mt) REVERT: J 218 ASP cc_start: 0.6857 (m-30) cc_final: 0.6599 (m-30) REVERT: K 20 TYR cc_start: 0.8038 (m-10) cc_final: 0.7571 (m-10) REVERT: K 53 ASP cc_start: 0.8098 (m-30) cc_final: 0.7836 (m-30) REVERT: L 3 THR cc_start: 0.9062 (m) cc_final: 0.8709 (m) REVERT: L 91 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8470 (tptm) REVERT: L 115 ASP cc_start: 0.7975 (t70) cc_final: 0.7372 (t0) REVERT: L 192 ASP cc_start: 0.6499 (t0) cc_final: 0.5698 (t0) REVERT: M 29 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7508 (tpm170) REVERT: M 56 ARG cc_start: 0.8861 (ttm170) cc_final: 0.8572 (ttm170) REVERT: N 22 MET cc_start: 0.7913 (tpp) cc_final: 0.7530 (tpp) REVERT: N 52 MET cc_start: 0.8960 (tmm) cc_final: 0.8706 (ttp) REVERT: N 89 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8944 (tm-30) REVERT: P 119 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7864 (tm-30) REVERT: P 158 TRP cc_start: 0.8701 (m100) cc_final: 0.8394 (m100) REVERT: P 184 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.5855 (mt) REVERT: Q 183 MET cc_start: 0.8297 (ttp) cc_final: 0.8096 (ttp) REVERT: R 37 SER cc_start: 0.8815 (t) cc_final: 0.8607 (t) REVERT: R 153 TYR cc_start: 0.8588 (p90) cc_final: 0.8342 (p90) REVERT: R 176 TYR cc_start: 0.8268 (t80) cc_final: 0.8036 (t80) REVERT: S 205 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7975 (ttm170) REVERT: S 230 TYR cc_start: 0.8326 (t80) cc_final: 0.8078 (t80) REVERT: T 68 ASP cc_start: 0.7783 (m-30) cc_final: 0.7387 (m-30) REVERT: T 223 ILE cc_start: 0.8388 (mm) cc_final: 0.7703 (mm) REVERT: T 227 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8375 (tm-30) REVERT: U 97 GLU cc_start: 0.7838 (tp30) cc_final: 0.7603 (tp30) REVERT: V 53 GLN cc_start: 0.8544 (tp40) cc_final: 0.8278 (tp40) REVERT: V 156 TYR cc_start: 0.8151 (t80) cc_final: 0.7909 (t80) REVERT: V 182 SER cc_start: 0.8730 (p) cc_final: 0.8504 (m) REVERT: W 174 ASP cc_start: 0.8766 (p0) cc_final: 0.8555 (p0) REVERT: X 25 CYS cc_start: 0.8804 (p) cc_final: 0.8485 (p) REVERT: Y 20 TYR cc_start: 0.8064 (m-10) cc_final: 0.7634 (m-10) REVERT: Y 53 ASP cc_start: 0.8096 (m-30) cc_final: 0.7827 (m-30) REVERT: Y 69 GLN cc_start: 0.7907 (mt0) cc_final: 0.7639 (mt0) REVERT: Z 3 THR cc_start: 0.9074 (m) cc_final: 0.8708 (m) REVERT: Z 111 MET cc_start: 0.7850 (ttm) cc_final: 0.7637 (ttm) REVERT: Z 115 ASP cc_start: 0.7909 (t70) cc_final: 0.6925 (t0) REVERT: Z 116 ASP cc_start: 0.7510 (p0) cc_final: 0.7307 (p0) REVERT: Z 192 ASP cc_start: 0.6528 (t0) cc_final: 0.6111 (t0) REVERT: a 29 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7516 (tpm170) REVERT: a 56 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8641 (ttm170) REVERT: b 52 MET cc_start: 0.9021 (tmm) cc_final: 0.8724 (ttp) REVERT: b 89 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8938 (tm-30) outliers start: 70 outliers final: 46 residues processed: 958 average time/residue: 0.5167 time to fit residues: 819.3738 Evaluate side-chains 847 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 797 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain b residue 73 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 312 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 468 optimal weight: 5.9990 chunk 383 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 564 optimal weight: 5.9990 chunk 609 optimal weight: 2.9990 chunk 502 optimal weight: 1.9990 chunk 559 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 452 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN L 89 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN b 192 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 51464 Z= 0.343 Angle : 0.653 17.091 69484 Z= 0.345 Chirality : 0.047 0.181 7764 Planarity : 0.004 0.062 8864 Dihedral : 7.325 66.317 7034 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.25 % Allowed : 13.36 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.03 (0.11), residues: 6250 helix: -0.10 (0.11), residues: 2138 sheet: -1.65 (0.14), residues: 1368 loop : -2.15 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 220 HIS 0.013 0.001 HIS b 155 PHE 0.023 0.002 PHE R 194 TYR 0.022 0.002 TYR V 118 ARG 0.007 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 863 time to evaluate : 4.622 Fit side-chains REVERT: A 166 CYS cc_start: 0.7493 (p) cc_final: 0.6987 (m) REVERT: B 39 ARG cc_start: 0.7613 (ptm160) cc_final: 0.7169 (ptm160) REVERT: B 119 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 158 TRP cc_start: 0.8760 (m100) cc_final: 0.8536 (m100) REVERT: B 184 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.5940 (mt) REVERT: C 110 LEU cc_start: 0.8708 (tp) cc_final: 0.8491 (tp) REVERT: C 155 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7923 (p0) REVERT: D 37 SER cc_start: 0.8938 (t) cc_final: 0.8700 (t) REVERT: D 66 ASP cc_start: 0.8459 (m-30) cc_final: 0.8078 (m-30) REVERT: D 99 ASP cc_start: 0.8355 (t0) cc_final: 0.8100 (t0) REVERT: D 153 TYR cc_start: 0.8715 (p90) cc_final: 0.8444 (p90) REVERT: E 114 GLU cc_start: 0.8280 (tp30) cc_final: 0.8013 (tt0) REVERT: E 121 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8449 (tt) REVERT: E 205 ARG cc_start: 0.8374 (ttm110) cc_final: 0.7963 (ttm170) REVERT: E 230 TYR cc_start: 0.8428 (t80) cc_final: 0.8105 (t80) REVERT: F 68 ASP cc_start: 0.7815 (m-30) cc_final: 0.7469 (m-30) REVERT: F 223 ILE cc_start: 0.8437 (mm) cc_final: 0.7720 (mm) REVERT: F 227 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8229 (tm-30) REVERT: G 57 LYS cc_start: 0.6126 (tmtt) cc_final: 0.5784 (tptp) REVERT: G 232 ILE cc_start: 0.8280 (mt) cc_final: 0.8049 (mt) REVERT: H 32 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7563 (mmt180) REVERT: H 80 GLU cc_start: 0.5347 (mp0) cc_final: 0.5109 (mt-10) REVERT: H 156 TYR cc_start: 0.8247 (t80) cc_final: 0.7994 (t80) REVERT: I 174 ASP cc_start: 0.8857 (p0) cc_final: 0.8590 (p0) REVERT: J 218 ASP cc_start: 0.6803 (m-30) cc_final: 0.6483 (m-30) REVERT: K 20 TYR cc_start: 0.8080 (m-10) cc_final: 0.7612 (m-10) REVERT: K 69 GLN cc_start: 0.8026 (mt0) cc_final: 0.7812 (mt0) REVERT: L 6 PHE cc_start: 0.8426 (m-10) cc_final: 0.8157 (m-10) REVERT: L 115 ASP cc_start: 0.8079 (t70) cc_final: 0.7449 (t0) REVERT: L 150 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: L 192 ASP cc_start: 0.6734 (t0) cc_final: 0.6090 (t0) REVERT: