Starting phenix.real_space_refine on Tue Jan 14 13:48:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f9p_50258/01_2025/9f9p_50258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f9p_50258/01_2025/9f9p_50258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f9p_50258/01_2025/9f9p_50258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f9p_50258/01_2025/9f9p_50258.map" model { file = "/net/cci-nas-00/data/ceres_data/9f9p_50258/01_2025/9f9p_50258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f9p_50258/01_2025/9f9p_50258.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 322 5.16 5 C 30556 2.51 5 N 8360 2.21 5 O 10358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 410 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 49596 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1884 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "C" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2126 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain: "D" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1864 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "E" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1757 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Chain: "F" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1722 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "G" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1724 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "I" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1663 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1555 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1586 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain: "L" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1578 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 199} Chain: "M" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1647 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "N" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1695 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "N" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "T" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "U" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "Y" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "Z" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "a" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "b" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Restraints were copied for chains: Z, b, R, P, O, Q, a, Y, X, T, V, U, S, W Time building chain proxies: 21.48, per 1000 atoms: 0.43 Number of scatterers: 49596 At special positions: 0 Unit cell: (152.46, 199.98, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 322 16.00 O 10358 8.00 N 8360 7.00 C 30556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 8.96 Conformation dependent library (CDL) restraints added in 4.8 seconds 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11548 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 74 sheets defined 39.1% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.515A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 80 through 103 Processing helix chain 'A' and resid 107 through 125 removed outlier: 3.864A pdb=" N ARG A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.529A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.508A pdb=" N TRP A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.816A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.610A pdb=" N PHE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.520A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.938A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.528A pdb=" N ASP B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 85 through 108 Processing helix chain 'C' and resid 112 through 128 removed outlier: 4.077A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 Processing helix chain 'C' and resid 190 through 207 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.744A pdb=" N LYS C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Proline residue: C 256 - end of helix removed outlier: 3.516A pdb=" N GLN C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.557A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.616A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.518A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.534A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.687A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.782A pdb=" N ASN E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.816A pdb=" N ILE E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.522A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 185 removed outlier: 3.737A pdb=" N THR E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 231 through 241 removed outlier: 3.770A pdb=" N ARG E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 removed outlier: 3.618A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 101 Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.802A pdb=" N HIS F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 177 removed outlier: 3.949A pdb=" N ALA F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS F 175 " --> pdb=" O THR F 171 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS F 176 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 184 through 198 removed outlier: 3.529A pdb=" N ALA F 198 " --> pdb=" O LYS F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 31 removed outlier: 3.535A pdb=" N ALA G 28 " --> pdb=" O TYR G 24 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 102 Processing helix chain 'G' and resid 106 through 121 removed outlier: 4.059A pdb=" N TYR G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 removed outlier: 3.548A pdb=" N THR G 172 " --> pdb=" O THR G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 199 removed outlier: 3.706A pdb=" N VAL G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 102 through 125 Processing helix chain 'H' and resid 129 through 144 Processing helix chain 'H' and resid 145 through 148 removed outlier: 3.799A pdb=" N ILE H 148 " --> pdb=" O LYS H 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 148' Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.882A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 Processing helix chain 'H' and resid 202 through 221 removed outlier: 3.696A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 251 through 259 Proline residue: H 256 - end of helix Processing helix chain 'I' and resid 114 through 137 Processing helix chain 'I' and resid 141 through 156 removed outlier: 3.614A pdb=" N TYR I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 208 removed outlier: 3.815A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 232 removed outlier: 3.601A pdb=" N GLY I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 177 removed outlier: 3.668A pdb=" N ARG J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 78 through 95 removed outlier: 3.720A pdb=" N ARG K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 163 through 182 Processing helix chain 'L' and resid 158 through 181 Processing helix chain 'L' and resid 185 through 200 Processing helix chain 'L' and resid 241 through 253 removed outlier: 5.078A pdb=" N GLY L 247 " --> pdb=" O ILE L 243 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL L 248 " --> pdb=" O TYR L 244 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN L 251 " --> pdb=" O GLY L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 277 removed outlier: 3.664A pdb=" N ARG L 276 " --> pdb=" O HIS L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 310 removed outlier: 3.649A pdb=" N ASP L 307 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 117 through 131 Processing helix chain 'M' and resid 174 through 188 Proline residue: M 180 - end of helix Processing helix chain 'M' and resid 200 through 219 Processing helix chain 'N' and resid 53 through 73 Processing helix chain 'N' and resid 79 through 97 Processing helix chain 'N' and resid 136 through 149 removed outlier: 4.544A pdb=" N LEU N 142 " --> pdb=" O ALA N 138 " (cutoff:3.500A) Proline residue: N 143 - end of helix Processing helix chain 'N' and resid 156 through 175 Processing helix chain 'N' and resid 206 through 209 Processing helix chain 'N' and resid 210 through 215 Processing helix chain 'O' and resid 19 through 32 removed outlier: 3.512A pdb=" N LYS O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 63 Processing helix chain 'O' and resid 80 through 103 Processing helix chain 'O' and resid 107 through 125 removed outlier: 3.863A pdb=" N ARG O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 123 " --> pdb=" O ALA O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 186 removed outlier: 3.531A pdb=" N LYS O 186 " --> pdb=" O GLU O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'O' and resid 194 through 211 Processing helix chain 'O' and resid 215 through 217 No H-bonds generated for 'chain 'O' and resid 215 through 217' Processing helix chain 'O' and resid 235 through 249 removed outlier: 3.509A pdb=" N TRP O 242 " --> pdb=" O ASP O 238 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA O 249 " --> pdb=" O ALA O 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 28 Processing helix chain 'P' and resid 77 through 100 removed outlier: 3.816A pdb=" N VAL P 83 " --> pdb=" O PRO P 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 119 removed outlier: 3.610A pdb=" N PHE P 119 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 176 removed outlier: 3.518A pdb=" N LYS P 174 " --> pdb=" O THR P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.941A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 229 removed outlier: 3.528A pdb=" N ASP P 226 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR P 227 " --> pdb=" O GLN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 85 through 108 Processing helix chain 'Q' and resid 112 through 128 removed outlier: 4.078A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR Q 128 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 185 Processing helix chain 'Q' and resid 190 through 207 Processing helix chain 'Q' and resid 250 through 267 removed outlier: 3.744A pdb=" N LYS Q 255 " --> pdb=" O GLU Q 251 " (cutoff:3.500A) Proline residue: Q 256 - end of helix removed outlier: 3.515A pdb=" N GLN Q 264 " --> pdb=" O GLU Q 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG Q 265 " --> pdb=" O ALA Q 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 29 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.558A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.615A pdb=" N THR R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.520A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.533A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.688A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 65 removed outlier: 3.783A pdb=" N ASN S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.817A pdb=" N ILE S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 120 removed outlier: 3.523A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 185 removed outlier: 3.737A pdb=" N THR S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU S 183 " --> pdb=" O THR S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 231 through 241 removed outlier: 3.770A pdb=" N ARG S 237 " --> pdb=" O THR S 233 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE S 238 " --> pdb=" O LYS S 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 31 removed outlier: 3.618A pdb=" N ALA T 28 " --> pdb=" O TYR T 24 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 101 Processing helix chain 'T' and resid 105 through 120 removed outlier: 3.805A pdb=" N HIS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 177 removed outlier: 3.949A pdb=" N ALA T 169 " --> pdb=" O ARG T 165 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS T 175 " --> pdb=" O THR T 171 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS T 176 " --> pdb=" O TYR T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 180 No H-bonds generated for 'chain 'T' and resid 178 through 180' Processing helix chain 'T' and resid 184 through 198 removed outlier: 3.534A pdb=" N ALA T 198 " --> pdb=" O LYS T 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 31 removed outlier: 3.536A pdb=" N ALA U 28 " --> pdb=" O TYR U 24 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 102 Processing helix chain 'U' and resid 106 through 121 removed outlier: 4.060A pdb=" N TYR U 121 " --> pdb=" O PHE U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 166 through 175 removed outlier: 3.551A pdb=" N THR U 172 " --> pdb=" O THR U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 199 removed outlier: 3.708A pdb=" N VAL U 188 " --> pdb=" O CYS U 184 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL U 189 " --> pdb=" O ASP U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 217 through 219 No H-bonds generated for 'chain 'U' and resid 217 through 219' Processing helix chain 'V' and resid 102 through 125 Processing helix chain 'V' and resid 129 through 144 Processing helix chain 'V' and resid 145 through 148 removed outlier: 3.795A pdb=" N ILE V 148 " --> pdb=" O LYS V 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 145 through 148' Processing helix chain 'V' and resid 183 through 188 removed outlier: 3.884A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 197 Processing helix chain 'V' and resid 202 through 221 removed outlier: 3.695A pdb=" N ARG V 220 " --> pdb=" O HIS V 216 " (cutoff:3.500A) Processing helix chain 'V' and resid 244 through 248 Processing helix chain 'V' and resid 251 through 259 Proline residue: V 256 - end of helix Processing helix chain 'W' and resid 114 through 137 Processing helix chain 'W' and resid 141 through 156 removed outlier: 3.612A pdb=" N TYR W 156 " --> pdb=" O HIS W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 208 removed outlier: 3.814A pdb=" N ALA W 203 " --> pdb=" O ALA W 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 213 through 232 removed outlier: 3.600A pdb=" N GLY W 228 " --> pdb=" O ALA W 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 142 through 154 Processing helix chain 'X' and resid 159 through 177 removed outlier: 3.668A pdb=" N ARG X 177 " --> pdb=" O SER X 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 71 Processing helix chain 'Y' and resid 78 through 95 removed outlier: 3.720A pdb=" N ARG Y 95 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 158 Processing helix chain 'Y' and resid 163 through 182 Processing helix chain 'Z' and resid 158 through 181 Processing helix chain 'Z' and resid 185 through 200 Processing helix chain 'Z' and resid 241 through 253 removed outlier: 5.077A pdb=" N GLY Z 247 " --> pdb=" O ILE Z 243 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL Z 248 " --> pdb=" O TYR Z 244 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN