Starting phenix.real_space_refine on Fri Dec 27 18:02:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f9p_50258/12_2024/9f9p_50258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f9p_50258/12_2024/9f9p_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_50258/12_2024/9f9p_50258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f9p_50258/12_2024/9f9p_50258.map" model { file = "/net/cci-nas-00/data/ceres_data/9f9p_50258/12_2024/9f9p_50258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f9p_50258/12_2024/9f9p_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 20.72, per 1000 atoms: 0.42 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: 8.71 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: 4.92 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: 17.02 Time building geometry restraints manager: 10.41 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.060 Extract box with map and model: 1.490 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 82.050 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.270 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:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.800 ------------------------------------------------------------------------------- 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 : 4.161 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: 1.6174 time to fit residues: 2397.1051 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 : 4.159 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8306 (p0) cc_final: 0.8069 (p0) REVERT: A 101 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8032 (tpt90) REVERT: A 197 ASP cc_start: 0.7821 (m-30) cc_final: 0.7474 (m-30) REVERT: A 238 ASP cc_start: 0.7820 (m-30) cc_final: 0.7137 (t0) REVERT: B 173 GLU cc_start: 0.7377 (tt0) cc_final: 0.7082 (mt-10) REVERT: B 210 ARG cc_start: 0.8604 (ttp-170) cc_final: 0.8294 (ttp-170) REVERT: B 212 SER cc_start: 0.8203 (p) cc_final: 0.7973 (t) REVERT: B 213 GLU cc_start: 0.8689 (mp0) cc_final: 0.8313 (mp0) REVERT: B 217 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7950 (pm20) REVERT: C 15 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 48 GLU cc_start: 0.7965 (tt0) cc_final: 0.7753 (pt0) REVERT: C 61 MET cc_start: 0.8555 (mmt) cc_final: 0.8173 (mmm) REVERT: C 148 HIS cc_start: 0.8471 (m-70) cc_final: 0.8258 (m-70) REVERT: C 186 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6675 (pttm) REVERT: C 214 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6362 (tp30) REVERT: C 234 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: C 250 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6841 (mtp180) REVERT: C 264 GLN cc_start: 0.7089 (mt0) cc_final: 0.6755 (mt0) REVERT: D 51 GLN cc_start: 0.6772 (mt0) cc_final: 0.6545 (mt0) REVERT: D 138 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5701 (tm-30) REVERT: D 183 ASP cc_start: 0.6995 (m-30) cc_final: 0.6766 (m-30) REVERT: D 211 ASN cc_start: 0.7691 (t0) cc_final: 0.7303 (t0) REVERT: E 66 LYS cc_start: 0.7810 (mtpt) cc_final: 0.7448 (mttp) REVERT: E 178 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6050 (mm-40) REVERT: E 185 TYR cc_start: 0.6847 (t80) cc_final: 0.6374 (t80) REVERT: E 196 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.6104 (p) REVERT: E 211 THR cc_start: 0.7469 (p) cc_final: 0.7261 (t) REVERT: E 232 GLN cc_start: 0.6182 (mt0) cc_final: 0.5674 (pm20) REVERT: F 51 ARG cc_start: 0.3869 (OUTLIER) cc_final: 0.2195 (mtm-85) REVERT: F 119 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7929 (mmt-90) REVERT: F 200 THR cc_start: 0.7335 (m) cc_final: 0.7003 (p) REVERT: G 55 ARG cc_start: 0.7816 (ptm-80) cc_final: 0.7470 (ptt90) REVERT: G 84 ARG cc_start: 0.8400 (tpt-90) cc_final: 0.7867 (tpt90) REVERT: G 176 LYS cc_start: 0.7639 (mttp) cc_final: 0.7395 (mttp) REVERT: H 198 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7644 (mptt) REVERT: I 96 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7877 (mpt180) REVERT: I 98 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7827 (mtmm) REVERT: I 260 GLU cc_start: 0.5118 (OUTLIER) cc_final: 0.4676 (tp30) REVERT: I 281 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6305 (mp0) REVERT: K 30 MET cc_start: 0.8411 (ptm) cc_final: 0.8177 (ptm) REVERT: K 75 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (mpt-90) REVERT: K 201 ILE cc_start: 0.8684 (mt) cc_final: 0.8344 (tt) REVERT: L 183 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7915 (mtt-85) REVERT: M 64 PHE cc_start: 0.8296 (m-80) cc_final: 0.8028 (m-80) REVERT: N 1 MET cc_start: 0.6705 (mtm) cc_final: 0.6248 (mmt) REVERT: N 98 PHE cc_start: 0.8333 (m-80) cc_final: 0.8122 (m-80) REVERT: N 157 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7832 (ttt-90) REVERT: N 218 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5358 (mpp80) REVERT: O 61 ASP cc_start: 0.8318 (p0) cc_final: 0.8076 (p0) REVERT: O 101 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8031 (tpt90) REVERT: O 197 ASP cc_start: 0.7822 (m-30) cc_final: 0.7472 (m-30) REVERT: O 238 ASP cc_start: 0.7819 (m-30) cc_final: 0.7137 (t0) REVERT: P 173 GLU cc_start: 0.7382 (tt0) cc_final: 0.7087 (mt-10) REVERT: P 210 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.8302 (ttp-170) REVERT: P 212 SER cc_start: 0.8206 (p) cc_final: 0.7973 (t) REVERT: P 213 GLU cc_start: 0.8683 (mp0) cc_final: 0.8307 (mp0) REVERT: P 217 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7944 (pm20) REVERT: Q 15 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: Q 48 GLU cc_start: 0.7971 (tt0) cc_final: 0.7755 (pt0) REVERT: Q 61 MET cc_start: 0.8557 (mmt) cc_final: 0.8173 (mmm) REVERT: Q 148 HIS cc_start: 0.8467 (m-70) cc_final: 0.8255 (m-70) REVERT: Q 186 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6681 (pttm) REVERT: Q 214 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6362 (tp30) REVERT: Q 234 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: Q 250 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6843 (mtp180) REVERT: Q 264 GLN cc_start: 0.7096 (mt0) cc_final: 0.6761 (mt0) REVERT: R 51 GLN cc_start: 0.6782 (mt0) cc_final: 0.6548 (mt0) REVERT: R 138 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5704 (tm-30) REVERT: R 139 ASN cc_start: 0.6647 (p0) cc_final: 0.6446 (p0) REVERT: R 183 ASP cc_start: 0.6996 (m-30) cc_final: 0.6768 (m-30) REVERT: R 211 ASN cc_start: 0.7685 (t0) cc_final: 0.7294 (t0) REVERT: S 66 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7474 (mttp) REVERT: S 178 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6028 (mm-40) REVERT: S 185 TYR cc_start: 0.6845 (t80) cc_final: 0.6369 (t80) REVERT: S 189 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7230 (mtp) REVERT: S 196 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.6097 (p) REVERT: S 211 THR cc_start: 0.7467 (p) cc_final: 0.7262 (t) REVERT: S 232 GLN cc_start: 0.6141 (mt0) cc_final: 0.5606 (pm20) REVERT: T 51 ARG cc_start: 0.3872 (OUTLIER) cc_final: 0.2200 (mtm-85) REVERT: T 119 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7929 (mmt-90) REVERT: T 200 THR cc_start: 0.7335 (m) cc_final: 0.6998 (p) REVERT: U 55 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7463 (ptt90) REVERT: U 84 ARG cc_start: 0.8398 (tpt-90) cc_final: 0.7866 (tpt90) REVERT: U 176 LYS cc_start: 0.7642 (mttp) cc_final: 0.7401 (mttp) REVERT: W 96 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7878 (mpt180) REVERT: W 98 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7827 (mtmm) REVERT: W 260 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4645 (tp30) REVERT: W 281 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6303 (mp0) REVERT: Y 30 MET cc_start: 0.8413 (ptm) cc_final: 0.8179 (ptm) REVERT: Y 75 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (mpt-90) REVERT: Y 201 ILE cc_start: 0.8682 (mt) cc_final: 0.8344 (tt) REVERT: Z 183 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7915 (mtt-85) REVERT: a 64 PHE cc_start: 0.8295 (m-80) cc_final: 0.8024 (m-80) REVERT: b 1 MET cc_start: 0.6697 (mtm) cc_final: 0.6240 (mmt) REVERT: b 98 PHE cc_start: 0.8329 (m-80) cc_final: 0.8115 (m-80) REVERT: b 157 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7835 (ttt-90) REVERT: b 218 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5371 (mpp80) outliers start: 136 outliers final: 27 residues processed: 1000 average time/residue: 1.5816 time to fit residues: 1899.9099 Evaluate side-chains 826 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 776 time to evaluate : 4.160 ------------------------------------------------------------------------------- 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 196 THR 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 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 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 51 ARG 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 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 308 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 462 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 556 optimal weight: 9.9990 chunk 601 optimal weight: 3.9990 chunk 495 optimal weight: 10.0000 chunk 552 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 446 