M 29 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7562 (tpm170) REVERT: M 56 ARG cc_start: 0.8942 (ttm170) cc_final: 0.8593 (ttm170) REVERT: M 188 ILE cc_start: 0.7323 (mm) cc_final: 0.6834 (mm) REVERT: N 52 MET cc_start: 0.9004 (tmm) cc_final: 0.8773 (ttp) REVERT: N 89 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8935 (tm-30) REVERT: O 145 MET cc_start: 0.7420 (mtm) cc_final: 0.7155 (mtt) REVERT: P 100 GLN cc_start: 0.8745 (mt0) cc_final: 0.8470 (mt0) REVERT: P 119 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7901 (tm-30) REVERT: P 158 TRP cc_start: 0.8787 (m100) cc_final: 0.8039 (m100) REVERT: P 209 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6684 (mm-30) REVERT: Q 183 MET cc_start: 0.8155 (ttp) cc_final: 0.7821 (ttp) REVERT: R 37 SER cc_start: 0.8864 (t) cc_final: 0.8628 (t) REVERT: R 153 TYR cc_start: 0.8693 (p90) cc_final: 0.8350 (p90) REVERT: R 176 TYR cc_start: 0.8399 (t80) cc_final: 0.8158 (t80) REVERT: S 205 ARG cc_start: 0.8343 (ttm110) cc_final: 0.7911 (ttm170) REVERT: S 230 TYR cc_start: 0.8433 (t80) cc_final: 0.8139 (t80) REVERT: T 68 ASP cc_start: 0.7833 (m-30) cc_final: 0.7559 (m-30) REVERT: T 223 ILE cc_start: 0.8446 (mm) cc_final: 0.7706 (mm) REVERT: T 227 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8235 (tm-30) REVERT: U 97 GLU cc_start: 0.7858 (tp30) cc_final: 0.7629 (tp30) REVERT: V 32 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7617 (mmt180) REVERT: V 53 GLN cc_start: 0.8604 (tp40) cc_final: 0.8380 (tp40) REVERT: V 156 TYR cc_start: 0.8232 (t80) cc_final: 0.7968 (t80) REVERT: V 182 SER cc_start: 0.8806 (p) cc_final: 0.8463 (m) REVERT: W 174 ASP cc_start: 0.8840 (p0) cc_final: 0.8600 (p0) REVERT: X 218 ASP cc_start: 0.6811 (m-30) cc_final: 0.6532 (m-30) REVERT: Y 20 TYR cc_start: 0.8102 (m-10) cc_final: 0.7619 (m-10) REVERT: Y 69 GLN cc_start: 0.7965 (mt0) cc_final: 0.7673 (mt0) REVERT: Z 115 ASP cc_start: 0.8097 (t70) cc_final: 0.7430 (t0) REVERT: Z 150 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: Z 192 ASP cc_start: 0.6772 (t0) cc_final: 0.6252 (t0) REVERT: a 29 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7467 (tpm170) REVERT: a 56 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8638 (ttm170) REVERT: a 211 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7923 (mt-10) REVERT: b 22 MET cc_start: 0.7951 (ttm) cc_final: 0.7637 (ttm) REVERT: b 52 MET cc_start: 0.9016 (tmm) cc_final: 0.8770 (ttp) REVERT: b 75 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (t0) REVERT: b 89 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8933 (tm-30) outliers start: 125 outliers final: 87 residues processed: 922 average time/residue: 0.5146 time to fit residues: 783.1512 Evaluate side-chains 855 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 762 time to evaluate : 4.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 208 MET Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 209 ILE Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 557 optimal weight: 0.9990 chunk 424 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 378 optimal weight: 0.8980 chunk 566 optimal weight: 0.1980 chunk 599 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 536 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS G 116 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 HIS L 151 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 176 GLN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS U 116 ASN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 177 HIS W 185 HIS Y 56 GLN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 155 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51464 Z= 0.182 Angle : 0.574 15.935 69484 Z= 0.305 Chirality : 0.044 0.187 7764 Planarity : 0.004 0.059 8864 Dihedral : 7.111 67.206 7034 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.25 % Allowed : 16.01 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.11), residues: 6250 helix: 0.29 (0.11), residues: 2128 sheet: -1.52 (0.14), residues: 1368 loop : -2.04 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 179 HIS 0.017 0.001 HIS b 155 PHE 0.014 0.001 PHE R 194 TYR 0.025 0.001 TYR H 118 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 931 time to evaluate : 4.461 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7262 (mtm-85) REVERT: A 139 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 39 ARG cc_start: 0.7480 (ptm160) cc_final: 0.7240 (ptm160) REVERT: B 119 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7871 (tm-30) REVERT: B 123 GLN cc_start: 0.7805 (tt0) cc_final: 0.7553 (tt0) REVERT: B 158 TRP cc_start: 0.8597 (m100) cc_final: 0.8261 (m100) REVERT: B 159 MET cc_start: 0.8171 (mmt) cc_final: 0.7675 (mmt) REVERT: B 184 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.5852 (mt) REVERT: C 41 ASP cc_start: 0.7896 (t0) cc_final: 0.7672 (m-30) REVERT: C 62 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.5878 (p90) REVERT: D 37 SER cc_start: 0.8827 (t) cc_final: 0.8564 (t) REVERT: D 99 ASP cc_start: 0.8324 (t0) cc_final: 0.8066 (t0) REVERT: E 114 GLU cc_start: 0.8311 (tp30) cc_final: 0.8010 (tt0) REVERT: E 121 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8447 (tt) REVERT: E 205 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7965 (ttm170) REVERT: E 230 TYR cc_start: 0.8341 (t80) cc_final: 0.8029 (t80) REVERT: F 68 ASP cc_start: 0.7768 (m-30) cc_final: 0.7494 (m-30) REVERT: F 223 ILE cc_start: 0.8454 (mm) cc_final: 0.7698 (mm) REVERT: G 97 GLU cc_start: 0.7818 (tp30) cc_final: 0.7554 (tp30) REVERT: G 117 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: H 32 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7407 (mmm160) REVERT: H 80 GLU cc_start: 0.5375 (mp0) cc_final: 0.5108 (mt-10) REVERT: H 156 TYR cc_start: 0.8196 (t80) cc_final: 0.7971 (t80) REVERT: I 53 GLU cc_start: 0.7959 (tt0) cc_final: 0.7569 (mt-10) REVERT: I 174 ASP cc_start: 0.8634 (p0) cc_final: 0.8381 (p0) REVERT: I 217 ILE cc_start: 0.6037 (mt) cc_final: 0.5812 (mt) REVERT: J 218 ASP cc_start: 0.6744 (m-30) cc_final: 0.6464 (m-30) REVERT: K 20 TYR cc_start: 0.8118 (m-10) cc_final: 0.7690 (m-10) REVERT: K 53 ASP cc_start: 0.8041 (m-30) cc_final: 0.7427 (m-30) REVERT: K 69 GLN cc_start: 0.7982 (mt0) cc_final: 0.7773 (mt0) REVERT: L 3 THR cc_start: 0.9079 (m) cc_final: 0.8744 (m) REVERT: L 6 PHE cc_start: 0.8291 (m-10) cc_final: 0.7975 (m-10) REVERT: L 88 TYR cc_start: 0.8625 (t80) cc_final: 0.7897 (t80) REVERT: L 115 ASP cc_start: 0.8015 (t70) cc_final: 0.7254 (t0) REVERT: L 192 ASP cc_start: 0.6564 (t0) cc_final: 0.5976 (t0) REVERT: M 29 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7519 (tpm170) REVERT: M 56 ARG cc_start: 0.8901 (ttm170) cc_final: 0.8554 (ttm170) REVERT: N 89 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8842 (tm-30) REVERT: N 197 MET cc_start: 0.8548 (mtm) cc_final: 0.8271 (mtm) REVERT: O 139 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8388 (mt) REVERT: P 100 GLN cc_start: 0.8457 (mt0) cc_final: 0.8196 (mm-40) REVERT: P 119 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7338 (tm-30) REVERT: P 158 TRP cc_start: 0.8563 (m100) cc_final: 0.8091 (m100) REVERT: P 171 MET cc_start: 0.8744 (tpp) cc_final: 0.8265 (mmm) REVERT: P 184 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.5802 (mt) REVERT: P 209 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6529 (mm-30) REVERT: Q 62 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.5770 (p90) REVERT: Q 183 MET cc_start: 0.7777 (ttp) cc_final: 0.7343 (ttp) REVERT: R 37 SER cc_start: 0.8767 (t) cc_final: 0.8509 (t) REVERT: R 153 TYR cc_start: 0.8664 (p90) cc_final: 0.8432 (p90) REVERT: R 176 TYR cc_start: 0.8357 (t80) cc_final: 0.8087 (t80) REVERT: S 205 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7925 (ttm170) REVERT: S 230 TYR cc_start: 0.8386 (t80) cc_final: 0.8137 (t80) REVERT: T 68 ASP cc_start: 0.7781 (m-30) cc_final: 0.7447 (m-30) REVERT: T 223 ILE cc_start: 0.8443 (mm) cc_final: 0.7684 (mm) REVERT: U 57 LYS cc_start: 0.6519 (tptp) cc_final: 0.6309 (tptt) REVERT: V 53 GLN cc_start: 0.8530 (tp40) cc_final: 0.8327 (tp40) REVERT: V 156 TYR cc_start: 0.8137 (t80) cc_final: 0.7916 (t80) REVERT: V 182 SER cc_start: 0.8605 (p) cc_final: 0.8217 (m) REVERT: W 53 GLU cc_start: 0.8127 (tt0) cc_final: 0.7746 (mt-10) REVERT: W 54 HIS cc_start: 0.7667 (t-90) cc_final: 0.7408 (t-90) REVERT: W 174 ASP cc_start: 0.8628 (p0) cc_final: 0.8289 (p0) REVERT: X 139 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (pp) REVERT: X 218 ASP cc_start: 0.6678 (m-30) cc_final: 0.6337 (m-30) REVERT: Y 20 TYR cc_start: 0.8126 (m-10) cc_final: 0.7679 (m-10) REVERT: Y 69 GLN cc_start: 0.7934 (mt0) cc_final: 0.7613 (mt0) REVERT: Z 3 THR cc_start: 0.9035 (m) cc_final: 0.8709 (m) REVERT: Z 115 ASP cc_start: 0.8016 (t70) cc_final: 0.7348 (t0) REVERT: Z 192 ASP cc_start: 0.6472 (t0) cc_final: 0.6040 (t0) REVERT: b 22 MET cc_start: 0.7930 (ttm) cc_final: 0.7605 (ttm) REVERT: b 75 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8164 (t0) REVERT: b 89 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8915 (tm-30) outliers start: 125 outliers final: 77 residues processed: 991 average time/residue: 0.5029 time to fit residues: 825.8528 Evaluate side-chains 884 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 798 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 56 GLN Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 499 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 446 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 511 optimal weight: 1.9990 chunk 414 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 537 optimal weight: 5.9990 chunk 151 optimal weight: 0.0370 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN D 97 ASN E 13 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN L 151 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 51464 Z= 0.248 Angle : 0.593 15.922 69484 Z= 0.313 Chirality : 0.045 0.210 7764 Planarity : 0.004 0.059 8864 Dihedral : 7.062 68.413 7034 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.06 % Allowed : 17.26 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.66 (0.11), residues: 6250 helix: 0.33 (0.11), residues: 2142 sheet: -1.51 (0.14), residues: 1378 loop : -2.01 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 179 HIS 0.009 0.001 HIS T 176 PHE 0.018 0.001 PHE Z 126 TYR 0.024 0.001 TYR H 118 ARG 0.006 0.000 ARG a 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 839 time to evaluate : 4.439 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8448 (mt) REVERT: B 39 ARG cc_start: 0.7523 (ptm160) cc_final: 0.7273 (ptm160) REVERT: B 119 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 158 TRP cc_start: 0.8607 (m100) cc_final: 0.8159 (m100) REVERT: B 159 MET cc_start: 0.8118 (mmt) cc_final: 0.7563 (mmt) REVERT: B 184 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.5841 (mt) REVERT: C 41 ASP cc_start: 0.7914 (t0) cc_final: 0.7252 (t0) REVERT: D 37 SER cc_start: 0.8864 (t) cc_final: 0.8586 (t) REVERT: D 66 ASP cc_start: 0.8414 (m-30) cc_final: 0.8129 (m-30) REVERT: D 99 ASP cc_start: 0.8391 (t0) cc_final: 0.7962 (t0) REVERT: E 114 GLU cc_start: 0.8322 (tp30) cc_final: 0.8038 (tt0) REVERT: E 205 ARG cc_start: 0.8469 (ttm110) cc_final: 0.8217 (ttm170) REVERT: F 68 ASP cc_start: 0.7788 (m-30) cc_final: 0.7526 (m-30) REVERT: F 223 ILE cc_start: 0.8148 (mm) cc_final: 0.7863 (mm) REVERT: G 57 LYS cc_start: 0.6345 (tmtt) cc_final: 0.6093 (tptp) REVERT: G 97 GLU cc_start: 0.7808 (tp30) cc_final: 0.7602 (tp30) REVERT: H 32 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7435 (mmm160) REVERT: H 156 TYR cc_start: 0.8225 (t80) cc_final: 0.7980 (t80) REVERT: I 53 GLU cc_start: 0.8022 (tt0) cc_final: 0.7632 (mt-10) REVERT: I 174 ASP cc_start: 0.8664 (p0) cc_final: 0.8344 (p0) REVERT: J 134 LEU cc_start: 0.8561 (mt) cc_final: 0.8300 (mt) REVERT: J 218 ASP cc_start: 0.6762 (m-30) cc_final: 0.6415 (m-30) REVERT: K 20 TYR cc_start: 0.8060 (m-10) cc_final: 0.7585 (m-10) REVERT: K 69 GLN cc_start: 0.8015 (mt0) cc_final: 0.7768 (mt0) REVERT: L 6 PHE cc_start: 0.8304 (m-10) cc_final: 0.8021 (m-10) REVERT: L 18 SER cc_start: 0.7964 (p) cc_final: 0.7631 (t) REVERT: L 115 ASP cc_start: 0.8074 (t70) cc_final: 0.7334 (t0) REVERT: L 192 ASP cc_start: 0.6675 (t0) cc_final: 0.5865 (t0) REVERT: M 56 ARG cc_start: 0.8947 (ttm170) cc_final: 0.8630 (ttm170) REVERT: N 89 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8901 (tm-30) REVERT: N 197 MET cc_start: 0.8596 (mtm) cc_final: 0.8305 (mtm) REVERT: P 100 GLN cc_start: 0.8464 (mt0) cc_final: 0.8166 (mm-40) REVERT: P 119 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7567 (tm-30) REVERT: P 158 TRP cc_start: 0.8575 (m100) cc_final: 0.8169 (m100) REVERT: P 184 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.5799 (mt) REVERT: P 209 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6473 (mm-30) REVERT: Q 183 MET cc_start: 0.7670 (ttp) cc_final: 0.7157 (ttp) REVERT: R 37 SER cc_start: 0.8876 (t) cc_final: 0.8600 (t) REVERT: R 153 TYR cc_start: 0.8674 (p90) cc_final: 0.8437 (p90) REVERT: R 176 TYR cc_start: 0.8406 (t80) cc_final: 0.8141 (t80) REVERT: T 68 ASP cc_start: 0.7776 (m-30) cc_final: 0.7515 (m-30) REVERT: T 223 ILE cc_start: 0.8097 (mm) cc_final: 0.7795 (mm) REVERT: V 36 ARG cc_start: 0.8661 (ttt-90) cc_final: 0.8317 (ttt-90) REVERT: V 156 TYR cc_start: 0.8209 (t80) cc_final: 0.7939 (t80) REVERT: V 182 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8334 (m) REVERT: W 53 GLU cc_start: 0.8105 (tt0) cc_final: 0.7764 (mt-10) REVERT: W 54 HIS cc_start: 0.7672 (t-90) cc_final: 0.7396 (t-90) REVERT: W 174 ASP cc_start: 0.8685 (p0) cc_final: 0.8343 (p0) REVERT: X 139 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8696 (pp) REVERT: Y 20 TYR cc_start: 0.8010 (m-10) cc_final: 0.7547 (m-10) REVERT: Y 69 GLN cc_start: 0.7990 (mt0) cc_final: 0.7634 (mt0) REVERT: Z 115 ASP cc_start: 0.8108 (t70) cc_final: 0.7415 (t0) REVERT: Z 192 ASP cc_start: 0.6600 (t0) cc_final: 0.6119 (t0) REVERT: a 29 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7366 (tpm170) REVERT: b 22 MET cc_start: 0.7925 (ttm) cc_final: 0.7613 (ttm) REVERT: b 75 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8263 (t0) REVERT: b 89 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8917 (tm-30) outliers start: 170 outliers final: 126 residues processed: 924 average time/residue: 0.4963 time to fit residues: 760.2248 Evaluate side-chains 907 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 775 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 154 CYS Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 201 MET Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 201 optimal weight: 2.9990 chunk 539 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 599 optimal weight: 0.8980 chunk 497 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 314 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 155 ASN E 13 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 HIS L 151 GLN M 190 ASN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN Z 151 GLN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 51464 Z= 0.179 Angle : 0.564 15.115 69484 Z= 0.299 Chirality : 0.044 0.207 7764 Planarity : 0.004 0.058 8864 Dihedral : 6.907 69.879 7030 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.13 % Allowed : 18.19 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.11), residues: 6250 helix: 0.49 (0.11), residues: 2154 sheet: -1.39 (0.14), residues: 1366 loop : -1.97 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 179 HIS 0.014 0.001 HIS T 176 PHE 0.016 0.001 PHE J 149 TYR 0.024 0.001 TYR H 118 ARG 0.006 0.000 ARG M 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 885 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8669 (mmp) cc_final: 0.8317 (tpp) REVERT: A 139 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8413 (mt) REVERT: B 39 ARG cc_start: 0.7572 (ptm160) cc_final: 0.7306 (ptm160) REVERT: B 119 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 158 TRP cc_start: 0.8549 (m100) cc_final: 0.8025 (m100) REVERT: B 184 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6089 (mt) REVERT: C 41 ASP cc_start: 0.7914 (t0) cc_final: 0.7657 (m-30) REVERT: C 130 TYR cc_start: 0.8773 (m-80) cc_final: 0.8486 (m-10) REVERT: C 226 TYR cc_start: 0.7545 (m-10) cc_final: 0.6364 (m-10) REVERT: D 37 SER cc_start: 0.8830 (t) cc_final: 0.8523 (t) REVERT: D 66 ASP cc_start: 0.8451 (m-30) cc_final: 0.8160 (m-30) REVERT: D 99 ASP cc_start: 0.8363 (t0) cc_final: 0.7897 (t0) REVERT: E 114 GLU cc_start: 0.8300 (tp30) cc_final: 0.8044 (tt0) REVERT: E 205 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8209 (ttm170) REVERT: F 68 ASP cc_start: 0.7780 (m-30) cc_final: 0.7536 (m-30) REVERT: H 32 ARG cc_start: 0.7997 (mmt-90) cc_final: 0.7598 (mmm160) REVERT: H 156 TYR cc_start: 0.8212 (t80) cc_final: 0.7974 (t80) REVERT: H 220 ASN cc_start: 0.8070 (p0) cc_final: 0.7728 (p0) REVERT: I 53 GLU cc_start: 0.7990 (tt0) cc_final: 0.7648 (mt-10) REVERT: I 174 ASP cc_start: 0.8466 (p0) cc_final: 0.8261 (p0) REVERT: I 217 ILE cc_start: 0.6063 (mt) cc_final: 0.5863 (mt) REVERT: J 218 ASP cc_start: 0.6655 (m-30) cc_final: 0.6279 (m-30) REVERT: K 20 TYR cc_start: 0.8020 (m-10) cc_final: 0.7595 (m-10) REVERT: K 69 GLN cc_start: 0.7989 (mt0) cc_final: 0.7733 (mt0) REVERT: L 3 THR cc_start: 0.9053 (m) cc_final: 0.8718 (m) REVERT: L 6 PHE cc_start: 0.8211 (m-10) cc_final: 0.7967 (m-10) REVERT: L 18 SER cc_start: 0.7918 (p) cc_final: 0.7548 (t) REVERT: L 115 ASP cc_start: 0.8076 (t70) cc_final: 0.7308 (t0) REVERT: L 192 ASP cc_start: 0.6594 (t0) cc_final: 0.5787 (t0) REVERT: M 29 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7261 (tpm170) REVERT: M 56 ARG cc_start: 0.8912 (ttm170) cc_final: 0.8596 (ttm170) REVERT: M 174 LEU cc_start: 0.8978 (mt) cc_final: 0.8754 (mt) REVERT: N 89 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8824 (tm-30) REVERT: N 197 MET cc_start: 0.8596 (mtm) cc_final: 0.8338 (mtm) REVERT: O 139 LEU cc_start: 0.8913 (mm) cc_final: 0.8525 (mt) REVERT: P 119 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7464 (tm-30) REVERT: P 123 GLN cc_start: 0.7757 (tt0) cc_final: 0.7524 (tt0) REVERT: P 158 TRP cc_start: 0.8475 (m100) cc_final: 0.8171 (m100) REVERT: P 184 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.5814 (mt) REVERT: P 209 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6500 (mm-30) REVERT: Q 87 ILE cc_start: 0.8783 (mm) cc_final: 0.8567 (mm) REVERT: Q 183 MET cc_start: 0.7495 (ttp) cc_final: 0.7043 (ttp) REVERT: R 37 SER cc_start: 0.8811 (t) cc_final: 0.8514 (t) REVERT: R 176 TYR cc_start: 0.8384 (t80) cc_final: 0.8124 (t80) REVERT: R 199 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6544 (tp) REVERT: T 68 ASP cc_start: 0.7782 (m-30) cc_final: 0.7527 (m-30) REVERT: V 156 TYR cc_start: 0.8191 (t80) cc_final: 0.7944 (t80) REVERT: V 182 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8218 (m) REVERT: V 220 ASN cc_start: 0.8034 (p0) cc_final: 0.7708 (p0) REVERT: W 53 GLU cc_start: 0.8071 (tt0) cc_final: 0.7769 (mt-10) REVERT: W 54 HIS cc_start: 0.7561 (t-90) cc_final: 0.7278 (t-90) REVERT: X 139 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8672 (pp) REVERT: Y 20 TYR cc_start: 0.8023 (m-10) cc_final: 0.7576 (m-10) REVERT: Y 69 GLN cc_start: 0.7948 (mt0) cc_final: 0.7611 (mt0) REVERT: Y 165 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: Z 3 THR cc_start: 0.8953 (m) cc_final: 0.8659 (m) REVERT: Z 18 SER cc_start: 0.7849 (p) cc_final: 0.7451 (t) REVERT: Z 115 ASP cc_start: 0.8060 (t70) cc_final: 0.7351 (t0) REVERT: Z 192 ASP cc_start: 0.6531 (t0) cc_final: 0.6058 (t0) REVERT: a 29 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7673 (tpm170) REVERT: a 39 THR cc_start: 0.8882 (t) cc_final: 0.8670 (m) REVERT: b 22 MET cc_start: 0.8057 (ttm) cc_final: 0.7774 (ttm) REVERT: b 75 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8275 (t0) REVERT: b 89 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8839 (tm-30) outliers start: 174 outliers final: 124 residues processed: 981 average time/residue: 0.4942 time to fit residues: 807.5433 Evaluate side-chains 927 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 795 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 154 CYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 140 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 209 ILE Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 578 optimal weight: 5.9990 chunk 67 optimal weight: 0.0270 chunk 341 optimal weight: 5.9990 chunk 438 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 504 optimal weight: 5.9990 chunk 334 optimal weight: 0.9990 chunk 597 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 364 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 ASN M 36 ASN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS U 54 ASN ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 222 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 51464 Z= 0.249 Angle : 0.592 15.649 69484 Z= 0.312 Chirality : 0.045 0.225 7764 Planarity : 0.004 0.059 8864 Dihedral : 6.932 70.141 7030 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.37 % Allowed : 18.75 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.11), residues: 6250 helix: 0.46 (0.11), residues: 2168 sheet: -1.41 (0.14), residues: 1366 loop : -1.96 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 179 HIS 0.008 0.001 HIS V 134 PHE 0.018 0.001 PHE D 194 TYR 0.026 0.001 TYR H 118 ARG 0.007 0.000 ARG Q 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 833 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7453 (mm) REVERT: B 119 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 158 TRP cc_start: 0.8536 (m100) cc_final: 0.8014 (m100) REVERT: B 159 MET cc_start: 0.7951 (mmt) cc_final: 0.7159 (mmt) REVERT: B 184 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6087 (mt) REVERT: C 41 ASP cc_start: 0.7930 (t0) cc_final: 0.7346 (t0) REVERT: C 130 TYR cc_start: 0.8770 (m-80) cc_final: 0.8471 (m-10) REVERT: D 37 SER cc_start: 0.8847 (t) cc_final: 0.8547 (t) REVERT: D 66 ASP cc_start: 0.8488 (m-30) cc_final: 0.8143 (m-30) REVERT: D 99 ASP cc_start: 0.8382 (t0) cc_final: 0.7898 (t0) REVERT: D 198 GLU cc_start: 0.7222 (tp30) cc_final: 0.6980 (pt0) REVERT: E 114 GLU cc_start: 0.8302 (tp30) cc_final: 0.8050 (tt0) REVERT: E 205 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8213 (ttm170) REVERT: F 68 ASP cc_start: 0.7803 (m-30) cc_final: 0.7557 (m-30) REVERT: F 227 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8298 (tm-30) REVERT: H 32 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7593 (mmm160) REVERT: H 156 TYR cc_start: 0.8216 (t80) cc_final: 0.7956 (t80) REVERT: I 53 GLU cc_start: 0.8056 (tt0) cc_final: 0.7712 (mt-10) REVERT: I 217 ILE cc_start: 0.6268 (mt) cc_final: 0.6000 (mt) REVERT: K 2 ASP cc_start: 0.7509 (p0) cc_final: 0.7249 (p0) REVERT: K 20 TYR cc_start: 0.8051 (m-10) cc_final: 0.7604 (m-10) REVERT: K 69 GLN cc_start: 0.8021 (mt0) cc_final: 0.7772 (mt0) REVERT: L 6 PHE cc_start: 0.8287 (m-10) cc_final: 0.7983 (m-10) REVERT: L 192 ASP cc_start: 0.6710 (t0) cc_final: 0.5857 (t0) REVERT: M 29 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7633 (tpm170) REVERT: M 56 ARG cc_start: 0.8916 (ttm170) cc_final: 0.8584 (ttm170) REVERT: M 174 LEU cc_start: 0.8993 (mt) cc_final: 0.8766 (mt) REVERT: N 89 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8832 (tm-30) REVERT: N 197 MET cc_start: 0.8590 (mtm) cc_final: 0.8300 (mtm) REVERT: O 139 LEU cc_start: 0.8994 (mm) cc_final: 0.8653 (mp) REVERT: O 253 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7968 (mm) REVERT: P 119 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7537 (tm-30) REVERT: P 184 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.5826 (mt) REVERT: Q 87 ILE cc_start: 0.8802 (mm) cc_final: 0.8586 (mm) REVERT: Q 183 MET cc_start: 0.7525 (ttp) cc_final: 0.7062 (ttp) REVERT: R 37 SER cc_start: 0.8838 (t) cc_final: 0.8528 (t) REVERT: R 176 TYR cc_start: 0.8411 (t80) cc_final: 0.8194 (t80) REVERT: S 212 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8935 (mm) REVERT: T 68 ASP cc_start: 0.7809 (m-30) cc_final: 0.7553 (m-30) REVERT: T 227 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8278 (tm-30) REVERT: U 197 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8410 (m-10) REVERT: V 156 TYR cc_start: 0.8228 (t80) cc_final: 0.7936 (t80) REVERT: V 182 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8237 (m) REVERT: V 220 ASN cc_start: 0.8169 (p0) cc_final: 0.7815 (p0) REVERT: W 53 GLU cc_start: 0.8080 (tt0) cc_final: 0.7788 (mt-10) REVERT: W 54 HIS cc_start: 0.7650 (t-90) cc_final: 0.7347 (t-90) REVERT: X 139 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8684 (pp) REVERT: Y 20 TYR cc_start: 0.8045 (m-10) cc_final: 0.7573 (m-10) REVERT: Y 69 GLN cc_start: 0.7999 (mt0) cc_final: 0.7653 (mt0) REVERT: Y 165 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: Z 115 ASP cc_start: 0.8177 (t70) cc_final: 0.7495 (t0) REVERT: Z 192 ASP cc_start: 0.6639 (t0) cc_final: 0.5926 (t0) REVERT: a 29 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7706 (tpm170) REVERT: b 22 MET cc_start: 0.8056 (ttm) cc_final: 0.7746 (ttm) REVERT: b 75 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8309 (t0) REVERT: b 89 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8840 (tm-30) outliers start: 187 outliers final: 150 residues processed: 937 average time/residue: 0.5077 time to fit residues: 794.2897 Evaluate side-chains 950 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 790 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 154 CYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 197 TYR Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 209 ILE Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 174 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 369 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 117 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 379 optimal weight: 4.9990 chunk 407 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 469 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 ASN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 51464 Z= 0.199 Angle : 0.576 15.796 69484 Z= 0.303 Chirality : 0.044 0.227 7764 Planarity : 0.004 0.062 8864 Dihedral : 6.875 72.341 7030 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.37 % Allowed : 18.97 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.11), residues: 6250 helix: 0.58 (0.11), residues: 2172 sheet: -1.37 (0.14), residues: 1364 loop : -1.93 (0.12), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 179 HIS 0.018 0.001 HIS F 176 PHE 0.014 0.001 PHE D 194 TYR 0.026 0.001 TYR I 36 ARG 0.006 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 855 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7358 (mm) REVERT: B 119 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 158 TRP cc_start: 0.8537 (m100) cc_final: 0.8135 (m100) REVERT: B 159 MET cc_start: 0.7827 (mmt) cc_final: 0.7224 (mmt) REVERT: B 184 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6077 (mt) REVERT: C 41 ASP cc_start: 0.7894 (t0) cc_final: 0.7644 (m-30) REVERT: C 130 TYR cc_start: 0.8869 (m-80) cc_final: 0.8607 (m-10) REVERT: C 224 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.5522 (mp10) REVERT: D 37 SER cc_start: 0.8815 (t) cc_final: 0.8497 (t) REVERT: D 66 ASP cc_start: 0.8499 (m-30) cc_final: 0.8148 (m-30) REVERT: D 99 ASP cc_start: 0.8369 (t0) cc_final: 0.7856 (t0) REVERT: E 114 GLU cc_start: 0.8281 (tp30) cc_final: 0.8048 (tt0) REVERT: E 205 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8215 (ttm170) REVERT: E 218 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7139 (mm-30) REVERT: F 68 ASP cc_start: 0.7782 (m-30) cc_final: 0.7542 (m-30) REVERT: F 227 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8239 (tm-30) REVERT: G 155 GLU cc_start: 0.8276 (mp0) cc_final: 0.7918 (mp0) REVERT: H 32 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7647 (mmm160) REVERT: H 138 LYS cc_start: 0.7601 (tptp) cc_final: 0.7124 (tptt) REVERT: H 156 TYR cc_start: 0.8214 (t80) cc_final: 0.7955 (t80) REVERT: H 220 ASN cc_start: 0.8090 (p0) cc_final: 0.7786 (p0) REVERT: I 53 GLU cc_start: 0.8036 (tt0) cc_final: 0.7741 (mt-10) REVERT: I 174 ASP cc_start: 0.8241 (p0) cc_final: 0.7995 (p0) REVERT: J 218 ASP cc_start: 0.6816 (m-30) cc_final: 0.6399 (m-30) REVERT: K 20 TYR cc_start: 0.8027 (m-10) cc_final: 0.7552 (m-10) REVERT: K 69 GLN cc_start: 0.8009 (mt0) cc_final: 0.7730 (mt0) REVERT: L 3 THR cc_start: 0.9060 (m) cc_final: 0.8779 (m) REVERT: L 6 PHE cc_start: 0.8267 (m-80) cc_final: 0.7995 (m-10) REVERT: L 115 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7821 (t0) REVERT: L 192 ASP cc_start: 0.6626 (t0) cc_final: 0.5816 (t0) REVERT: M 29 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7629 (tpm170) REVERT: M 56 ARG cc_start: 0.8893 (ttm170) cc_final: 0.8582 (ttm170) REVERT: N 89 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8824 (tm-30) REVERT: N 197 MET cc_start: 0.8608 (mtm) cc_final: 0.8325 (mtm) REVERT: O 139 LEU cc_start: 0.8972 (mm) cc_final: 0.8635 (mp) REVERT: O 253 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7851 (mm) REVERT: P 119 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7466 (tm-30) REVERT: P 184 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6076 (mt) REVERT: Q 183 MET cc_start: 0.7481 (ttp) cc_final: 0.7017 (ttp) REVERT: Q 224 GLN cc_start: 0.6423 (OUTLIER) cc_final: 0.5587 (mp10) REVERT: R 37 SER cc_start: 0.8856 (t) cc_final: 0.8489 (t) REVERT: R 79 ASP cc_start: 0.7806 (m-30) cc_final: 0.7121 (m-30) REVERT: R 125 ARG cc_start: 0.8603 (ttp80) cc_final: 0.7886 (ttp80) REVERT: R 176 TYR cc_start: 0.8370 (t80) cc_final: 0.8155 (t80) REVERT: S 14 THR cc_start: 0.8153 (p) cc_final: 0.7910 (p) REVERT: S 212 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8935 (mm) REVERT: T 68 ASP cc_start: 0.7791 (m-30) cc_final: 0.7549 (m-30) REVERT: T 227 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8265 (tm-30) REVERT: U 197 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: V 156 TYR cc_start: 0.8242 (t80) cc_final: 0.7957 (t80) REVERT: V 182 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8256 (m) REVERT: V 220 ASN cc_start: 0.8058 (p0) cc_final: 0.7727 (p0) REVERT: W 53 GLU cc_start: 0.8084 (tt0) cc_final: 0.7813 (mt-10) REVERT: W 54 HIS cc_start: 0.7634 (t-90) cc_final: 0.7324 (t-90) REVERT: X 129 ASN cc_start: 0.8022 (p0) cc_final: 0.7731 (p0) REVERT: X 139 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8650 (pp) REVERT: Y 2 ASP cc_start: 0.7495 (p0) cc_final: 0.7220 (p0) REVERT: Y 20 TYR cc_start: 0.8025 (m-10) cc_final: 0.7532 (m-10) REVERT: Y 69 GLN cc_start: 0.7978 (mt0) cc_final: 0.7618 (mt0) REVERT: Y 165 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: Z 3 THR cc_start: 0.9054 (m) cc_final: 0.8715 (m) REVERT: Z 115 ASP cc_start: 0.8153 (t70) cc_final: 0.7447 (t0) REVERT: Z 192 ASP cc_start: 0.6567 (t0) cc_final: 0.6107 (t0) REVERT: b 22 MET cc_start: 0.8043 (ttm) cc_final: 0.7741 (ttm) REVERT: b 75 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8292 (t0) REVERT: b 89 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8843 (tm-30) outliers start: 187 outliers final: 140 residues processed: 960 average time/residue: 0.4943 time to fit residues: 791.1863 Evaluate side-chains 954 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 801 time to evaluate : 5.