Z 251 " --> pdb=" O GLY Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 258 through 277 removed outlier: 3.664A pdb=" N ARG Z 276 " --> pdb=" O HIS Z 272 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 310 removed outlier: 3.646A pdb=" N ASP Z 307 " --> pdb=" O THR Z 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 111 Processing helix chain 'a' and resid 117 through 131 Processing helix chain 'a' and resid 174 through 188 Proline residue: a 180 - end of helix Processing helix chain 'a' and resid 200 through 219 Processing helix chain 'b' and resid 53 through 73 Processing helix chain 'b' and resid 79 through 97 Processing helix chain 'b' and resid 136 through 149 removed outlier: 4.544A pdb=" N LEU b 142 " --> pdb=" O ALA b 138 " (cutoff:3.500A) Proline residue: b 143 - end of helix Processing helix chain 'b' and resid 156 through 175 Processing helix chain 'b' and resid 206 through 209 Processing helix chain 'b' and resid 210 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.249A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.696A pdb=" N ILE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.715A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.613A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.693A pdb=" N HIS D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.574A pdb=" N ILE D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.763A pdb=" N MET E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP E 147 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 159 through 162 removed outlier: 5.414A pdb=" N GLY F 217 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 64 through 68 removed outlier: 6.419A pdb=" N VAL F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'G' and resid 65 through 69 removed outlier: 6.443A pdb=" N ALA G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA G 140 " --> pdb=" O GLY G 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 179 through 182 Processing sheet with id=AB8, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AB9, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.437A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 190 through 193 removed outlier: 6.621A pdb=" N VAL I 239 " --> pdb=" O GLY I 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY I 254 " --> pdb=" O VAL I 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.611A pdb=" N GLU I 88 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 100 through 104 removed outlier: 6.468A pdb=" N ILE I 107 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA I 163 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 277 through 284 removed outlier: 3.903A pdb=" N ARG I 279 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.905A pdb=" N LEU J 28 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.618A pdb=" N ILE J 49 " --> pdb=" O ILE J 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 54 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.704A pdb=" N CYS K 191 " --> pdb=" O VAL K 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.678A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.622A pdb=" N LYS K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 235 through 238 removed outlier: 3.535A pdb=" N SER L 298 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS L 288 " --> pdb=" O GLN L 296 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLN L 296 " --> pdb=" O HIS L 288 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS L 290 " --> pdb=" O TRP L 294 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'L' and resid 144 through 146 removed outlier: 4.028A pdb=" N MET L 210 " --> pdb=" O THR L 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 168 through 172 removed outlier: 5.739A pdb=" N THR M 42 " --> pdb=" O ASP M 57 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 60 through 61 removed outlier: 3.514A pdb=" N THR M 68 " --> pdb=" O LEU M 60 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 75 through 79 removed outlier: 6.518A pdb=" N THR M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.612A pdb=" N THR N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 3 through 4 Processing sheet with id=AD9, first strand: chain 'N' and resid 131 through 134 Processing sheet with id=AE1, first strand: chain 'N' and resid 24 through 26 removed outlier: 6.917A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 167 through 171 removed outlier: 6.252A pdb=" N LEU O 35 " --> pdb=" O GLN O 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 66 through 70 removed outlier: 6.697A pdb=" N ILE O 73 " --> pdb=" O ILE O 69 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 158 through 161 Processing sheet with id=AE5, first strand: chain 'P' and resid 63 through 67 removed outlier: 6.715A pdb=" N VAL P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 167 through 170 Processing sheet with id=AE7, first strand: chain 'Q' and resid 71 through 75 removed outlier: 6.612A pdb=" N ILE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE Q 140 " --> pdb=" O THR Q 156 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.692A pdb=" N HIS R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AF1, first strand: chain 'R' and resid 62 through 66 removed outlier: 6.574A pdb=" N ILE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF3, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.762A pdb=" N MET S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP S 147 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 159 through 162 removed outlier: 5.415A pdb=" N GLY T 217 " --> pdb=" O PRO T 221 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 64 through 68 removed outlier: 6.421A pdb=" N VAL T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 160 through 163 Processing sheet with id=AF7, first strand: chain 'U' and resid 65 through 69 removed outlier: 6.443A pdb=" N ALA U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA U 140 " --> pdb=" O GLY U 143 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 179 through 182 Processing sheet with id=AF9, first strand: chain 'V' and resid 74 through 75 Processing sheet with id=AG1, first strand: chain 'V' and resid 88 through 92 removed outlier: 6.437A pdb=" N ILE V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 190 through 193 removed outlier: 6.618A pdb=" N VAL W 239 " --> pdb=" O GLY W 254 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY W 254 " --> pdb=" O VAL W 239 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 86 through 88 removed outlier: 6.612A pdb=" N GLU W 88 " --> pdb=" O VAL W 92 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL W 92 " --> pdb=" O GLU W 88 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 100 through 104 removed outlier: 6.468A pdb=" N ILE W 107 " --> pdb=" O MET W 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA W 163 " --> pdb=" O ALA W 112 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 277 through 284 removed outlier: 3.902A pdb=" N ARG W 279 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS X 194 " --> pdb=" O THR X 191 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.906A pdb=" N LEU X 28 " --> pdb=" O ILE X 35 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 42 through 46 removed outlier: 6.616A pdb=" N ILE X 49 " --> pdb=" O ILE X 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR X 54 " --> pdb=" O GLU X 106 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 140 through 143 removed outlier: 4.704A pdb=" N CYS Y 191 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 22 through 24 removed outlier: 6.676A pdb=" N PHE Y 24 " --> pdb=" O LYS Y 28 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS Y 28 " --> pdb=" O PHE Y 24 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 36 through 40 removed outlier: 6.621A pdb=" N LYS Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 235 through 238 removed outlier: 3.535A pdb=" N SER Z 298 " --> pdb=" O VAL Z 286 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS Z 288 " --> pdb=" O GLN Z 296 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN Z 296 " --> pdb=" O HIS Z 288 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS Z 290 " --> pdb=" O TRP Z 294 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP Z 294 " --> pdb=" O HIS Z 290 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 130 through 131 Processing sheet with id=AH4, first strand: chain 'Z' and resid 144 through 146 removed outlier: 4.029A pdb=" N MET Z 210 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 168 through 172 removed outlier: 5.742A pdb=" N THR a 42 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 60 through 61 removed outlier: 3.513A pdb=" N THR a 68 " --> pdb=" O LEU a 60 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 75 through 79 removed outlier: 6.518A pdb=" N THR a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 3 through 4 removed outlier: 3.614A pdb=" N THR b 45 " --> pdb=" O VAL b 41 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 3 through 4 Processing sheet with id=AI1, first strand: chain 'b' and resid 131 through 134 Processing sheet with id=AI2, first strand: chain 'b' and resid 24 through 26 removed outlier: 6.917A pdb=" N LEU b 24 " --> pdb=" O LYS b 31 " (cutoff:3.500A) 2741 hydrogen bonds defined for protein. 7857 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: 18.25 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 9567 1.32 - 1.47: 17849 1.47 - 1.61: 21522 1.61 - 1.75: 0 1.75 - 1.90: 490 Bond restraints: 49428 Sorted by residual: bond pdb=" C ALA V 155 " pdb=" O ALA V 155 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.22e-02 6.72e+03 2.01e+01 bond pdb=" C ALA H 155 " pdb=" O ALA H 155 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.22e-02 6.72e+03 2.01e+01 bond pdb=" CD2 HIS b 66 " pdb=" NE2 HIS b 66 " ideal model delta sigma weight residual 1.374 1.423 -0.049 1.10e-02 8.26e+03 1.99e+01 bond pdb=" CD2 HIS N 66 " pdb=" NE2 HIS N 66 " ideal model delta sigma weight residual 1.374 1.423 -0.049 1.10e-02 8.26e+03 1.95e+01 bond pdb=" CE1 HIS T 100 " pdb=" NE2 HIS T 100 " ideal model delta sigma weight residual 1.321 1.365 -0.044 1.00e-02 1.00e+04 1.94e+01 ... (remaining 49423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 61166 2.94 - 5.87: 5267 5.87 - 8.81: 407 8.81 - 11.75: 28 11.75 - 14.68: 12 Bond angle restraints: 66880 Sorted by residual: angle pdb=" C LYS P 48 " pdb=" CA LYS P 48 " pdb=" CB LYS P 48 " ideal model delta sigma weight residual 111.70 97.02 14.68 1.48e+00 4.57e-01 9.84e+01 angle pdb=" C LYS B 48 " pdb=" CA LYS B 48 " pdb=" CB LYS B 48 " ideal model delta sigma weight residual 111.70 97.05 14.65 1.48e+00 4.57e-01 9.80e+01 angle pdb=" C PHE a 177 " pdb=" CA PHE a 177 " pdb=" CB PHE a 177 " ideal model delta sigma weight residual 110.79 98.29 12.50 1.68e+00 3.54e-01 5.54e+01 angle pdb=" C PHE M 177 " pdb=" CA PHE M 177 " pdb=" CB PHE M 177 " ideal model delta sigma weight residual 110.79 98.31 12.48 1.68e+00 3.54e-01 5.52e+01 angle pdb=" CA ASP G 142 " pdb=" CB ASP G 142 " pdb=" CG ASP G 142 " ideal model delta sigma weight residual 112.60 119.96 -7.36 1.00e+00 1.00e+00 5.42e+01 ... (remaining 66875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 26432 17.82 - 35.65: 2296 35.65 - 53.47: 584 53.47 - 71.29: 210 71.29 - 89.12: 98 Dihedral angle restraints: 29620 sinusoidal: 11554 harmonic: 18066 Sorted by residual: dihedral pdb=" C CYS b 103 " pdb=" N CYS b 103 " pdb=" CA CYS b 103 " pdb=" CB CYS b 103 " ideal model delta harmonic sigma weight residual -122.60 -106.33 -16.27 0 2.50e+00 1.60e-01 4.24e+01 dihedral pdb=" C CYS N 103 " pdb=" N CYS N 103 " pdb=" CA CYS N 103 " pdb=" CB CYS N 103 " ideal model delta harmonic sigma weight residual -122.60 -106.37 -16.23 0 2.50e+00 1.60e-01 4.21e+01 dihedral pdb=" CA ASP G 42 " pdb=" C ASP G 42 " pdb=" N GLY G 43 " pdb=" CA GLY G 43 " ideal model delta harmonic sigma weight residual -180.00 -149.90 -30.10 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 29617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5179 0.095 - 0.191: 2047 0.191 - 0.286: 256 0.286 - 0.382: 26 0.382 - 0.477: 4 Chirality restraints: 7512 Sorted by residual: chirality pdb=" CA TYR V 218 " pdb=" N TYR V 218 " pdb=" C TYR V 218 " pdb=" CB TYR V 218 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CA TYR H 218 " pdb=" N TYR H 218 " pdb=" C TYR H 218 " pdb=" CB TYR H 218 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA PRO D 12 " pdb=" N PRO D 12 " pdb=" C PRO D 12 " pdb=" CB PRO D 12 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 7509 not shown) Planarity restraints: 8644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 70 " 0.076 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR R 70 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR R 70 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR R 70 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR R 70 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR R 70 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR R 70 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 70 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 127 " -0.050 2.00e-02 2.50e+03 3.44e-02 2.96e+01 pdb=" CG TRP b 127 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP b 127 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP b 127 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP b 127 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP b 127 " 0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP b 127 " 0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 127 " -0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 127 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP b 127 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 127 " 0.050 2.00e-02 2.50e+03 3.44e-02 2.96e+01 pdb=" CG TRP N 127 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP N 127 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP N 127 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP N 127 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP N 127 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP N 127 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 127 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 127 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP N 127 " 0.047 2.00e-02 2.50e+03 ... (remaining 8641 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 241 2.54 - 3.13: 35777 3.13 - 3.72: 72228 3.72 - 4.31: 114199 4.31 - 4.90: 185110 Nonbonded interactions: 407555 Sorted by model distance: nonbonded pdb=" ND1 HIS S 99 " pdb=" O HOH S 301 " model vdw 1.949 3.120 nonbonded pdb=" ND1 HIS E 99 " pdb=" O HOH E 301 " model vdw 1.959 3.120 nonbonded pdb=" O ASP Z 277 " pdb=" O HOH Z 401 " model vdw 2.178 3.040 nonbonded pdb=" O ASP L 277 " pdb=" O HOH L 401 " model vdw 2.179 3.040 nonbonded pdb=" O ILE W 229 " pdb=" O HOH W 301 " model vdw 2.190 3.040 ... (remaining 407550 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: 0.18 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'W' } 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: 4.810 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: 1.540 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 85.600 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.012 0.093 49428 Z= 0.762 Angle : 1.725 14.682 66880 Z= 1.134 Chirality : 0.093 0.477 7512 Planarity : 0.016 0.202 8644 Dihedral : 16.328 89.117 18072 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.63 % Favored : 96.95 % Rotamer: Outliers : 4.39 % Allowed : 7.87 % Favored : 87.74 % Cbeta Deviations : 0.31 % 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: -1.54 (0.09), residues: 6200 helix: -1.50 (0.09), residues: 2286 sheet: 0.48 (0.13), residues: 1394 loop : -1.28 (0.10), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.015 TRP Q 145 HIS 0.029 0.006 HIS b 90 PHE 0.060 0.012 PHE K 85 TYR 0.076 0.013 TYR R 70 ARG 0.033 0.004 ARG L 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1099 time to evaluate : 4.