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 15 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 70 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 49428 Z= 0.293 Angle : 0.709 9.109 66880 Z= 0.393 Chirality : 0.049 0.205 7512 Planarity : 0.006 0.063 8644 Dihedral : 6.668 76.253 6947 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 2.63 % Allowed : 13.28 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 6200 helix: 1.80 (0.10), residues: 2348 sheet: 1.14 (0.13), residues: 1386 loop : -0.74 (0.11), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP V 245 HIS 0.009 0.002 HIS b 90 PHE 0.021 0.003 PHE L 271 TYR 0.027 0.002 TYR P 116 ARG 0.007 0.001 ARG D 233 *********************** 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 878 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 742 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8124 (tpt90) REVERT: A 146 ASP cc_start: 0.7419 (p0) cc_final: 0.7097 (p0) REVERT: B 173 GLU cc_start: 0.7525 (tt0) cc_final: 0.7231 (mt-10) REVERT: B 210 ARG cc_start: 0.8619 (ttp-170) cc_final: 0.8224 (ttp-170) REVERT: B 217 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7883 (mp0) REVERT: B 227 TYR cc_start: 0.8060 (m-80) cc_final: 0.7839 (m-80) REVERT: C 15 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 61 MET cc_start: 0.8566 (mmt) cc_final: 0.8340 (mmt) REVERT: C 148 HIS cc_start: 0.8418 (m-70) cc_final: 0.8198 (m-70) REVERT: C 186 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6673 (pttm) REVERT: C 214 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6382 (tp30) REVERT: C 234 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: C 250 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6801 (mtp180) REVERT: D 5 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7962 (tpp80) REVERT: D 103 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7598 (t0) REVERT: D 138 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.5965 (tm-30) REVERT: D 177 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.5979 (mm-40) REVERT: D 211 ASN cc_start: 0.7671 (t0) cc_final: 0.7401 (t0) REVERT: D 230 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4794 (mm-30) REVERT: E 148 GLU cc_start: 0.7867 (pt0) cc_final: 0.7537 (pm20) REVERT: E 178 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6263 (mp10) REVERT: E 185 TYR cc_start: 0.6895 (t80) cc_final: 0.6637 (t80) REVERT: E 187 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6119 (mpp-170) REVERT: E 196 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.6076 (m) REVERT: E 226 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7057 (tptp) REVERT: E 228 GLU cc_start: 0.7733 (tt0) cc_final: 0.7416 (mt-10) REVERT: E 232 GLN cc_start: 0.6164 (mt0) cc_final: 0.5626 (pm20) REVERT: F 119 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7934 (mmt-90) REVERT: F 200 THR cc_start: 0.7405 (m) cc_final: 0.6982 (p) REVERT: G 41 THR cc_start: 0.6730 (p) cc_final: 0.5941 (m) REVERT: G 55 ARG cc_start: 0.7836 (ptm-80) cc_final: 0.7483 (ptt90) REVERT: H 198 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7665 (mmtp) REVERT: I 98 LYS cc_start: 0.8282 (mmmm) cc_final: 0.7837 (mtmm) REVERT: I 280 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: K 30 MET cc_start: 0.8479 (ptm) cc_final: 0.8182 (ptm) REVERT: K 75 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7500 (mpt-90) REVERT: K 201 ILE cc_start: 0.8613 (mt) cc_final: 0.8368 (tt) REVERT: L 134 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: L 183 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7937 (mtt-85) REVERT: M 64 PHE cc_start: 0.8329 (m-80) cc_final: 0.8041 (m-80) REVERT: N 1 MET cc_start: 0.6698 (mtm) cc_final: 0.6478 (mtp) REVERT: N 150 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7666 (mm-30) REVERT: N 157 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7896 (ttt-90) REVERT: O 101 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8119 (tpt90) REVERT: O 146 ASP cc_start: 0.7418 (p0) cc_final: 0.7095 (p0) REVERT: P 173 GLU cc_start: 0.7524 (tt0) cc_final: 0.7230 (mt-10) REVERT: P 183 GLU cc_start: 0.7451 (tp30) cc_final: 0.7233 (mm-30) REVERT: P 210 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8227 (ttp-170) REVERT: P 217 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7880 (mp0) REVERT: P 227 TYR cc_start: 0.8057 (m-80) cc_final: 0.7802 (m-80) REVERT: Q 15 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: Q 61 MET cc_start: 0.8567 (mmt) cc_final: 0.8339 (mmt) REVERT: Q 148 HIS cc_start: 0.8424 (m-70) cc_final: 0.8213 (m-70) REVERT: Q 186 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6642 (pttm) REVERT: Q 214 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6409 (tp30) REVERT: Q 234 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: Q 250 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6815 (mtp180) REVERT: R 5 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7962 (tpp80) REVERT: R 46 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: R 103 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7595 (t0) REVERT: R 138 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5953 (tm-30) REVERT: R 139 ASN cc_start: 0.6707 (p0) cc_final: 0.6471 (p0) REVERT: R 177 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.5969 (mm-40) REVERT: R 211 ASN cc_start: 0.7659 (t0) cc_final: 0.7389 (t0) REVERT: R 230 GLU cc_start: 0.5280 (OUTLIER) cc_final: 0.4803 (mm-30) REVERT: S 148 GLU cc_start: 0.7853 (pt0) cc_final: 0.7522 (pm20) REVERT: S 178 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6265 (mp10) REVERT: S 185 TYR cc_start: 0.6880 (t80) cc_final: 0.6655 (t80) REVERT: S 196 THR cc_start: 0.6276 (OUTLIER) cc_final: 0.6070 (m) REVERT: S 226 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7056 (tptp) REVERT: S 228 GLU cc_start: 0.7736 (tt0) cc_final: 0.7416 (mt-10) REVERT: S 232 GLN cc_start: 0.6155 (mt0) cc_final: 0.5625 (pm20) REVERT: T 119 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7938 (mmt-90) REVERT: T 200 THR cc_start: 0.7404 (m) cc_final: 0.6978 (p) REVERT: U 55 ARG cc_start: 0.7841 (ptm-80) cc_final: 0.7497 (ptt90) REVERT: W 98 LYS cc_start: 0.8287 (mmmm) cc_final: 0.7843 (mtmm) REVERT: W 280 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: Y 30 MET cc_start: 0.8480 (ptm) cc_final: 0.8181 (ptm) REVERT: Y 75 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7493 (mpt-90) REVERT: Y 201 ILE cc_start: 0.8611 (mt) cc_final: 0.8366 (tt) REVERT: Z 134 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: Z 183 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: Z 216 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: a 64 PHE cc_start: 0.8340 (m-80) cc_final: 0.8045 (m-80) REVERT: b 1 MET cc_start: 0.6698 (mtm) cc_final: 0.6480 (mtp) REVERT: b 150 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7660 (mm-30) REVERT: b 157 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7886 (ttt-90) outliers start: 136 outliers final: 52 residues processed: 827 average time/residue: 1.6327 time to fit residues: 1615.3685 Evaluate side-chains 804 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 721 time to evaluate : 4.170 ------------------------------------------------------------------------------- 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 186 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 5 ARG 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 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 E residue 187 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 160 THR 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 K residue 204 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 183 ARG 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 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 186 LYS Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain R residue 5 ARG 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 46 VAL Chi-restraints excluded: chain S residue 140 SER Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 143 MET 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 Y residue 204 THR Chi-restraints excluded: chain Z residue 134 GLN 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 220 SER Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 57 ASP Chi-restraints excluded: chain a residue 131 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 7.9990 chunk 418 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 558 optimal weight: 8.9990 chunk 591 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 529 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN C 94 ASN D 68 HIS E 182 ASN ** L 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN N 97 GLN O 93 GLN P 61 GLN P 223 GLN Q 60 ASN Q 94 ASN R 68 HIS S 182 ASN ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 302 GLN b 97 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 49428 Z= 0.386 Angle : 0.786 9.819 66880 Z= 0.435 Chirality : 0.053 0.211 7512 Planarity : 0.006 0.078 8644 Dihedral : 6.683 59.274 6926 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.77 % Rotamer: Outliers : 3.02 % Allowed : 13.46 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 6200 helix: 1.67 (0.10), residues: 2320 sheet: 1.05 (0.13), residues: 