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 197 TYR Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 543 optimal weight: 3.9990 chunk 572 optimal weight: 5.9990 chunk 522 optimal weight: 1.9990 chunk 556 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 437 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 503 optimal weight: 0.1980 chunk 526 optimal weight: 1.9990 chunk 554 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS I 54 HIS ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 51464 Z= 0.199 Angle : 0.578 15.788 69484 Z= 0.304 Chirality : 0.044 0.245 7764 Planarity : 0.004 0.066 8864 Dihedral : 6.850 74.725 7030 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.06 % Allowed : 19.63 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.11), residues: 6250 helix: 0.66 (0.11), residues: 2162 sheet: -1.34 (0.14), residues: 1364 loop : -1.89 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 179 HIS 0.021 0.001 HIS F 176 PHE 0.016 0.001 PHE T 178 TYR 0.029 0.001 TYR L 88 ARG 0.009 0.000 ARG a 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 844 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7368 (mm) REVERT: B 119 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 158 TRP cc_start: 0.8550 (m100) cc_final: 0.8138 (m100) REVERT: B 159 MET cc_start: 0.7790 (mmt) cc_final: 0.7194 (mmt) REVERT: B 184 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6067 (mt) REVERT: C 41 ASP cc_start: 0.7893 (t0) cc_final: 0.7652 (m-30) REVERT: C 130 TYR cc_start: 0.8862 (m-80) cc_final: 0.8597 (m-10) REVERT: C 224 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.5531 (mp10) REVERT: D 37 SER cc_start: 0.8825 (t) cc_final: 0.8506 (t) REVERT: D 66 ASP cc_start: 0.8495 (m-30) cc_final: 0.8148 (m-30) REVERT: D 79 ASP cc_start: 0.7776 (m-30) cc_final: 0.7570 (m-30) REVERT: D 99 ASP cc_start: 0.8365 (t0) cc_final: 0.7833 (t0) REVERT: E 205 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8217 (ttm170) REVERT: E 218 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7199 (mm-30) REVERT: F 68 ASP cc_start: 0.7777 (m-30) cc_final: 0.7549 (m-30) REVERT: G 155 GLU cc_start: 0.8324 (mp0) cc_final: 0.7938 (mp0) REVERT: G 188 ASN cc_start: 0.6799 (t0) cc_final: 0.6580 (t0) REVERT: H 32 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7703 (mmm160) REVERT: H 138 LYS cc_start: 0.7612 (tptp) cc_final: 0.7171 (tptt) REVERT: H 156 TYR cc_start: 0.8213 (t80) cc_final: 0.7965 (t80) REVERT: I 53 GLU cc_start: 0.8045 (tt0) cc_final: 0.7766 (mt-10) REVERT: I 174 ASP cc_start: 0.8252 (p0) cc_final: 0.8033 (p0) REVERT: K 20 TYR cc_start: 0.8029 (m-10) cc_final: 0.7545 (m-10) REVERT: K 69 GLN cc_start: 0.8005 (mt0) cc_final: 0.7755 (mt0) REVERT: K 165 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: L 115 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7827 (t0) REVERT: L 192 ASP cc_start: 0.6669 (t0) cc_final: 0.6021 (t0) REVERT: M 29 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7633 (tpm170) REVERT: M 56 ARG cc_start: 0.8901 (ttm170) cc_final: 0.8582 (ttm170) REVERT: N 89 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8824 (tm-30) REVERT: N 197 MET cc_start: 0.8616 (mtm) cc_final: 0.8329 (mtm) REVERT: O 139 LEU cc_start: 0.8979 (mm) cc_final: 0.8632 (mp) REVERT: O 253 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7876 (mm) REVERT: P 119 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7695 (tm-30) REVERT: P 184 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6074 (mt) REVERT: Q 183 MET cc_start: 0.7465 (ttp) cc_final: 0.6987 (ttp) REVERT: Q 224 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5605 (mp10) REVERT: R 37 SER cc_start: 0.8866 (t) cc_final: 0.8502 (t) REVERT: R 79 ASP cc_start: 0.7787 (m-30) cc_final: 0.7483 (m-30) REVERT: S 14 THR cc_start: 0.8169 (p) cc_final: 0.7913 (p) REVERT: S 212 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8791 (mm) REVERT: T 68 ASP cc_start: 0.7787 (m-30) cc_final: 0.7543 (m-30) REVERT: U 197 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8268 (m-10) REVERT: V 138 LYS cc_start: 0.7589 (tptp) cc_final: 0.7171 (tptt) REVERT: V 156 TYR cc_start: 0.8358 (t80) cc_final: 0.8038 (t80) REVERT: V 182 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8238 (m) REVERT: W 53 GLU cc_start: 0.8108 (tt0) cc_final: 0.7807 (mt-10) REVERT: W 54 HIS cc_start: 0.7624 (t-90) cc_final: 0.7315 (t-90) REVERT: X 139 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8648 (pp) REVERT: X 218 ASP cc_start: 0.6594 (m-30) cc_final: 0.6105 (m-30) REVERT: Y 20 TYR cc_start: 0.8076 (m-10) cc_final: 0.7566 (m-10) REVERT: Y 69 GLN cc_start: 0.7983 (mt0) cc_final: 0.7626 (mt0) REVERT: Y 165 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: Z 3 THR cc_start: 0.9070 (m) cc_final: 0.8712 (m) REVERT: Z 18 SER cc_start: 0.7876 (p) cc_final: 0.7506 (t) REVERT: Z 115 ASP cc_start: 0.8138 (t70) cc_final: 0.7419 (t0) REVERT: Z 192 ASP cc_start: 0.6590 (t0) cc_final: 0.6080 (t0) REVERT: a 29 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7512 (tpm170) REVERT: b 22 MET cc_start: 0.8037 (ttm) cc_final: 0.7747 (ttm) REVERT: b 75 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8286 (t0) REVERT: b 89 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8843 (tm-30) outliers start: 170 outliers final: 142 residues processed: 937 average time/residue: 0.5026 time to fit residues: 785.4669 Evaluate side-chains 978 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 822 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 154 CYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 197 TYR Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 365 optimal weight: 0.8980 chunk 588 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 409 optimal weight: 7.9990 chunk 617 optimal weight: 0.6980 chunk 568 optimal weight: 0.8980 chunk 491 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 379 optimal weight: 0.0770 chunk 301 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS I 54 HIS ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 176 GLN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 178 HIS ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 51464 Z= 0.175 Angle : 0.579 15.564 69484 Z= 0.304 Chirality : 0.044 0.247 7764 Planarity : 0.004 0.067 8864 Dihedral : 6.812 77.782 7030 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.88 % Allowed : 20.08 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.11), residues: 