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8349 (p0) cc_final: 0.8113 (p0) REVERT: A 101 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8192 (tpt90) REVERT: A 183 LYS cc_start: 0.8238 (mttp) cc_final: 0.7990 (ttpm) REVERT: A 227 GLU cc_start: 0.8018 (tt0) cc_final: 0.7790 (tm-30) REVERT: A 238 ASP cc_start: 0.8063 (m-30) cc_final: 0.7384 (t0) REVERT: A 241 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: A 244 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7475 (t) REVERT: B 37 LYS cc_start: 0.8608 (tttp) cc_final: 0.8341 (tttt) REVERT: B 173 GLU cc_start: 0.7417 (tt0) cc_final: 0.7169 (mt-10) REVERT: B 175 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7231 (mtp-110) REVERT: B 180 MET cc_start: 0.8003 (mtp) cc_final: 0.7622 (mtp) REVERT: B 181 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7547 (pt0) REVERT: B 210 ARG cc_start: 0.8676 (ttp-170) cc_final: 0.8375 (ttp-170) REVERT: B 215 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8060 (tttp) REVERT: B 217 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8072 (pm20) REVERT: B 223 GLN cc_start: 0.8317 (mt0) cc_final: 0.7960 (mt0) REVERT: C 48 GLU cc_start: 0.7937 (tt0) cc_final: 0.7710 (pt0) REVERT: C 148 HIS cc_start: 0.8461 (m-70) cc_final: 0.8255 (m-70) REVERT: C 186 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6913 (pttp) REVERT: C 214 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6504 (tp30) REVERT: C 234 GLU cc_start: 0.7994 (mp0) cc_final: 0.7718 (mt-10) REVERT: C 250 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6649 (mpt-90) REVERT: C 264 GLN cc_start: 0.7146 (mt0) cc_final: 0.6849 (mt0) REVERT: D 51 GLN cc_start: 0.6790 (mt0) cc_final: 0.6580 (mt0) REVERT: D 54 GLN cc_start: 0.8266 (tp40) cc_final: 0.7940 (tp-100) REVERT: D 110 TYR cc_start: 0.9089 (t80) cc_final: 0.8880 (t80) REVERT: D 138 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5636 (tm-30) REVERT: D 139 ASN cc_start: 0.6489 (p0) cc_final: 0.6285 (p0) REVERT: D 172 MET cc_start: 0.8476 (mtm) cc_final: 0.8255 (mtp) REVERT: D 173 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6997 (mm-30) REVERT: D 174 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6803 (mttm) REVERT: D 183 ASP cc_start: 0.7248 (m-30) cc_final: 0.6942 (m-30) REVERT: D 195 GLU cc_start: 0.5880 (mm-30) cc_final: 0.5647 (mm-30) REVERT: D 211 ASN cc_start: 0.7849 (t0) cc_final: 0.7532 (t0) REVERT: D 213 LYS cc_start: 0.7122 (mttt) cc_final: 0.6722 (tttm) REVERT: D 222 LEU cc_start: 0.7230 (tp) cc_final: 0.6949 (tp) REVERT: D 228 GLU cc_start: 0.6059 (tt0) cc_final: 0.5826 (tt0) REVERT: E 9 ASP cc_start: 0.5606 (t70) cc_final: 0.5392 (t0) REVERT: E 18 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: E 20 ARG cc_start: 0.8516 (mtt180) cc_final: 0.8289 (mtt180) REVERT: E 78 LEU cc_start: 0.8725 (pp) cc_final: 0.8501 (pp) REVERT: E 148 GLU cc_start: 0.7875 (pt0) cc_final: 0.7634 (pm20) REVERT: E 168 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: E 178 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7007 (mt0) REVERT: E 188 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6834 (m110) REVERT: E 189 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7259 (mtp) REVERT: E 211 THR cc_start: 0.7583 (p) cc_final: 0.7332 (t) REVERT: F 41 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8211 (mtpp) REVERT: F 42 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8178 (p0) REVERT: F 51 ARG cc_start: 0.3870 (OUTLIER) cc_final: 0.2356 (mtm-85) REVERT: F 115 GLU cc_start: 0.8743 (tt0) cc_final: 0.8511 (mt-10) REVERT: F 119 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8142 (mmt-90) REVERT: F 176 HIS cc_start: 0.8353 (m90) cc_final: 0.8147 (m-70) REVERT: F 200 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6793 (p) REVERT: F 207 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.7224 (m110) REVERT: G 6 HIS cc_start: 0.8460 (p-80) cc_final: 0.8185 (p-80) REVERT: G 41 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6085 (m) REVERT: G 55 ARG cc_start: 0.7915 (ptm-80) cc_final: 0.7521 (ptm-80) REVERT: G 176 LYS cc_start: 0.7806 (mttp) cc_final: 0.7456 (mttp) REVERT: H 81 VAL cc_start: 0.8928 (m) cc_final: 0.8708 (p) REVERT: H 198 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7728 (mptt) REVERT: H 204 GLU cc_start: 0.8301 (mp0) cc_final: 0.8075 (mp0) REVERT: H 239 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8173 (mt-10) REVERT: I 96 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.8045 (mpt180) REVERT: I 98 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8134 (mmmt) REVERT: I 109 CYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8308 (m) REVERT: I 148 MET cc_start: 0.8875 (mtp) cc_final: 0.8614 (mtp) REVERT: I 281 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6443 (mt-10) REVERT: J 124 MET cc_start: 0.8808 (mtt) cc_final: 0.8586 (mtm) REVERT: J 162 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7856 (tt0) REVERT: J 194 LYS cc_start: 0.8088 (pttp) cc_final: 0.7853 (pttm) REVERT: K 3 GLU cc_start: 0.8107 (mp0) cc_final: 0.7860 (pm20) REVERT: K 75 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6882 (mpt-90) REVERT: K 98 ASP cc_start: 0.7830 (m-30) cc_final: 0.7580 (m-30) REVERT: K 201 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8400 (OUTLIER) REVERT: M 64 PHE cc_start: 0.8320 (m-80) cc_final: 0.8020 (m-80) REVERT: M 80 GLU cc_start: 0.8711 (pm20) cc_final: 0.8424 (mm-30) REVERT: M 147 ASP cc_start: 0.8093 (p0) cc_final: 0.7882 (p0) REVERT: N 1 MET cc_start: 0.6946 (mtm) cc_final: 0.6436 (mmt) REVERT: N 150 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7643 (mm-30) REVERT: N 157 ARG cc_start: 0.8638 (ttm110) cc_final: 0.7909 (ttt-90) REVERT: N 218 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5471 (mpp80) REVERT: O 61 ASP cc_start: 0.8364 (p0) cc_final: 0.8127 (p0) REVERT: O 101 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8190 (tpt90) REVERT: O 183 LYS cc_start: 0.8240 (mttp) cc_final: 0.7991 (ttpm) REVERT: O 227 GLU cc_start: 0.8012 (tt0) cc_final: 0.7786 (tm-30) REVERT: O 238 ASP cc_start: 0.8065 (m-30) cc_final: 0.7383 (t0) REVERT: O 241 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: O 244 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7473 (t) REVERT: P 37 LYS cc_start: 0.8607 (tttp) cc_final: 0.8339 (tttt) REVERT: P 173 GLU cc_start: 0.7416 (tt0) cc_final: 0.7164 (mt-10) REVERT: P 175 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7231 (mtp-110) REVERT: P 180 MET cc_start: 0.8006 (mtp) cc_final: 0.7620 (mtp) REVERT: P 181 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7566 (pt0) REVERT: P 210 ARG cc_start: 0.8682 (ttp-170) cc_final: 0.8277 (ttp-170) REVERT: P 215 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8065 (tttp) REVERT: P 217 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8037 (mp0) REVERT: P 223 GLN cc_start: 0.8311 (mt0) cc_final: 0.7957 (mt0) REVERT: Q 48 GLU cc_start: 0.7937 (tt0) cc_final: 0.7710 (pt0) REVERT: Q 148 HIS cc_start: 0.8457 (m-70) cc_final: 0.8257 (m-70) REVERT: Q 157 ASP cc_start: 0.8799 (p0) cc_final: 0.8564 (p0) REVERT: Q 186 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6913 (pttp) REVERT: Q 214 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6507 (tp30) REVERT: Q 234 GLU cc_start: 0.7992 (mp0) cc_final: 0.7709 (mt-10) REVERT: Q 250 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6704 (mmt90) REVERT: Q 264 GLN cc_start: 0.7147 (mt0) cc_final: 0.6882 (mt0) REVERT: R 51 GLN cc_start: 0.6779 (mt0) cc_final: 0.6569 (mt0) REVERT: R 54 GLN cc_start: 0.8262 (tp40) cc_final: 0.7935 (tp-100) REVERT: R 110 TYR cc_start: 0.9089 (t80) cc_final: 0.8880 (t80) REVERT: R 138 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5619 (tm-30) REVERT: R 139 ASN cc_start: 0.6512 (p0) cc_final: 0.6307 (p0) REVERT: R 172 MET cc_start: 0.8475 (mtm) cc_final: 0.8257 (mtp) REVERT: R 173 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7001 (mm-30) REVERT: R 174 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6792 (mttm) REVERT: R 183 ASP cc_start: 0.7250 (m-30) cc_final: 0.6948 (m-30) REVERT: R 195 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5666 (mm-30) REVERT: R 211 ASN cc_start: 0.7844 (t0) cc_final: 0.7524 (t0) REVERT: R 213 LYS cc_start: 0.7110 (mttt) cc_final: 0.6723 (tttm) REVERT: R 222 LEU cc_start: 0.7236 (tp) cc_final: 0.6949 (tp) REVERT: R 228 GLU cc_start: 0.6070 (tt0) cc_final: 0.5837 (tt0) REVERT: S 9 ASP cc_start: 0.5623 (t70) cc_final: 0.5406 (t0) REVERT: S 18 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: S 20 ARG cc_start: 0.8513 (mtt180) cc_final: 0.8273 (mtt90) REVERT: S 78 LEU cc_start: 0.8724 (pp) cc_final: 0.8498 (pp) REVERT: S 148 GLU cc_start: 0.7879 (pt0) cc_final: 0.7634 (pm20) REVERT: S 168 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: S 178 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7005 (mt0) REVERT: S 188 ASN cc_start: 0.7018 (OUTLIER) cc_final: 0.6816 (m110) REVERT: S 189 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7278 (mtp) REVERT: S 211 THR cc_start: 0.7580 (p) cc_final: 0.7336 (t) REVERT: T 41 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8206 (mtpp) REVERT: T 42 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8160 (p0) REVERT: T 51 ARG cc_start: 0.3859 (OUTLIER) cc_final: 0.2340 (mtm-85) REVERT: T 84 MET cc_start: 0.8307 (ttt) cc_final: 0.8104 (tmt) REVERT: T 115 GLU cc_start: 0.8744 (tt0) cc_final: 0.8513 (mt-10) REVERT: T 119 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8140 (mmt-90) REVERT: T 176 HIS cc_start: 0.8354 (m90) cc_final: 0.8148 (m-70) REVERT: T 200 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6783 (p) REVERT: T 207 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.7197 (m110) REVERT: U 6 HIS cc_start: 0.8461 (p-80) cc_final: 0.8190 (p-80) REVERT: U 41 THR cc_start: 0.6529 (OUTLIER) cc_final: 0.6095 (m) REVERT: U 55 ARG cc_start: 0.7922 (ptm-80) cc_final: 0.7523 (ptm-80) REVERT: U 176 LYS cc_start: 0.7796 (mttp) cc_final: 0.7445 (mttp) REVERT: V 81 VAL cc_start: 0.8927 (m) cc_final: 0.8708 (p) REVERT: V 204 GLU cc_start: 0.8300 (mp0) cc_final: 0.8073 (mp0) REVERT: V 239 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8169 (mt-10) REVERT: W 96 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.8046 (mpt180) REVERT: W 98 LYS cc_start: 0.8385 (mmmm) cc_final: 0.8135 (mmmt) REVERT: W 109 CYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8309 (m) REVERT: W 148 MET cc_start: 0.8874 (mtp) cc_final: 0.8614 (mtp) REVERT: W 281 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6442 (mt-10) REVERT: X 124 MET cc_start: 0.8808 (mtt) cc_final: 0.8580 (mtm) REVERT: X 162 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7856 (tt0) REVERT: X 194 LYS cc_start: 0.8091 (pttp) cc_final: 0.7855 (pttm) REVERT: Y 3 GLU cc_start: 0.8106 (mp0) cc_final: 0.7862 (pm20) REVERT: Y 75 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6873 (mpt-90) REVERT: Y 98 ASP cc_start: 0.7811 (m-30) cc_final: 0.7582 (m-30) REVERT: Y 201 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8399 (OUTLIER) REVERT: a 64 PHE cc_start: 0.8317 (m-80) cc_final: 0.8014 (m-80) REVERT: a 80 GLU cc_start: 0.8714 (pm20) cc_final: 0.8422 (mm-30) REVERT: a 147 ASP cc_start: 0.8105 (p0) cc_final: 0.7893 (p0) REVERT: b 1 MET cc_start: 0.6945 (mtm) cc_final: 0.6435 (mmt) REVERT: b 150 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7642 (mm-30) REVERT: b 157 ARG cc_start: 0.8638 (ttm110) cc_final: 0.7915 (ttt-90) REVERT: b 218 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5494 (mpp80) outliers start: 227 outliers final: 56 residues processed: 1239 average time/residue: 1.6418 time to fit residues: 2432.0858 Evaluate side-chains 913 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 821 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 168 GLN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 234 ASP Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 244 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain P residue 218 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 155 HIS Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain R residue 12 PRO Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 168 GLN Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain S residue 227 LEU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 170 ARG Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain T residue 207 ASN Chi-restraints excluded: chain U residue 40 CYS Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 103 THR Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 109 CYS Chi-restraints excluded: chain W residue 206 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 201 ILE Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 226 VAL Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain b residue 218 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 0.9990 chunk 463 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 312 optimal weight: 0.9990 chunk 247 optimal weight: 0.4980 chunk 479 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 357 optimal weight: 2.9990 chunk 555 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 93 GLN B 61 GLN C 60 ASN C 94 ASN C 149 HIS D 54 GLN D 164 ASN E 155 GLN E 168 GLN E 182 ASN E 188 ASN E 232 GLN F 61 GLN F 104 ASN G 223 GLN H 115 ASN H 211 GLN J 201 ASN K 11 ASN K 73 HIS K 143 HIS K 186 ASN L 180 ASN L 233 HIS L 251 GLN L 272 HIS L 302 GLN M 210 ASN O 89 GLN O 93 GLN P 61 GLN Q 60 ASN Q 94 ASN R 54 GLN R 85 ASN R 164 ASN S 155 GLN S 168 GLN S 182 ASN S 188 ASN S 232 GLN T 61 GLN T 104 ASN U 223 GLN V 115 ASN V 211 GLN X 201 ASN Y 11 ASN Y 143 HIS Y 186 ASN Z 180 ASN Z 233 HIS Z 251 GLN Z 272 HIS Z 302 GLN a 210 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105617 restraints weight = 50191.238| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.20 r_work: 0.3080 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 49428 Z= 0.173 Angle : 0.604 7.727 66880 Z= 0.338 Chirality : 0.045 0.178 7512 Planarity : 0.004 0.057 8644 Dihedral : 7.443 80.250 7055 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.94 % Favored : 98.03 % Rotamer: Outliers : 2.63 % Allowed : 11.54 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 6200 helix: 1.36 (0.10), residues: 2334 sheet: 1.00 (0.13), residues: 1436 loop : -0.76 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 154 HIS 0.004 0.001 HIS U 119 PHE 0.015 0.002 PHE X 20 TYR 0.018 0.002 TYR P 116 ARG 0.004 0.000 ARG J 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 927 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8103 (p0) cc_final: 0.7857 (p0) REVERT: A 197 ASP cc_start: 0.7468 (m-30) cc_final: 0.7109 (m-30) REVERT: A 238 ASP cc_start: 0.7381 (m-30) cc_final: 0.6716 (t0) REVERT: B 173 GLU cc_start: 0.6939 (tt0) cc_final: 0.6630 (mt-10) REVERT: B 210 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8114 (ttp-170) REVERT: B 212 SER cc_start: 0.8283 (p) cc_final: 0.8081 (t) REVERT: B 213 GLU cc_start: 0.8252 (mp0) cc_final: 0.7971 (mp0) REVERT: C 15 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 48 GLU cc_start: 0.7354 (tt0) cc_final: 0.7044 (pt0) REVERT: C 61 MET cc_start: 0.8621 (mmt) cc_final: 0.8288 (mmm) REVERT: C 148 HIS cc_start: 0.8239 (m-70) cc_final: 0.7943 (m-70) REVERT: C 186 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6612 (pttm) REVERT: C 234 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: C 264 GLN cc_start: 0.7131 (mt0) cc_final: 0.6783 (mt0) REVERT: D 51 GLN cc_start: 0.6701 (mt0) cc_final: 0.6499 (mt0) REVERT: D 54 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7626 (tp-100) REVERT: D 138 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5422 (tm-30) REVERT: D 139 ASN cc_start: 0.6609 (p0) cc_final: 0.6378 (p0) REVERT: D 173 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6752 (mt-10) REVERT: D 183 ASP cc_start: 0.6721 (m-30) cc_final: 0.6516 (m-30) REVERT: D 211 ASN cc_start: 0.7659 (t0) cc_final: 0.7264 (t0) REVERT: E 66 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7242 (mttp) REVERT: E 178 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.5716 (mm-40) REVERT: E 185 TYR cc_start: 0.6591 (t80) cc_final: 0.6219 (t80) REVERT: E 189 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.7035 (mtp) REVERT: E 196 THR cc_start: 0.6290 (OUTLIER) cc_final: 0.6047 (p) REVERT: E 232 GLN cc_start: 0.6040 (mt0) cc_final: 0.5693 (pm20) REVERT: F 42 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7792 (p0) REVERT: F 51 ARG cc_start: 0.3539 (OUTLIER) cc_final: 0.1932 (mtm-85) REVERT: F 119 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7770 (mmt-90) REVERT: F 200 THR cc_start: 0.7291 (m) cc_final: 0.7081 (p) REVERT: G 55 ARG cc_start: 0.7469 (ptm-80) cc_final: 0.7104 (ptt90) REVERT: G 84 ARG cc_start: 0.8263 (tpt-90) cc_final: 0.7735 (tpt90) REVERT: G 176 LYS cc_start: 0.7585 (mttp) cc_final: 0.7377 (mttp) REVERT: H 126 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7594 (mppt) REVERT: I 98 LYS cc_start: 0.8024 (mmmm) cc_final: 0.7627 (mtmm) REVERT: I 156 TYR cc_start: 0.8719 (m-80) cc_final: 0.8476 (m-80) REVERT: I 260 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4326 (tp30) REVERT: I 281 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6094 (mp0) REVERT: J 194 LYS cc_start: 0.8067 (pttp) cc_final: 0.7860 (ptpp) REVERT: K 30 MET cc_start: 0.8416 (ptm) cc_final: 0.8216 (ptm) REVERT: K 75 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7135 (mpt-90) REVERT: K 201 ILE cc_start: 0.8641 (mt) cc_final: 0.8295 (tt) REVERT: L 183 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7724 (mtt-85) REVERT: L 216 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: M 64 PHE cc_start: 0.7915 (m-80) cc_final: 0.7657 (m-80) REVERT: N 1 MET cc_start: 0.5903 (mtm) cc_final: 0.5561 (mmt) REVERT: N 98 PHE cc_start: 0.8387 (m-80) cc_final: 0.8153 (m-80) REVERT: N 151 LYS cc_start: 0.7534 (ptpt) cc_final: 0.7307 (ptmm) REVERT: N 157 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7750 (ttt-90) REVERT: N 162 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7686 (ttp-110) REVERT: N 218 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5133 (mpp80) REVERT: O 61 ASP cc_start: 0.8107 (p0) cc_final: 0.7856 (p0) REVERT: O 197 ASP cc_start: 0.7475 (m-30) cc_final: 0.7114 (m-30) REVERT: O 238 ASP cc_start: 0.7380 (m-30) cc_final: 0.6711 (t0) REVERT: P 173 GLU cc_start: 0.6953 (tt0) cc_final: 0.6645 (mt-10) REVERT: P 210 ARG cc_start: 0.8459 (ttp-170) cc_final: 0.8121 (ttp-170) REVERT: P 212 SER cc_start: 0.8286 (p) cc_final: 0.8084 (t) REVERT: P 213 GLU cc_start: 0.8245 (mp0) cc_final: 0.7969 (mp0) REVERT: Q 15 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: Q 48 GLU cc_start: 0.7369 (tt0) cc_final: 0.7050 (pt0) REVERT: Q 61 MET cc_start: 0.8619 (mmt) cc_final: 0.8287 (mmm) REVERT: Q 148 HIS cc_start: 0.8239 (m-70) cc_final: 0.7943 (m-70) REVERT: Q 186 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6611 (pttm) REVERT: Q 234 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: Q 264 GLN cc_start: 0.7142 (mt0) cc_final: 0.6796 (mt0) REVERT: R 51 GLN cc_start: 0.6704 (mt0) cc_final: 0.6497 (mt0) REVERT: R 54 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7623 (tp-100) REVERT: R 138 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5424 (tm-30) REVERT: R 139 ASN cc_start: 0.6602 (p0) cc_final: 0.6352 (p0) REVERT: R 173 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6758 (mt-10) REVERT: R 183 ASP cc_start: 0.6711 (m-30) cc_final: 0.6510 (m-30) REVERT: R 211 ASN cc_start: 0.7661 (t0) cc_final: 0.7266 (t0) REVERT: S 66 LYS cc_start: 0.7712 (mtpt) cc_final: 0.7274 (mttp) REVERT: S 178 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.5693 (mm-40) REVERT: S 185 TYR cc_start: 0.6591 (t80) cc_final: 0.6212 (t80) REVERT: S 189 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.7044 (mtp) REVERT: S 196 THR cc_start: 0.6291 (OUTLIER) cc_final: 0.6049 (p) REVERT: S 232 GLN cc_start: 0.6010 (mt0) cc_final: 0.5626 (pm20) REVERT: T 42 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7781 (p0) REVERT: T 51 ARG cc_start: 0.3534 (OUTLIER) cc_final: 0.1921 (mtm-85) REVERT: T 119 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7769 (mmt-90) REVERT: T 200 THR cc_start: 0.7288 (m) cc_final: 0.7079 (p) REVERT: T 207 ASN cc_start: 0.7008 (OUTLIER) cc_final: 0.6794 (m110) REVERT: U 55 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.7095 (ptt90) REVERT: U 84 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.7737 (tpt90) REVERT: U 176 LYS cc_start: 0.7586 (mttp) cc_final: 0.7379 (mttp) REVERT: V 126 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7589 (mppt) REVERT: W 96 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7585 (mpt180) REVERT: W 98 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7624 (mtmm) REVERT: W 156 TYR cc_start: 0.8717 (m-80) cc_final: 0.8476 (m-80) REVERT: W 260 GLU cc_start: 0.4841 (OUTLIER) cc_final: 0.4291 (tp30) REVERT: W 281 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6100 (mp0) REVERT: X 194 LYS cc_start: 0.8067 (pttp) cc_final: 0.7860 (ptpp) REVERT: Y 30 MET cc_start: 0.8417 (ptm) cc_final: 0.8217 (ptm) REVERT: Y 75 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7124 (mpt-90) REVERT: Y 201 ILE cc_start: 0.8640 (mt) cc_final: 0.8296 (tt) REVERT: Z 183 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7740 (mtt-85) REVERT: a 64 PHE cc_start: 0.7914 (m-80) cc_final: 0.7652 (m-80) REVERT: b 1 MET cc_start: 0.5909 (mtm) cc_final: 0.5558 (mmt) REVERT: b 98 PHE cc_start: 0.8384 (m-80) cc_final: 0.8146 (m-80) REVERT: b 151 LYS cc_start: 0.7531 (ptpt) cc_final: 0.7305 (ptmm) REVERT: b 157 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7757 (ttt-90) REVERT: b 162 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7679 (ttp-110) REVERT: b 218 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5146 (mpp80) outliers start: 136 outliers final: 27 residues processed: 1000 average time/residue: 1.5898 time to fit residues: 1917.6121 Evaluate side-chains 833 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 776 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 183 ARG Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 207 ASN Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 126 LYS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 260 GLU Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Z residue 183 ARG Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain b residue 218 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 279 optimal weight: 9.9990 chunk 462 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 405 optimal weight: 0.8980 chunk 420 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 416 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 166 HIS B 61 GLN C 60 ASN C 94 ASN C 149 HIS C 161 ASN C 230 GLN D 143 HIS E 155 GLN E 182 ASN K 22 ASN ** L 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN O 93 GLN O 166 HIS P 61 GLN Q 60 ASN Q 94 ASN Q 161 ASN Q 230 GLN R 143 HIS S 155 GLN S 182 ASN Y 22 ASN Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 70 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104480 restraints weight = 50593.363| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.19 r_work: 0.3058 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 49428 Z= 0.221 Angle : 0.634 8.680 66880 Z= 0.352 Chirality : 0.046 0.181 7512 Planarity : 0.005 0.047 8644 Dihedral : 6.512 82.423 6956 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 2.44 % Allowed : 13.23 % Favored : 84.34 % 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: 1.18 (0.10), residues: 6200 helix: 2.02 (0.11), residues: 2346 sheet: 1.10 (0.13), residues: 1410 loop : -0.63 (0.11), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 245 HIS 0.006 0.001 HIS N 90 PHE 0.018 0.002 PHE L 271 TYR 0.024 0.002 TYR B 116 ARG 0.009 0.001 ARG O 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 769 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8181 (p0) cc_final: 0.7963 (p0) REVERT: B 173 GLU cc_start: 0.7002 (tt0) cc_final: 0.6685 (mt-10) REVERT: B 210 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8192 (ttp-170) REVERT: C 15 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: C 48 GLU cc_start: 0.7398 (tt0) cc_final: 0.7177 (pt0) REVERT: C 61 MET cc_start: 0.8626 (mmt) cc_final: 0.8420 (mmt) REVERT: C 148 HIS cc_start: 0.8188 (m-70) cc_final: 0.7907 (m-70) REVERT: C 178 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: C 186 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6515 (pttm) REVERT: C 234 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: C 264 GLN cc_start: 0.7058 (mt0) cc_final: 0.6542 (mt0) REVERT: D 46 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: D 54 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7608 (tp40) REVERT: D 103 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7176 (t70) REVERT: D 138 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5702 (tm-30) REVERT: D 139 ASN cc_start: 0.6608 (p0) cc_final: 0.6343 (p0) REVERT: D 173 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6736 (mt-10) REVERT: D 177 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.5681 (mm-40) REVERT: D 211 ASN cc_start: 0.7671 (t0) cc_final: 0.7453 (t0) REVERT: D 213 LYS cc_start: 0.6089 (mtmt) cc_final: 0.5789 (tttm) REVERT: D 230 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.4828 (mm-30) REVERT: E 178 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.5960 (mp10) REVERT: E 185 TYR cc_start: 0.6623 (t80) cc_final: 0.6316 (t80) REVERT: E 189 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6870 (mtp) REVERT: E 226 LYS cc_start: 0.7614 (mmtt) cc_final: 0.6969 (tptp) REVERT: E 228 GLU cc_start: 0.7388 (tt0) cc_final: 0.7083 (mt-10) REVERT: E 232 GLN cc_start: 0.5995 (mt0) cc_final: 0.5654 (pm20) REVERT: F 87 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7943 (ttt90) REVERT: F 200 THR cc_start: 0.7417 (m) cc_final: 0.7160 (p) REVERT: G 55 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.7102 (ptt90) REVERT: G 84 ARG cc_start: 0.8324 (tpt-90) cc_final: 0.7762 (tpt90) REVERT: G 176 LYS cc_start: 0.7571 (mttp) cc_final: 0.7338 (mttp) REVERT: H 144 ASN cc_start: 0.8385 (m-40) cc_final: 0.8185 (m110) REVERT: I 156 TYR cc_start: 0.8647 (m-80) cc_final: 0.8403 (m-80) REVERT: I 280 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: I 281 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6358 (mt-10) REVERT: J 194 LYS cc_start: 0.8042 (pttp) cc_final: 0.7768 (pttp) REVERT: K 30 MET cc_start: 0.8473 (ptm) cc_final: 0.8175 (ptm) REVERT: K 75 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7251 (mpt-90) REVERT: K 169 ASP cc_start: 0.8042 (m-30) cc_final: 0.7837 (m-30) REVERT: K 201 ILE cc_start: 0.8560 (mt) cc_final: 0.8318 (tt) REVERT: L 183 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7764 (mtt-85) REVERT: L 216 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: M 64 PHE cc_start: 0.7952 (m-80) cc_final: 0.7660 (m-80) REVERT: N 150 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7428 (mm-30) REVERT: N 151 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7279 (ptmm) REVERT: N 157 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7773 (ttt-90) REVERT: N 162 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7723 (ttp-110) REVERT: O 61 ASP cc_start: 0.8183 (p0) cc_final: 0.7961 (p0) REVERT: P 173 GLU cc_start: 0.7006 (tt0) cc_final: 0.6684 (mt-10) REVERT: P 210 ARG cc_start: 0.8452 (ttp-170) cc_final: 0.8196 (ttp-170) REVERT: Q 15 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: Q 61 MET cc_start: 0.8625 (mmt) cc_final: 0.8416 (mmt) REVERT: Q 148 HIS cc_start: 0.8185 (m-70) cc_final: 0.7911 (m-70) REVERT: Q 178 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: Q 186 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6537 (pttm) REVERT: Q 234 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: R 46 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: R 54 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7608 (tp40) REVERT: R 103 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7178 (t70) REVERT: R 138 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5692 (tm-30) REVERT: R 139 ASN cc_start: 0.6617 (p0) cc_final: 0.6369 (p0) REVERT: R 173 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6716 (mt-10) REVERT: R 177 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.5676 (mm-40) REVERT: R 211 ASN cc_start: 0.7674 (t0) cc_final: 0.7458 (t0) REVERT: R 213 LYS cc_start: 0.6092 (mtmt) cc_final: 0.5789 (tttm) REVERT: R 230 GLU cc_start: 0.5262 (OUTLIER) cc_final: 0.4834 (mm-30) REVERT: S 178 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.5965 (mp10) REVERT: S 185 TYR cc_start: 0.6627 (t80) cc_final: 0.6319 (t80) REVERT: S 189 