6250 helix: 0.75 (0.11), residues: 2166 sheet: -1.27 (0.14), residues: 1358 loop : -1.87 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 179 HIS 0.012 0.001 HIS F 176 PHE 0.020 0.001 PHE X 149 TYR 0.025 0.001 TYR I 36 ARG 0.010 0.000 ARG A 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 882 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7416 (mm) REVERT: B 119 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 158 TRP cc_start: 0.8534 (m100) cc_final: 0.7959 (m100) REVERT: B 159 MET cc_start: 0.7762 (mmt) cc_final: 0.7182 (mmt) REVERT: B 184 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6071 (mt) REVERT: C 41 ASP cc_start: 0.7874 (t0) cc_final: 0.7640 (m-30) REVERT: C 130 TYR cc_start: 0.8869 (m-80) cc_final: 0.8524 (m-10) REVERT: C 224 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5507 (mp10) REVERT: D 37 SER cc_start: 0.8855 (t) cc_final: 0.8493 (t) REVERT: D 66 ASP cc_start: 0.8493 (m-30) cc_final: 0.8139 (m-30) REVERT: D 79 ASP cc_start: 0.7750 (m-30) cc_final: 0.7531 (m-30) REVERT: D 99 ASP cc_start: 0.8350 (t0) cc_final: 0.7792 (t0) REVERT: E 205 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8262 (ttm170) REVERT: F 68 ASP cc_start: 0.7767 (m-30) cc_final: 0.7537 (m-30) REVERT: G 57 LYS cc_start: 0.6410 (tptp) cc_final: 0.5860 (pttm) REVERT: G 155 GLU cc_start: 0.8317 (mp0) cc_final: 0.7953 (mp0) REVERT: H 32 ARG cc_start: 0.8087 (mmt-90) cc_final: 0.7675 (mmm160) REVERT: H 138 LYS cc_start: 0.7530 (tptp) cc_final: 0.7090 (tptt) REVERT: H 156 TYR cc_start: 0.8357 (t80) cc_final: 0.8087 (t80) REVERT: I 53 GLU cc_start: 0.8049 (tt0) cc_final: 0.7787 (mt-10) REVERT: J 84 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7458 (tmt) REVERT: K 20 TYR cc_start: 0.8011 (m-10) cc_final: 0.7542 (m-10) REVERT: K 69 GLN cc_start: 0.7995 (mt0) cc_final: 0.7724 (mt0) REVERT: L 3 THR cc_start: 0.8943 (m) cc_final: 0.8636 (m) REVERT: L 115 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7779 (t0) REVERT: L 192 ASP cc_start: 0.6674 (t0) cc_final: 0.6164 (t0) REVERT: M 29 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7610 (tpm170) REVERT: M 56 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8575 (ttm170) REVERT: N 89 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8832 (tm-30) REVERT: N 197 MET cc_start: 0.8615 (mtm) cc_final: 0.8330 (mtm) REVERT: O 139 LEU cc_start: 0.8930 (mm) cc_final: 0.8586 (mp) REVERT: O 230 GLU cc_start: 0.7330 (pm20) cc_final: 0.6952 (pm20) REVERT: O 253 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7774 (mm) REVERT: P 119 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7637 (tm-30) REVERT: P 184 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.6107 (mt) REVERT: Q 183 MET cc_start: 0.7381 (ttp) cc_final: 0.6909 (ttp) REVERT: Q 224 GLN cc_start: 0.6415 (OUTLIER) cc_final: 0.5619 (mp10) REVERT: R 37 SER cc_start: 0.8820 (t) cc_final: 0.8457 (t) REVERT: S 14 THR cc_start: 0.8126 (p) cc_final: 0.7904 (p) REVERT: T 68 ASP cc_start: 0.7773 (m-30) cc_final: 0.7541 (m-30) REVERT: T 88 MET cc_start: 0.8067 (mtp) cc_final: 0.7629 (mtp) REVERT: U 57 LYS cc_start: 0.6385 (tptp) cc_final: 0.5908 (pttm) REVERT: U 197 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: V 138 LYS cc_start: 0.7529 (tptp) cc_final: 0.7119 (tptt) REVERT: V 156 TYR cc_start: 0.8296 (t80) cc_final: 0.7991 (t80) REVERT: V 182 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8298 (m) REVERT: V 218 MET cc_start: 0.8343 (mmm) cc_final: 0.8041 (mmm) REVERT: V 220 ASN cc_start: 0.7923 (p0) cc_final: 0.7637 (p0) REVERT: W 53 GLU cc_start: 0.8055 (tt0) cc_final: 0.7656 (mt-10) REVERT: W 54 HIS cc_start: 0.7604 (t-90) cc_final: 0.7309 (t-90) REVERT: W 60 GLN cc_start: 0.8808 (tt0) cc_final: 0.8597 (tt0) REVERT: X 139 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8590 (pp) REVERT: X 218 ASP cc_start: 0.6574 (m-30) cc_final: 0.6107 (m-30) REVERT: Y 2 ASP cc_start: 0.7489 (p0) cc_final: 0.7274 (p0) REVERT: Y 20 TYR cc_start: 0.8068 (m-10) cc_final: 0.7591 (m-10) REVERT: Y 69 GLN cc_start: 0.7966 (mt0) cc_final: 0.7610 (mt0) REVERT: Y 165 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8234 (tt0) REVERT: Z 3 THR cc_start: 0.9050 (m) cc_final: 0.8703 (m) REVERT: Z 115 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7163 (t0) REVERT: Z 116 ASP cc_start: 0.7703 (p0) cc_final: 0.7437 (p0) REVERT: Z 192 ASP cc_start: 0.6520 (t0) cc_final: 0.5860 (t0) REVERT: a 29 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7570 (tpm170) REVERT: a 39 THR cc_start: 0.8855 (t) cc_final: 0.8623 (m) REVERT: b 22 MET cc_start: 0.8030 (ttm) cc_final: 0.7738 (ttm) REVERT: b 75 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8288 (t0) REVERT: b 89 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8840 (tm-30) outliers start: 160 outliers final: 128 residues processed: 969 average time/residue: 0.4932 time to fit residues: 798.6926 Evaluate side-chains 978 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 837 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 154 CYS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 197 TYR Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 390 optimal weight: 5.9990 chunk 523 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 453 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 492 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 505 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 HIS ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123507 restraints weight = 70150.421| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.28 r_work: 0.3406 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 51464 Z= 0.339 Angle : 0.647 16.363 69484 Z= 0.339 Chirality : 0.047 0.252 7764 Planarity : 0.004 0.069 8864 Dihedral : 6.965 71.710 7030 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.01 % Allowed : 19.97 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.11), residues: 6250 helix: 0.59 (0.11), residues: 2170 sheet: -1.38 (0.14), residues: 1364 loop : -1.92 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 179 HIS 0.009 0.001 HIS H 134 PHE 0.020 0.002 PHE X 149 TYR 0.029 0.002 TYR B 101 ARG 0.009 0.001 ARG O 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12834.11 seconds wall clock time: 223 minutes 21.60 seconds (13401.60 seconds total)