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6889 (mtp) REVERT: S 226 LYS cc_start: 0.7618 (mmtt) cc_final: 0.6975 (tptp) REVERT: S 228 GLU cc_start: 0.7385 (tt0) cc_final: 0.7085 (mt-10) REVERT: S 232 GLN cc_start: 0.6019 (mt0) cc_final: 0.5667 (pm20) REVERT: T 87 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7947 (ttt90) REVERT: T 200 THR cc_start: 0.7419 (m) cc_final: 0.7165 (p) REVERT: U 55 ARG cc_start: 0.7444 (ptm-80) cc_final: 0.7128 (ptt90) REVERT: U 84 ARG cc_start: 0.8326 (tpt-90) cc_final: 0.7766 (tpt90) REVERT: U 176 LYS cc_start: 0.7581 (mttp) cc_final: 0.7342 (mttp) REVERT: W 156 TYR cc_start: 0.8646 (m-80) cc_final: 0.8404 (m-80) REVERT: W 280 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: W 281 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6373 (mt-10) REVERT: X 194 LYS cc_start: 0.8047 (pttp) cc_final: 0.7775 (pttp) REVERT: Y 30 MET cc_start: 0.8473 (ptm) cc_final: 0.8178 (ptm) REVERT: Y 75 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7249 (mpt-90) REVERT: Y 169 ASP cc_start: 0.8036 (m-30) cc_final: 0.7830 (m-30) REVERT: Y 201 ILE cc_start: 0.8566 (mt) cc_final: 0.8322 (tt) REVERT: Z 183 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7759 (mtt-85) REVERT: Z 216 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: a 64 PHE cc_start: 0.7950 (m-80) cc_final: 0.7664 (m-80) REVERT: b 150 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7425 (mm-30) REVERT: b 151 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7274 (ptmm) REVERT: b 157 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7783 (ttt-90) REVERT: b 162 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7726 (ttp-110) outliers start: 126 outliers final: 40 residues processed: 844 average time/residue: 1.6525 time to fit residues: 1667.2525 Evaluate side-chains 810 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 736 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 183 ARG Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain P residue 212 SER Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 230 GLU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Z residue 155 MET Chi-restraints excluded: chain Z residue 183 ARG Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain b residue 151 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 197 optimal weight: 7.9990 chunk 395 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 606 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 461 optimal weight: 4.9990 chunk 336 optimal weight: 0.0570 chunk 190 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN D 141 GLN E 155 GLN E 182 ASN L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN P 61 GLN Q 60 ASN Q 264 GLN R 141 GLN S 155 GLN S 182 ASN Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107493 restraints weight = 50515.971| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.18 r_work: 0.3109 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 49428 Z= 0.141 Angle : 0.523 8.304 66880 Z= 0.291 Chirality : 0.043 0.164 7512 Planarity : 0.004 0.045 8644 Dihedral : 5.965 75.778 6930 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.47 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 14.19 % Favored : 83.84 % 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: 1.55 (0.10), residues: 6200 helix: 2.44 (0.11), residues: 2350 sheet: 1.03 (0.13), residues: 1524 loop : -0.45 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 165 HIS 0.003 0.001 HIS Q 104 PHE 0.014 0.001 PHE Q 140 TYR 0.015 0.001 TYR P 116 ARG 0.005 0.000 ARG O 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 786 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6807 (tmm160) REVERT: A 61 ASP cc_start: 0.8161 (p0) cc_final: 0.7914 (p0) REVERT: A 197 ASP cc_start: 0.7393 (m-30) cc_final: 0.7066 (m-30) REVERT: B 173 GLU cc_start: 0.6931 (tt0) cc_final: 0.6542 (mt-10) REVERT: B 175 ARG cc_start: 0.7226 (mtp-110) cc_final: 0.6666 (ttm-80) REVERT: B 210 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.8201 (ttp-170) REVERT: B 213 GLU cc_start: 0.8219 (mp0) cc_final: 0.8012 (mp0) REVERT: C 15 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: C 61 MET cc_start: 0.8612 (mmt) cc_final: 0.8371 (mmt) REVERT: C 148 HIS cc_start: 0.8205 (m-70) cc_final: 0.7917 (m-70) REVERT: C 186 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6565 (pttm) REVERT: C 260 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6318 (tp30) REVERT: C 264 GLN cc_start: 0.7010 (mt0) cc_final: 0.6694 (mt0) REVERT: D 38 LYS cc_start: 0.7366 (mmmm) cc_final: 0.7144 (mmtp) REVERT: D 46 GLU cc_start: 0.7765 (tt0) cc_final: 0.7548 (pt0) REVERT: D 54 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7550 (tp-100) REVERT: D 103 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6982 (t70) REVERT: D 138 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5638 (tm-30) REVERT: D 173 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6713 (mt-10) REVERT: D 177 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5724 (mm-40) REVERT: D 211 ASN cc_start: 0.7596 (t0) cc_final: 0.7314 (t0) REVERT: E 178 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.5843 (mp10) REVERT: E 185 TYR cc_start: 0.6664 (t80) cc_final: 0.6397 (t80) REVERT: E 189 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6356 (ptp) REVERT: E 226 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7009 (tptp) REVERT: E 228 GLU cc_start: 0.7381 (tt0) cc_final: 0.7074 (mt-10) REVERT: E 232 GLN cc_start: 0.5956 (mt0) cc_final: 0.5693 (pm20) REVERT: F 200 THR cc_start: 0.7430 (m) cc_final: 0.7187 (p) REVERT: G 55 ARG cc_start: 0.7359 (ptm-80) cc_final: 0.7084 (ptt90) REVERT: G 84 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7732 (tpt90) REVERT: H 260 ASP cc_start: 0.8212 (m-30) cc_final: 0.7842 (p0) REVERT: I 156 TYR cc_start: 0.8643 (m-80) cc_final: 0.8370 (m-80) REVERT: I 157 GLN cc_start: 0.8517 (mt0) cc_final: 0.8194 (mt0) REVERT: I 280 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: I 281 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6345 (mt-10) REVERT: J 194 LYS cc_start: 0.8023 (pttp) cc_final: 0.7772 (pttp) REVERT: K 30 MET cc_start: 0.8387 (ptm) cc_final: 0.8085 (ptm) REVERT: K 75 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7268 (mpt-90) REVERT: K 135 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8221 (ttp) REVERT: L 216 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: M 64 PHE cc_start: 0.7939 (m-80) cc_final: 0.7654 (m-80) REVERT: N 98 PHE cc_start: 0.8319 (m-80) cc_final: 0.8059 (m-80) REVERT: N 150 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7472 (mm-30) REVERT: N 151 LYS cc_start: 0.7535 (ptpt) cc_final: 0.7230 (ptmm) REVERT: N 157 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7692 (ttt-90) REVERT: N 162 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7602 (ttp-110) REVERT: O 40 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.6806 (tmm160) REVERT: O 61 ASP cc_start: 0.8158 (p0) cc_final: 0.7904 (p0) REVERT: O 197 ASP cc_start: 0.7391 (m-30) cc_final: 0.7062 (m-30) REVERT: P 173 GLU cc_start: 0.6935 (tt0) cc_final: 0.6589 (mt-10) REVERT: P 175 ARG cc_start: 0.7224 (mtp-110) cc_final: 0.6663 (ttm-80) REVERT: P 210 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8164 (ttp-170) REVERT: P 213 GLU cc_start: 0.8221 (mp0) cc_final: 0.8013 (mp0) REVERT: P 227 TYR cc_start: 0.7884 (m-80) cc_final: 0.7672 (m-80) REVERT: Q 15 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: Q 61 MET cc_start: 0.8610 (mmt) cc_final: 0.8362 (mmt) REVERT: Q 148 HIS cc_start: 0.8205 (m-70) cc_final: 0.7950 (m-70) REVERT: Q 186 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6563 (pttm) REVERT: Q 260 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6351 (tp30) REVERT: R 38 LYS cc_start: 0.7333 (mmmm) cc_final: 0.7111 (mmtp) REVERT: R 46 GLU cc_start: 0.7755 (tt0) cc_final: 0.7544 (pt0) REVERT: R 54 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7555 (tp-100) REVERT: R 103 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6981 (t70) REVERT: R 138 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5630 (tm-30) REVERT: R 173 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6711 (mt-10) REVERT: R 177 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.5736 (mm-40) REVERT: R 211 ASN cc_start: 0.7599 (t0) cc_final: 0.7324 (t0) REVERT: S 178 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.5848 (mp10) REVERT: S 185 TYR cc_start: 0.6668 (t80) cc_final: 0.6406 (t80) REVERT: S 187 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5818 (mpp-170) REVERT: S 189 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6375 (ptp) REVERT: S 226 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7016 (tptp) REVERT: S 228 GLU cc_start: 0.7369 (tt0) cc_final: 0.7071 (mt-10) REVERT: S 232 GLN cc_start: 0.5963 (mt0) cc_final: 0.5699 (pm20) REVERT: T 200 THR cc_start: 0.7424 (m) cc_final: 0.7186 (p) REVERT: U 55 ARG cc_start: 0.7404 (ptm-80) cc_final: 0.7094 (ptt90) REVERT: U 84 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7732 (tpt90) REVERT: W 96 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7834 (mtt90) REVERT: W 156 TYR cc_start: 0.8640 (m-80) cc_final: 0.8367 (m-80) REVERT: W 157 GLN cc_start: 0.8517 (mt0) cc_final: 0.8197 (mt0) REVERT: W 280 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: W 281 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6352 (mt-10) REVERT: X 194 LYS cc_start: 0.8020 (pttp) cc_final: 0.7769 (pttp) REVERT: Y 30 MET cc_start: 0.8389 (ptm) cc_final: 0.8090 (ptm) REVERT: Y 75 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7263 (mpt-90) REVERT: Y 135 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8221 (ttp) REVERT: Z 216 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: a 64 PHE cc_start: 0.7942 (m-80) cc_final: 0.7650 (m-80) REVERT: b 98 PHE cc_start: 0.8313 (m-80) cc_final: 0.8047 (m-80) REVERT: b 150 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7466 (mm-30) REVERT: b 151 LYS cc_start: 0.7534 (ptpt) cc_final: 0.7228 (ptmm) REVERT: b 157 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7684 (ttt-90) REVERT: b 162 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7605 (ttp-110) outliers start: 102 outliers final: 29 residues processed: 850 average time/residue: 1.6789 time to fit residues: 1704.3212 Evaluate side-chains 798 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 741 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 135 MET Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain L residue 302 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 187 ARG Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 84 ARG Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 96 ARG Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 31 GLN Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 135 MET Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 302 GLN Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 131 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 499 optimal weight: 6.9990 chunk 496 optimal weight: 3.9990 chunk 578 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 438 optimal weight: 8.9990 chunk 466 optimal weight: 9.9990 chunk 180 optimal weight: 0.0030 chunk 290 optimal weight: 5.9990 chunk 459 optimal weight: 1.9990 chunk 475 optimal weight: 0.9980 chunk 335 optimal weight: 0.3980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN C 163 ASN E 155 GLN E 182 ASN K 22 ASN L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN Q 264 GLN S 155 GLN S 182 ASN Y 22 ASN Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108092 restraints weight = 50777.188| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.19 r_work: 0.3115 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 49428 Z= 0.138 Angle : 0.509 8.488 66880 Z= 0.282 Chirality : 0.043 0.163 7512 Planarity : 0.004 0.045 8644 Dihedral : 5.738 71.993 6924 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Rotamer: Outliers : 1.80 % Allowed : 14.68 % Favored : 83.53 % 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: 1.70 (0.11), residues: 6200 helix: 2.55 (0.11), residues: 2354 sheet: 1.11 (0.13), residues: 1522 loop : -0.37 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 165 HIS 0.003 0.001 HIS X 147 PHE 0.015 0.001 PHE X 20 TYR 0.015 0.001 TYR P 116 ARG 0.005 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 774 time to evaluate : 4.374 Fit side-chains REVERT: A 40 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6783 (tmm160) REVERT: A 56 ARG cc_start: 0.7373 (ttp80) cc_final: 0.6856 (ttp-170) REVERT: A 197 ASP cc_start: 0.7355 (m-30) cc_final: 0.7035 (m-30) REVERT: B 173 GLU cc_start: 0.6960 (tt0) cc_final: 0.6589 (mt-10) REVERT: B 175 ARG cc_start: 0.7136 (mtp-110) cc_final: 0.6644 (ttm-80) REVERT: B 210 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8178 (ttp-170) REVERT: C 15 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: C 61 MET cc_start: 0.8625 (mmt) cc_final: 0.8388 (mmt) REVERT: C 148 HIS cc_start: 0.8224 (m-70) cc_final: 0.7951 (m-70) REVERT: C 178 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: C 186 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6550 (pttm) REVERT: C 260 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6254 (tp30) REVERT: C 264 GLN cc_start: 0.6932 (mt0) cc_final: 0.6711 (mt0) REVERT: D 38 LYS cc_start: 0.7346 (mmmm) cc_final: 0.7118 (mmtp) REVERT: D 54 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7530 (tp-100) REVERT: D 103 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6931 (t70) REVERT: D 138 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5677 (tm-30) REVERT: D 177 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.5774 (mm-40) REVERT: D 197 VAL cc_start: 0.6543 (OUTLIER) cc_final: 0.6183 (p) REVERT: D 211 ASN cc_start: 0.7635 (t0) cc_final: 0.7384 (t0) REVERT: D 230 GLU cc_start: 0.5264 (OUTLIER) cc_final: 0.4874 (mm-30) REVERT: E 178 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.5873 (mp10) REVERT: E 185 TYR cc_start: 0.6624 (t80) cc_final: 0.6364 (t80) REVERT: E 189 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6407 (ptp) REVERT: E 226 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7025 (tptp) REVERT: E 228 GLU cc_start: 0.7355 (tt0) cc_final: 0.7044 (mt-10) REVERT: E 232 GLN cc_start: 0.5863 (mt0) cc_final: 0.5644 (pm20) REVERT: F 200 THR cc_start: 0.7469 (m) cc_final: 0.7210 (p) REVERT: G 41 THR cc_start: 0.6666 (p) cc_final: 0.5937 (m) REVERT: G 55 ARG cc_start: 0.7349 (ptm-80) cc_final: 0.7058 (ptt90) REVERT: I 156 TYR cc_start: 0.8625 (m-80) cc_final: 0.8413 (m-80) REVERT: I 280 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: I 281 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6329 (mt-10) REVERT: J 194 LYS cc_start: 0.8012 (pttp) cc_final: 0.7693 (pttm) REVERT: K 30 MET cc_start: 0.8391 (ptm) cc_final: 0.8077 (ptm) REVERT: K 75 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7316 (mpt-90) REVERT: L 216 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: M 64 PHE cc_start: 0.7943 (m-80) cc_final: 0.7645 (m-80) REVERT: N 98 PHE cc_start: 0.8244 (m-80) cc_final: 0.7999 (m-80) REVERT: N 150 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7464 (mm-30) REVERT: N 151 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7263 (ptmm) REVERT: N 157 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7691 (ttt-90) REVERT: N 162 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7592 (ttp-110) REVERT: N 205 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: O 40 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6758 (tmm160) REVERT: O 197 ASP cc_start: 0.7364 (m-30) cc_final: 0.7040 (m-30) REVERT: P 173 GLU cc_start: 0.6954 (tt0) cc_final: 0.6584 (mt-10) REVERT: P 175 ARG cc_start: 0.7149 (mtp-110) cc_final: 0.6661 (ttm-80) REVERT: P 210 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8243 (ttp-170) REVERT: Q 15 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: Q 61 MET cc_start: 0.8629 (mmt) cc_final: 0.8363 (mmt) REVERT: Q 148 HIS cc_start: 0.8227 (m-70) cc_final: 0.7948 (m-70) REVERT: Q 178 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: Q 186 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6548 (pttm) REVERT: R 38 LYS cc_start: 0.7318 (mmmm) cc_final: 0.7069 (mmtp) REVERT: R 54 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7541 (tp-100) REVERT: R 103 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6933 (t70) REVERT: R 138 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: R 177 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.5780 (mm-40) REVERT: R 197 VAL cc_start: 0.6545 (OUTLIER) cc_final: 0.6176 (p) REVERT: R 211 ASN cc_start: 0.7634 (t0) cc_final: 0.7385 (t0) REVERT: R 230 GLU cc_start: 0.5296 (OUTLIER) cc_final: 0.4900 (mm-30) REVERT: S 65 ASN cc_start: 0.6781 (m-40) cc_final: 0.6438 (m110) REVERT: S 178 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: S 185 TYR cc_start: 0.6628 (t80) cc_final: 0.6367 (t80) REVERT: S 189 MET cc_start: 0.7006 (ptm) cc_final: 0.6423 (ptp) REVERT: S 226 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7039 (tptp) REVERT: S 228 GLU cc_start: 0.7359 (tt0) cc_final: 0.7062 (mt-10) REVERT: S 232 GLN cc_start: 0.5855 (mt0) cc_final: 0.5654 (pm20) REVERT: T 200 THR cc_start: 0.7466 (m) cc_final: 0.7200 (p) REVERT: U 55 ARG cc_start: 0.7350 (ptm-80) cc_final: 0.7054 (ptt90) REVERT: V 237 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: W 156 TYR cc_start: 0.8629 (m-80) cc_final: 0.8417 (m-80) REVERT: W 280 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: W 281 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6356 (mt-10) REVERT: X 194 LYS cc_start: 0.8009 (pttp) cc_final: 0.7694 (pttm) REVERT: Y 30 MET cc_start: 0.8395 (ptm) cc_final: 0.8081 (ptm) REVERT: Y 75 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7302 (mpt-90) REVERT: Z 216 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: Z 304 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7995 (mttt) REVERT: a 64 PHE cc_start: 0.7952 (m-80) cc_final: 0.7650 (m-80) REVERT: b 98 PHE cc_start: 0.8244 (m-80) cc_final: 0.7998 (m-80) REVERT: b 150 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7459 (mm-30) REVERT: b 151 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7255 (ptmm) REVERT: b 157 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7690 (ttt-90) REVERT: b 162 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7589 (ttp-110) REVERT: b 205 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7678 (mp0) outliers start: 93 outliers final: 26 residues processed: 830 average time/residue: 1.6609 time to fit residues: 1646.8478 Evaluate side-chains 806 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 747 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain N residue 205 GLU Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 230 GLU Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain X residue 31 GLN Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain b residue 151 LYS Chi-restraints excluded: chain b residue 205 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 373 optimal weight: 6.9990 chunk 493 optimal weight: 0.0070 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 604 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 380 optimal weight: 2.9990 chunk 541 optimal weight: 10.0000 chunk 455 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN C 163 ASN E 155 GLN E 182 ASN L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN Q 264 GLN S 155 GLN S 182 ASN Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106208 restraints weight = 50479.405| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.18 r_work: 0.3084 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 49428 Z= 0.177 Angle : 0.557 8.635 66880 Z= 0.308 Chirality : 0.044 0.163 7512 Planarity : 0.004 0.044 8644 Dihedral : 5.823 64.109 6921 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 1.82 % Allowed : 14.93 % Favored : 83.26 % 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: 1.60 (0.10), residues: 6200 helix: 2.49 (0.11), residues: 2344 sheet: 1.04 (0.13), residues: 1496 loop : -0.39 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 154 HIS 0.005 0.001 HIS b 90 PHE 0.017 0.002 PHE X 20 TYR 0.018 0.002 TYR B 116 ARG 0.005 0.000 ARG M 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 773 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6772 (tmm160) REVERT: A 197 ASP cc_start: 0.7389 (m-30) cc_final: 0.7082 (m-30) REVERT: B 173 GLU cc_start: 0.7042 (tt0) cc_final: 0.6671 (mt-10) REVERT: B 210 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8226 (ttp-170) REVERT: C 15 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: C 61 MET cc_start: 0.8616 (mmt) cc_final: 0.8373 (mmt) REVERT: C 148 HIS cc_start: 0.8216 (m-70) cc_final: 0.7936 (m-70) REVERT: C 178 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: C 260 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6288 (tp30) REVERT: D 38 LYS cc_start: 0.7351 (mmmm) cc_final: 0.7112 (mmtp) REVERT: D 54 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7528 (tp-100) REVERT: D 103 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7039 (t70) REVERT: D 138 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5781 (tm-30) REVERT: D 177 GLN cc_start: 0.6527 (mt0) cc_final: 0.5754 (mm-40) REVERT: D 197 VAL cc_start: 0.6466 (OUTLIER) cc_final: 0.6042 (p) REVERT: D 211 ASN cc_start: 0.7660 (t0) cc_final: 0.7378 (t0) REVERT: D 219 ASP cc_start: 0.5731 (t0) cc_final: 0.5413 (t70) REVERT: E 9 ASP cc_start: 0.5599 (t70) cc_final: 0.5348 (t0) REVERT: E 60 ASP cc_start: 0.7241 (m-30) cc_final: 0.6919 (m-30) REVERT: E 178 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.5945 (mp-120) REVERT: E 185 TYR cc_start: 0.6672 (t80) cc_final: 0.6419 (t80) REVERT: E 189 MET cc_start: 0.6966 (ptm) cc_final: 0.6441 (ptp) REVERT: E 226 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7091 (tptp) REVERT: E 228 GLU cc_start: 0.7437 (tt0) cc_final: 0.7111 (mt-10) REVERT: F 200 THR cc_start: 0.7395 (m) cc_final: 0.7110 (p) REVERT: G 41 THR cc_start: 0.6710 (p) cc_final: 0.6000 (m) REVERT: G 55 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.7130 (ptt90) REVERT: G 84 ARG cc_start: 0.8259 (tpt-90) cc_final: 0.7784 (tpt90) REVERT: H 237 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: I 156 TYR cc_start: 0.8641 (m-80) cc_final: 0.8434 (m-80) REVERT: I 280 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: I 281 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6357 (mt-10) REVERT: J 194 LYS cc_start: 0.8017 (pttp) cc_final: 0.7693 (pttm) REVERT: K 30 MET cc_start: 0.8430 (ptm) cc_final: 0.8096 (ptm) REVERT: K 75 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7399 (mpt-90) REVERT: L 216 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: M 64 PHE cc_start: 0.7972 (m-80) cc_final: 0.7648 (m-80) REVERT: N 98 PHE cc_start: 0.8251 (m-80) cc_final: 0.8015 (m-80) REVERT: N 150 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7450 (mm-30) REVERT: N 151 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7239 (ptmm) REVERT: N 157 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7741 (ttt-90) REVERT: N 162 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7640 (ttp-110) REVERT: O 40 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6770 (tmm160) REVERT: O 197 ASP cc_start: 0.7398 (m-30) cc_final: 0.7084 (m-30) REVERT: Q 15 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: Q 61 MET cc_start: 0.8599 (mmt) cc_final: 0.8383 (mmt) REVERT: Q 148 HIS cc_start: 0.8218 (m-70) cc_final: 0.7936 (m-70) REVERT: Q 178 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: R 38 LYS cc_start: 0.7358 (mmmm) cc_final: 0.7103 (mmtp) REVERT: R 54 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7542 (tp-100) REVERT: R 103 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7042 (t70) REVERT: R 138 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5770 (tm-30) REVERT: R 177 GLN cc_start: 0.6523 (mt0) cc_final: 0.5752 (mm-40) REVERT: R 197 VAL cc_start: 0.6468 (OUTLIER) cc_final: 0.6043 (p) REVERT: R 211 ASN cc_start: 0.7667 (t0) cc_final: 0.7385 (t0) REVERT: R 219 ASP cc_start: 0.5719 (t0) cc_final: 0.5403 (t70) REVERT: S 9 ASP cc_start: 0.5591 (t70) cc_final: 0.5343 (t0) REVERT: S 60 ASP cc_start: 0.7241 (m-30) cc_final: 0.6923 (m-30) REVERT: S 178 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.5936 (mp-120) REVERT: S 185 TYR cc_start: 0.6680 (t80) cc_final: 0.6431 (t80) REVERT: S 189 MET cc_start: 0.7028 (ptm) cc_final: 0.6455 (ptp) REVERT: S 226 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7068 (tptp) REVERT: S 228 GLU cc_start: 0.7425 (tt0) cc_final: 0.7106 (mt-10) REVERT: S 232 GLN cc_start: 0.5916 (mt0) cc_final: 0.5712 (pm20) REVERT: T 200 THR cc_start: 0.7392 (m) cc_final: 0.7104 (p) REVERT: U 41 THR cc_start: 0.6713 (p) cc_final: 0.6005 (m) REVERT: U 55 ARG cc_start: 0.7405 (ptm-80) cc_final: 0.7121 (ptt90) REVERT: U 84 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.7786 (tpt90) REVERT: V 237 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: W 156 TYR cc_start: 0.8635 (m-80) cc_final: 0.8429 (m-80) REVERT: W 280 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: X 194 LYS cc_start: 0.8001 (pttp) cc_final: 0.7684 (pttm) REVERT: Y 30 MET cc_start: 0.8430 (ptm) cc_final: 0.8097 (ptm) REVERT: Y 75 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7392 (mpt-90) REVERT: Z 216 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: a 64 PHE cc_start: 0.7960 (m-80) cc_final: 0.7637 (m-80) REVERT: b 98 PHE cc_start: 0.8254 (m-80) cc_final: 0.8016 (m-80) REVERT: b 150 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7445 (mm-30) REVERT: b 151 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7241 (ptmm) REVERT: b 157 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7743 (ttt-90) REVERT: b 162 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7655 (ttp-110) outliers start: 94 outliers final: 37 residues processed: 843 average time/residue: 1.6088 time to fit residues: 1627.4668 Evaluate side-chains 808 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 747 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 302 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 302 GLN Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain b residue 151 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 610 optimal weight: 0.2980 chunk 242 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 467 optimal weight: 0.0010 chunk 267 optimal weight: 8.9990 chunk 561 optimal weight: 9.9990 chunk 474 optimal weight: 0.9980 chunk 551 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 chunk 485 optimal weight: 10.0000 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN C 163 ASN E 155 GLN E 182 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN Q 264 GLN S 155 GLN S 182 ASN Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105837 restraints weight = 50492.877| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.17 r_work: 0.3080 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 49428 Z= 0.192 Angle : 0.573 9.302 66880 Z= 0.317 Chirality : 0.045 0.165 7512 Planarity : 0.004 0.043 8644 Dihedral : 5.781 59.317 6910 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.95 % Allowed : 14.81 % Favored : 83.24 % 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: 1.56 (0.10), residues: 6200 helix: 2.45 (0.11), residues: 2344 sheet: 1.08 (0.13), residues: 1462 loop : -0.43 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 154 HIS 0.005 0.001 HIS N 90 PHE 0.017 0.002 PHE J 20 TYR 0.018 0.002 TYR B 116 ARG 0.005 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 767 time to evaluate : 5.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6732 (tmm160) REVERT: A 197 ASP cc_start: 0.7407 (m-30) cc_final: 0.7098 (m-30) REVERT: B 173 GLU cc_start: 0.7062 (tt0) cc_final: 0.6684 (mt-10) REVERT: B 210 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8096 (ttp-170) REVERT: C 15 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: C 61 MET cc_start: 0.8619 (mmt) cc_final: 0.8408 (mmt) REVERT: C 148 HIS cc_start: 0.8220 (m-70) cc_final: 0.7945 (m-70) REVERT: C 178 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: D 38 LYS cc_start: 0.7357 (mmmm) cc_final: 0.7110 (mmtp) REVERT: D 54 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7531 (tp-100) REVERT: D 103 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7113 (t70) REVERT: D 138 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5748 (tm-30) REVERT: D 177 GLN cc_start: 0.6433 (mt0) cc_final: 0.5667 (mm-40) REVERT: D 197 VAL cc_start: 0.6491 (OUTLIER) cc_final: 0.6038 (p) REVERT: D 211 ASN cc_start: 0.7681 (t0) cc_final: 0.7410 (t0) REVERT: D 219 ASP cc_start: 0.5717 (OUTLIER) cc_final: 0.5438 (t70) REVERT: E 9 ASP cc_start: 0.5580 (t70) cc_final: 0.5339 (t0) REVERT: E 10 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6555 (ptm160) REVERT: E 60 ASP cc_start: 0.7214 (m-30) cc_final: 0.6886 (m-30) REVERT: E 65 ASN cc_start: 0.6823 (m-40) cc_final: 0.6492 (m110) REVERT: E 132 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5077 (mp) REVERT: E 178 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.5824 (mp-120) REVERT: E 185 TYR cc_start: 0.6690 (t80) cc_final: 0.6419 (t80) REVERT: E 189 MET cc_start: 0.6967 (ptm) cc_final: 0.6409 (ptp) REVERT: E 226 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7091 (tptp) REVERT: E 228 GLU cc_start: 0.7495 (tt0) cc_final: 0.7139 (mt-10) REVERT: F 87 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7945 (ttt90) REVERT: F 200 THR cc_start: 0.7378 (m) cc_final: 0.7076 (p) REVERT: G 41 THR cc_start: 0.6746 (p) cc_final: 0.6014 (m) REVERT: G 55 ARG cc_start: 0.7363 (ptm-80) cc_final: 0.7071 (ptt90) REVERT: H 147 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7611 (m-40) REVERT: H 237 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: I 156 TYR cc_start: 0.8625 (m-80) cc_final: 0.8416 (m-80) REVERT: I 280 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: K 30 MET cc_start: 0.8437 (ptm) cc_final: 0.8092 (ptm) REVERT: K 75 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7424 (mpt-90) REVERT: L 216 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: M 64 PHE cc_start: 0.7972 (m-80) cc_final: 0.7625 (m-80) REVERT: N 98 PHE cc_start: 0.8254 (m-80) cc_final: 0.8015 (m-80) REVERT: N 150 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7495 (mm-30) REVERT: N 151 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7263 (ptmm) REVERT: N 157 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7754 (ttt-90) REVERT: N 162 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7658 (ttp-110) REVERT: O 40 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6737 (tmm160) REVERT: O 197 ASP cc_start: 0.7418 (m-30) cc_final: 0.7108 (m-30) REVERT: P 173 GLU cc_start: 0.7056 (tt0) cc_final: 0.6684 (mt-10) REVERT: Q 15 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: Q 61 MET cc_start: 0.8616 (mmt) cc_final: 0.8403 (mmt) REVERT: Q 148 HIS cc_start: 0.8213 (m-70) cc_final: 0.7928 (m-70) REVERT: Q 178 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: R 38 LYS cc_start: 0.7353 (mmmm) cc_final: 0.7079 (mmtp) REVERT: R 54 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7546 (tp-100) REVERT: R 103 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7116 (t70) REVERT: R 138 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5732 (tm-30) REVERT: R 177 GLN cc_start: 0.6482 (mt0) cc_final: 0.5722 (mm-40) REVERT: R 197 VAL cc_start: 0.6419 (OUTLIER) cc_final: 0.5961 (p) REVERT: R 211 ASN cc_start: 0.7686 (t0) cc_final: 0.7414 (t0) REVERT: R 219 ASP cc_start: 0.5714 (OUTLIER) cc_final: 0.5438 (t70) REVERT: S 9 ASP cc_start: 0.5573 (t70) cc_final: 0.5333 (t0) REVERT: S 10 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6541 (ptm160) REVERT: S 60 ASP cc_start: 0.7219 (m-30) cc_final: 0.6886 (m-30) REVERT: S 65 ASN cc_start: 0.6827 (m-40) cc_final: 0.6491 (m110) REVERT: S 132 LEU cc_start: 0.5750 (OUTLIER) cc_final: 0.5057 (mp) REVERT: S 178 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.5885 (mp-120) REVERT: S 185 TYR cc_start: 0.6687 (t80) cc_final: 0.6415 (t80) REVERT: S 189 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6463 (ptp) REVERT: S 226 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7102 (tptp) REVERT: S 228 GLU cc_start: 0.7460 (tt0) cc_final: 0.7090 (mt-10) REVERT: S 232 GLN cc_start: 0.5955 (mt0) cc_final: 0.5729 (pm20) REVERT: T 87 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7945 (ttt90) REVERT: T 200 THR cc_start: 0.7376 (m) cc_final: 0.7070 (p) REVERT: U 41 THR cc_start: 0.6724 (p) cc_final: 0.6000 (m) REVERT: U 55 ARG cc_start: 0.7377 (ptm-80) cc_final: 0.7077 (ptt90) REVERT: V 147 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: V 237 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: W 156 TYR cc_start: 0.8623 (m-80) cc_final: 0.8414 (m-80) REVERT: W 280 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: Y 30 MET cc_start: 0.8442 (ptm) cc_final: 0.8098 (ptm) REVERT: Y 75 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7414 (mpt-90) REVERT: Z 216 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: Z 304 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: a 64 PHE cc_start: 0.7960 (m-80) cc_final: 0.7613 (m-80) REVERT: b 98 PHE cc_start: 0.8251 (m-80) cc_final: 0.8012 (m-80) REVERT: b 150 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7487 (mm-30) REVERT: b 151 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7261 (ptmm) REVERT: b 157 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7763 (ttt-90) REVERT: b 162 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7664 (ttp-110) outliers start: 101 outliers final: 42 residues processed: 834 average time/residue: 1.6387 time to fit residues: 1650.4527 Evaluate side-chains 832 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 754 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 302 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 147 ASN Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 31 GLN Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 302 GLN Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 151 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 44 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 587 optimal weight: 0.7980 chunk 552 optimal weight: 0.9980 chunk 523 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 605 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 390 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 207 GLN B 61 GLN C 60 ASN C 163 ASN E 182 ASN L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN O 207 GLN P 61 GLN Q 60 ASN Q 163 ASN Q 264 GLN S 182 ASN Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105609 restraints weight = 50440.181| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.16 r_work: 0.3078 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 49428 Z= 0.199 Angle : 0.582 9.190 66880 Z= 0.322 Chirality : 0.045 0.167 7512 Planarity : 0.004 0.047 8644 Dihedral : 5.788 58.980 6910 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 1.91 % Allowed : 15.10 % Favored : 82.99 % 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: 1.53 (0.10), residues: 6200 helix: 2.41 (0.11), residues: 2342 sheet: 1.06 (0.13), residues: 1462 loop : -0.43 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 154 HIS 0.005 0.001 HIS N 90 PHE 0.017 0.002 PHE J 20 TYR 0.019 0.002 TYR P 116 ARG 0.007 0.001 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 769 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6732 (tmm160) REVERT: A 197 ASP cc_start: 0.7401 (m-30) cc_final: 0.7100 (m-30) REVERT: B 173 GLU cc_start: 0.7116 (tt0) cc_final: 0.6737 (mt-10) REVERT: B 210 ARG cc_start: 0.8420 (ttp-170) cc_final: 0.8113 (ttp-170) REVERT: C 15 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: C 61 MET cc_start: 0.8618 (mmt) cc_final: 0.8408 (mmt) REVERT: C 148 HIS cc_start: 0.8211 (m-70) cc_final: 0.7939 (m-70) REVERT: C 178 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: D 38 LYS cc_start: 0.7341 (mmmm) cc_final: 0.7098 (mmtp) REVERT: D 54 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7522 (tp-100) REVERT: D 103 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7111 (t70) REVERT: D 138 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5735 (tm-30) REVERT: D 177 GLN cc_start: 0.6455 (mt0) cc_final: 0.5676 (mm-40) REVERT: D 197 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.5956 (p) REVERT: D 211 ASN cc_start: 0.7669 (t0) cc_final: 0.7465 (t0) REVERT: D 219 ASP cc_start: 0.5655 (OUTLIER) cc_final: 0.5404 (t70) REVERT: E 9 ASP cc_start: 0.5576 (t70) cc_final: 0.5331 (t0) REVERT: E 10 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6617 (ptm160) REVERT: E 60 ASP cc_start: 0.7218 (m-30) cc_final: 0.6908 (m-30) REVERT: E 65 ASN cc_start: 0.6840 (m-40) cc_final: 0.6512 (m110) REVERT: E 132 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5090 (mp) REVERT: E 178 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.5686 (mp10) REVERT: E 185 TYR cc_start: 0.6692 (t80) cc_final: 0.6412 (t80) REVERT: E 189 MET cc_start: 0.6987 (ptm) cc_final: 0.6418 (ptp) REVERT: E 226 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7085 (tptp) REVERT: E 228 GLU cc_start: 0.7464 (tt0) cc_final: 0.7089 (mt-10) REVERT: F 87 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7933 (ttt90) REVERT: F 200 THR cc_start: 0.7380 (m) cc_final: 0.7077 (p) REVERT: G 55 ARG cc_start: 0.7332 (ptm-80) cc_final: 0.7069 (ptt90) REVERT: G 84 ARG cc_start: 0.8289 (tpt-90) cc_final: 0.7810 (tpt90) REVERT: H 147 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7606 (m-40) REVERT: H 237 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: H 260 ASP cc_start: 0.8263 (m-30) cc_final: 0.7916 (p0) REVERT: I 156 TYR cc_start: 0.8618 (m-80) cc_final: 0.8401 (m-80) REVERT: I 157 GLN cc_start: 0.8499 (mt0) cc_final: 0.8175 (mt0) REVERT: I 280 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: J 194 LYS cc_start: 0.8096 (pttp) cc_final: 0.7711 (pttm) REVERT: K 30 MET cc_start: 0.8449 (ptm) cc_final: 0.8100 (ptm) REVERT: K 75 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7389 (mpt-90) REVERT: L 216 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: M 64 PHE cc_start: 0.7960 (m-80) cc_final: 0.7633 (m-80) REVERT: N 98 PHE cc_start: 0.8285 (m-80) cc_final: 0.8049 (m-80) REVERT: N 150 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7503 (mm-30) REVERT: N 151 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7258 (ptmm) REVERT: N 157 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7782 (ttt-90) REVERT: N 162 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7667 (ttp-110) REVERT: O 40 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6726 (tmm160) REVERT: O 197 ASP cc_start: 0.7420 (m-30) cc_final: 0.7118 (m-30) REVERT: P 173 GLU cc_start: 0.7107 (tt0) cc_final: 0.6730 (mt-10) REVERT: Q 15 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: Q 61 MET cc_start: 0.8616 (mmt) cc_final: 0.8403 (mmt) REVERT: Q 148 HIS cc_start: 0.8209 (m-70) cc_final: 0.7936 (m-70) REVERT: Q 178 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: R 38 LYS cc_start: 0.7352 (mmmm) cc_final: 0.7078 (mmtp) REVERT: R 54 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7537 (tp-100) REVERT: R 103 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7112 (t70) REVERT: R 138 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: R 177 GLN cc_start: 0.6459 (mt0) cc_final: 0.5680 (mm-40) REVERT: R 197 VAL cc_start: 0.6450 (OUTLIER) cc_final: 0.5954 (p) REVERT: R 211 ASN cc_start: 0.7675 (t0) cc_final: 0.7470 (t0) REVERT: R 219 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.5439 (t70) REVERT: S 9 ASP cc_start: 0.5561 (t70) cc_final: 0.5321 (t0) REVERT: S 10 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6632 (ptm160) REVERT: S 60 ASP cc_start: 0.7214 (m-30) cc_final: 0.6886 (m-30) REVERT: S 65 ASN cc_start: 0.6831 (m-40) cc_final: 0.6498 (m110) REVERT: S 132 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5082 (mp) REVERT: S 178 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.5913 (mp10) REVERT: S 185 TYR cc_start: 0.6690 (t80) cc_final: 0.6392 (t80) REVERT: S 189 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6467 (ptp) REVERT: S 226 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7098 (tptp) REVERT: S 228 GLU cc_start: 0.7445 (tt0) cc_final: 0.7091 (mt-10) REVERT: S 232 GLN cc_start: 0.5958 (mt0) cc_final: 0.5752 (pm20) REVERT: T 87 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7939 (ttt90) REVERT: T 200 THR cc_start: 0.7375 (m) cc_final: 0.7068 (p) REVERT: U 55 ARG cc_start: 0.7377 (ptm-80) cc_final: 0.7083 (ptt90) REVERT: U 84 ARG cc_start: 0.8286 (tpt-90) cc_final: 0.7807 (tpt90) REVERT: V 147 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7597 (m-40) REVERT: V 237 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: W 156 TYR cc_start: 0.8618 (m-80) cc_final: 0.8402 (m-80) REVERT: W 157 GLN cc_start: 0.8500 (mt0) cc_final: 0.8179 (mt0) REVERT: W 280 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: X 194 LYS cc_start: 0.8092 (pttp) cc_final: 0.7710 (pttm) REVERT: Y 30 MET cc_start: 0.8452 (ptm) cc_final: 0.8105 (ptm) REVERT: Y 75 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7396 (mpt-90) REVERT: Z 216 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: a 64 PHE cc_start: 0.7962 (m-80) cc_final: 0.7631 (m-80) REVERT: b 98 PHE cc_start: 0.8285 (m-80) cc_final: 0.8049 (m-80) REVERT: b 150 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7493 (mm-30) REVERT: b 151 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7258 (ptmm) REVERT: b 157 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7789 (ttt-90) REVERT: b 162 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7682 (ttp-110) outliers start: 99 outliers final: 42 residues processed: 839 average time/residue: 1.6212 time to fit residues: 1630.2522 Evaluate side-chains 838 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 761 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 302 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 101 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain V residue 147 ASN Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 31 GLN Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 302 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 151 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 163 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 357 optimal weight: 7.9990 chunk 585 optimal weight: 8.9990 chunk 501 optimal weight: 0.2980 chunk 103 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN C 163 ASN E 182 ASN K 22 ASN L 251 GLN L 302 GLN O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN Q 264 GLN S 182 ASN Y 22 ASN Z 251 GLN Z 302 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104489 restraints weight = 50211.762| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.18 r_work: 0.3057 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 49428 Z= 0.256 Angle : 0.645 9.600 66880 Z= 0.357 Chirality : 0.047 0.192 7512 Planarity : 0.005 0.051 8644 Dihedral : 5.936 58.626 6910 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 14.91 % Favored : 83.12 % 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: 1.38 (0.10), residues: 6200 helix: 2.25 (0.11), residues: 2334 sheet: 1.09 (0.13), residues: 1424 loop : -0.52 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP V 245 HIS 0.007 0.001 HIS b 90 PHE 0.019 0.002 PHE J 20 TYR 0.023 0.002 TYR O 9 ARG 0.005 0.001 ARG N 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 761 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6738 (tmm160) REVERT: B 173 GLU cc_start: 0.7139 (tt0) cc_final: 0.6760 (mt-10) REVERT: C 15 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: C 148 HIS cc_start: 0.8187 (m-70) cc_final: 0.7877 (m-70) REVERT: C 250 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6687 (mmp80) REVERT: D 38 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7083 (mmtp) REVERT: D 54 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7556 (tp-100) REVERT: D 103 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7158 (t70) REVERT: D 138 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5687 (tm-30) REVERT: D 177 GLN cc_start: 0.6438 (mt0) cc_final: 0.5665 (mm-40) REVERT: D 197 VAL cc_start: 0.6471 (OUTLIER) cc_final: 0.5980 (p) REVERT: D 219 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5519 (t70) REVERT: E 9 ASP cc_start: 0.5620 (t70) cc_final: 0.5362 (t0) REVERT: E 10 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6635 (ptm160) REVERT: E 60 ASP cc_start: 0.7257 (m-30) cc_final: 0.6944 (m-30) REVERT: E 65 ASN cc_start: 0.6885 (m-40) cc_final: 0.6565 (m110) REVERT: E 132 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5156 (mp) REVERT: E 178 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.5832 (mp10) REVERT: E 185 TYR cc_start: 0.6684 (t80) cc_final: 0.6402 (t80) REVERT: E 189 MET cc_start: 0.7058 (ptm) cc_final: 0.6507 (ptp) REVERT: E 226 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7061 (tptp) REVERT: E 228 GLU cc_start: 0.7451 (tt0) cc_final: 0.7067 (mt-10) REVERT: F 87 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8003 (ttt90) REVERT: G 55 ARG cc_start: 0.7403 (ptm-80) cc_final: 0.7095 (ptt90) REVERT: G 204 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6305 (m-30) REVERT: H 147 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7604 (m-40) REVERT: H 237 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: I 156 TYR cc_start: 0.8618 (m-80) cc_final: 0.8406 (m-80) REVERT: I 157 GLN cc_start: 0.8514 (mt0) cc_final: 0.8176 (mt0) REVERT: I 280 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: K 30 MET cc_start: 0.8506 (ptm) cc_final: 0.8169 (ptm) REVERT: K 75 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7435 (mpt-90) REVERT: L 216 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: M 57 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8256 (p0) REVERT: M 64 PHE cc_start: 0.7965 (m-80) cc_final: 0.7623 (m-80) REVERT: N 98 PHE cc_start: 0.8334 (m-80) cc_final: 0.8112 (m-80) REVERT: N 150 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7474 (mm-30) REVERT: N 151 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6981 (ptpt) REVERT: N 157 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7808 (ttt-90) REVERT: N 162 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7694 (ttp-110) REVERT: O 40 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6760 (tmm160) REVERT: P 173 GLU cc_start: 0.7135 (tt0) cc_final: 0.6754 (mt-10) REVERT: Q 15 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: Q 61 MET cc_start: 0.8623 (mmt) cc_final: 0.8406 (mmt) REVERT: Q 148 HIS cc_start: 0.8193 (m-70) cc_final: 0.7882 (m-70) REVERT: Q 178 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: Q 250 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6683 (mmp80) REVERT: R 38 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7060 (mmtp) REVERT: R 54 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7568 (tp-100) REVERT: R 103 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7152 (t70) REVERT: R 138 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5682 (tm-30) REVERT: R 177 GLN cc_start: 0.6427 (mt0) cc_final: 0.5654 (mm-40) REVERT: R 197 VAL cc_start: 0.6474 (OUTLIER) cc_final: 0.5983 (p) REVERT: R 219 ASP cc_start: 0.5749 (OUTLIER) cc_final: 0.5518 (t70) REVERT: S 9 ASP cc_start: 0.5634 (t70) cc_final: 0.5381 (t0) REVERT: S 10 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6642 (ptm160) REVERT: S 60 ASP cc_start: 0.7246 (m-30) cc_final: 0.6917 (m-30) REVERT: S 65 ASN cc_start: 0.6880 (m-40) cc_final: 0.6559 (m110) REVERT: S 132 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5199 (mp) REVERT: S 178 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.5839 (mp10) REVERT: S 185 TYR cc_start: 0.6687 (t80) cc_final: 0.6407 (t80) REVERT: S 189 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6515 (ptp) REVERT: S 226 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7087 (tptp) REVERT: S 228 GLU cc_start: 0.7453 (tt0) cc_final: 0.7078 (mt-10) REVERT: S 232 GLN cc_start: 0.5967 (mt0) cc_final: 0.5748 (pm20) REVERT: T 87 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7998 (ttt90) REVERT: U 204 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6309 (m-30) REVERT: V 147 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7597 (m-40) REVERT: V 237 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: W 156 TYR cc_start: 0.8610 (m-80) cc_final: 0.8396 (m-80) REVERT: W 157 GLN cc_start: 0.8514 (mt0) cc_final: 0.8178 (mt0) REVERT: W 280 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: Y 30 MET cc_start: 0.8509 (ptm) cc_final: 0.8173 (ptm) REVERT: Y 75 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7418 (mpt-90) REVERT: Z 216 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: a 57 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8252 (p0) REVERT: a 64 PHE cc_start: 0.7965 (m-80) cc_final: 0.7620 (m-80) REVERT: b 98 PHE cc_start: 0.8331 (m-80) cc_final: 0.8106 (m-80) REVERT: b 150 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7469 (mm-30) REVERT: b 151 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6981 (ptpt) REVERT: b 157 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7801 (ttt-90) REVERT: b 162 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7705 (ttp-110) outliers start: 102 outliers final: 47 residues processed: 825 average time/residue: 1.6091 time to fit residues: 1592.8587 Evaluate side-chains 826 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 741 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 101 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 147 ASN Chi-restraints excluded: chain V residue 198 LYS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 31 GLN Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 302 GLN Chi-restraints excluded: chain a residue 57 ASP Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 151 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 488 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 552 optimal weight: 2.9990 chunk 497 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 319 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN C 163 ASN E 182 ASN L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN Q 264 GLN S 182 ASN Z 251 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 70 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106654 restraints weight = 50570.100| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.18 r_work: 0.3093 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 49428 Z= 0.168 Angle : 0.557 9.080 66880 Z= 0.308 Chirality : 0.044 0.193 7512 Planarity : 0.004 0.043 8644 Dihedral : 5.680 59.111 6910 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 1.49 % Allowed : 15.35 % Favored : 83.16 % 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: 1.55 (0.10), residues: 6200 helix: 2.43 (0.11), residues: 2346 sheet: 1.07 (0.13), residues: 1474 loop : -0.44 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 154 HIS 0.004 0.001 HIS N 90 PHE 0.015 0.002 PHE J 20 TYR 0.019 0.001 TYR O 9 ARG 0.006 0.000 ARG a 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12400 Ramachandran restraints generated. 6200 Oldfield, 0 Emsley, 6200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 766 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6724 (tmm160) REVERT: A 197 ASP cc_start: 0.7370 (m-30) cc_final: 0.7049 (m-30) REVERT: B 173 GLU cc_start: 0.7120 (tt0) cc_final: 0.6723 (mt-10) REVERT: C 15 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: C 148 HIS cc_start: 0.8219 (m-70) cc_final: 0.7914 (m-70) REVERT: C 250 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6754 (mmp80) REVERT: C 262 ASP cc_start: 0.6488 (m-30) cc_final: 0.6066 (t70) REVERT: D 38 LYS cc_start: 0.7346 (mmmm) cc_final: 0.7088 (mmtp) REVERT: D 54 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7524 (tp-100) REVERT: D 103 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7085 (t70) REVERT: D 138 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5592 (tm-30) REVERT: D 177 GLN cc_start: 0.6447 (mt0) cc_final: 0.5695 (mm-40) REVERT: D 197 VAL cc_start: 0.6457 (OUTLIER) cc_final: 0.6252 (m) REVERT: D 219 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5513 (t70) REVERT: E 9 ASP cc_start: 0.5505 (t70) cc_final: 0.5259 (t0) REVERT: E 10 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6552 (ptm160) REVERT: E 60 ASP cc_start: 0.7194 (m-30) cc_final: 0.6866 (m-30) REVERT: E 65 ASN cc_start: 0.6826 (m-40) cc_final: 0.6498 (m110) REVERT: E 132 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5173 (mp) REVERT: E 178 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.5836 (mp10) REVERT: E 185 TYR cc_start: 0.6689 (t80) cc_final: 0.6330 (t80) REVERT: E 189 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6348 (ptp) REVERT: E 226 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7062 (tptp) REVERT: E 228 GLU cc_start: 0.7419 (tt0) cc_final: 0.7067 (mt-10) REVERT: F 87 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7928 (ttt90) REVERT: F 200 THR cc_start: 0.7317 (m) cc_final: 0.7047 (p) REVERT: G 55 ARG cc_start: 0.7327 (ptm-80) cc_final: 0.6953 (pmm-80) REVERT: G 84 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.7797 (tpt90) REVERT: G 204 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6282 (m-30) REVERT: H 237 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: H 260 ASP cc_start: 0.8239 (m-30) cc_final: 0.7905 (p0) REVERT: I 156 TYR cc_start: 0.8591 (m-80) cc_final: 0.8368 (m-80) REVERT: I 157 GLN cc_start: 0.8492 (mt0) cc_final: 0.8164 (mt0) REVERT: I 280 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: J 194 LYS cc_start: 0.8095 (pttp) cc_final: 0.7710 (pttm) REVERT: K 30 MET cc_start: 0.8430 (ptm) cc_final: 0.8129 (ptm) REVERT: K 75 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7396 (mpt-90) REVERT: L 216 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: M 64 PHE cc_start: 0.7950 (m-80) cc_final: 0.7618 (m-80) REVERT: N 98 PHE cc_start: 0.8251 (m-80) cc_final: 0.8017 (m-80) REVERT: N 150 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7463 (mm-30) REVERT: N 151 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7245 (ptmm) REVERT: N 157 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7759 (ttt-90) REVERT: N 162 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7635 (ttp-110) REVERT: O 40 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6725 (tmm160) REVERT: O 197 ASP cc_start: 0.7385 (m-30) cc_final: 0.7058 (m-30) REVERT: P 173 GLU cc_start: 0.7059 (tt0) cc_final: 0.6695 (mt-10) REVERT: Q 15 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: Q 61 MET cc_start: 0.8607 (mmt) cc_final: 0.8391 (mmt) REVERT: Q 148 HIS cc_start: 0.8219 (m-70) cc_final: 0.7912 (m-70) REVERT: Q 178 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: Q 250 ARG cc_start: 0.7019 (mtp180) cc_final: 0.6751 (mmp80) REVERT: R 38 LYS cc_start: 0.7344 (mmmm) cc_final: 0.7077 (mmtp) REVERT: R 54 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7539 (tp-100) REVERT: R 103 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7085 (t70) REVERT: R 138 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5575 (tm-30) REVERT: R 177 GLN cc_start: 0.6455 (mt0) cc_final: 0.5705 (mm-40) REVERT: R 197 VAL cc_start: 0.6472 (OUTLIER) cc_final: 0.6264 (m) REVERT: R 219 ASP cc_start: 0.5730 (OUTLIER) cc_final: 0.5506 (t70) REVERT: S 9 ASP cc_start: 0.5496 (t70) cc_final: 0.5250 (t0) REVERT: S 10 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6557 (ptm160) REVERT: S 60 ASP cc_start: 0.7215 (m-30) cc_final: 0.6887 (m-30) REVERT: S 65 ASN cc_start: 0.6840 (m-40) cc_final: 0.6504 (m110) REVERT: S 178 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.5820 (mp10) REVERT: S 185 TYR cc_start: 0.6688 (t80) cc_final: 0.6339 (t80) REVERT: S 189 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6391 (ptp) REVERT: S 226 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7081 (tptp) REVERT: S 228 GLU cc_start: 0.7421 (tt0) cc_final: 0.7074 (mt-10) REVERT: S 232 GLN cc_start: 0.6000 (mt0) cc_final: 0.5777 (pm20) REVERT: T 87 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7908 (ttt90) REVERT: T 200 THR cc_start: 0.7315 (m) cc_final: 0.7041 (p) REVERT: U 84 ARG cc_start: 0.8262 (tpt-90) cc_final: 0.7792 (tpt90) REVERT: U 204 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6284 (m-30) REVERT: V 237 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: W 156 TYR cc_start: 0.8594 (m-80) cc_final: 0.8371 (m-80) REVERT: W 157 GLN cc_start: 0.8491 (mt0) cc_final: 0.8164 (mt0) REVERT: W 280 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: X 194 LYS cc_start: 0.8092 (pttp) cc_final: 0.7712 (pttm) REVERT: Y 30 MET cc_start: 0.8437 (ptm) cc_final: 0.8118 (ptm) REVERT: Y 75 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7377 (mpt-90) REVERT: Z 216 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: Z 304 LYS cc_start: 0.8261 (mmtp) cc_final: 0.7958 (mttt) REVERT: a 64 PHE cc_start: 0.7954 (m-80) cc_final: 0.7619 (m-80) REVERT: b 98 PHE cc_start: 0.8247 (m-80) cc_final: 0.8017 (m-80) REVERT: b 150 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7450 (mm-30) REVERT: b 151 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7238 (ptmm) REVERT: b 157 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7760 (ttt-90) REVERT: b 162 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7650 (ttp-110) outliers start: 77 outliers final: 38 residues processed: 821 average time/residue: 1.6020 time to fit residues: 1579.9364 Evaluate side-chains 831 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 759 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 216 GLN Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 302 GLN Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain N residue 151 LYS Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 101 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 178 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 151 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 388 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 599 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 307 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 385 optimal weight: 3.9990 chunk 391 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 61 GLN C 60 ASN C 163 ASN D 85 ASN E 182 ASN ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 251 GLN L 302 GLN ** M 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN S 182 ASN Y 165 GLN Z 251 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 70 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106633 restraints weight = 50354.781| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.17 r_work: 0.3091 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 49428 Z= 0.202 Angle : 0.643 59.200 66880 Z= 0.365 Chirality : 0.045 0.820 7512 Planarity : 0.004 0.041 8644 Dihedral : 5.685 59.067 6910 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.62 % Allowed : 15.56 % Favored : 82.81 % Cbeta Deviations : 0.02 % 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: 1.56 (0.10), residues: 6200 helix: 2.44 (0.11), residues: 2346 sheet: 1.07 (0.13), residues: 1476 loop : -0.43 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 154 HIS 0.005 0.001 HIS N 90 PHE 0.015 0.002 PHE X 20 TYR 0.018 0.002 TYR O 9 ARG 0.004 0.000 ARG A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38603.91 seconds wall clock time: 658 minutes 23.62 seconds (39503.62 seconds total)