1382 loop : -0.74 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP V 245 HIS 0.010 0.002 HIS b 90 PHE 0.022 0.003 PHE D 43 TYR 0.028 0.003 TYR Y 101 ARG 0.008 0.001 ARG O 101 *********************** 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 896 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 740 time to evaluate : 5.148 Fit side-chains REVERT: A 40 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7358 (tmm160) REVERT: A 101 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8144 (tpt90) REVERT: A 146 ASP cc_start: 0.7467 (p0) cc_final: 0.7158 (p0) REVERT: B 181 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7258 (pt0) REVERT: B 210 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8286 (ttp-170) REVERT: B 217 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8097 (pm20) REVERT: C 15 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: C 148 HIS cc_start: 0.8423 (m-70) cc_final: 0.8221 (m-70) REVERT: C 186 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6633 (pttm) REVERT: C 214 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6395 (tp30) REVERT: C 230 GLN cc_start: 0.5533 (OUTLIER) cc_final: 0.5163 (tp40) REVERT: C 250 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6819 (mmp80) REVERT: D 5 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.8008 (tpp80) REVERT: D 103 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7667 (t0) REVERT: D 138 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5988 (tm-30) REVERT: D 175 SER cc_start: 0.6879 (m) cc_final: 0.6274 (p) REVERT: D 197 VAL cc_start: 0.6417 (OUTLIER) cc_final: 0.6042 (p) REVERT: D 211 ASN cc_start: 0.7720 (t0) cc_final: 0.7454 (t0) REVERT: D 219 ASP cc_start: 0.6029 (m-30) cc_final: 0.5528 (p0) REVERT: E 9 ASP cc_start: 0.5550 (t70) cc_final: 0.5320 (t0) REVERT: E 53 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6823 (ttt180) REVERT: E 132 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5046 (mp) REVERT: E 148 GLU cc_start: 0.7856 (pt0) cc_final: 0.7504 (pm20) REVERT: E 178 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6504 (mp10) REVERT: E 183 GLU cc_start: 0.6705 (tt0) cc_final: 0.6394 (tm-30) REVERT: E 185 TYR cc_start: 0.6938 (t80) cc_final: 0.6657 (t80) REVERT: E 226 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7066 (tptp) REVERT: E 232 GLN cc_start: 0.6128 (mt0) cc_final: 0.5704 (pm20) REVERT: F 119 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.7974 (mmt-90) REVERT: G 55 ARG cc_start: 0.7799 (ptm-80) cc_final: 0.7580 (ptm-80) REVERT: H 147 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7675 (m-40) REVERT: H 198 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7672 (mmtp) REVERT: I 76 GLU cc_start: 0.8351 (mp0) cc_final: 0.7928 (pt0) REVERT: I 96 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8052 (ttm170) REVERT: I 98 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7859 (mtmm) REVERT: J 85 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8630 (mttt) REVERT: K 30 MET cc_start: 0.8454 (ptm) cc_final: 0.8110 (ptm) REVERT: K 201 ILE cc_start: 0.8577 (mt) cc_final: 0.8356 (tt) REVERT: L 134 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: M 64 PHE cc_start: 0.8372 (m-80) cc_final: 0.8065 (m-80) REVERT: M 131 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: N 1 MET cc_start: 0.6613 (mtm) cc_final: 0.6393 (mtp) REVERT: N 157 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7874 (ttt-90) REVERT: O 40 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7354 (tmm160) REVERT: O 101 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8141 (tpt90) REVERT: O 146 ASP cc_start: 0.7467 (p0) cc_final: 0.7144 (p0) REVERT: P 181 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7276 (pt0) REVERT: P 210 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.8284 (ttp-170) REVERT: P 217 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8083 (pm20) REVERT: Q 15 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: Q 148 HIS cc_start: 0.8422 (m-70) cc_final: 0.8220 (m-70) REVERT: Q 186 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6634 (pttm) REVERT: Q 214 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6387 (tp30) REVERT: Q 230 GLN cc_start: 0.5532 (OUTLIER) cc_final: 0.5164 (tp40) REVERT: Q 250 ARG cc_start: 0.7109 (mtt180) cc_final: 0.6824 (mmp80) REVERT: R 5 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.8004 (tpp80) REVERT: R 103 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7665 (t0) REVERT: R 138 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6002 (tm-30) REVERT: R 139 ASN cc_start: 0.6553 (p0) cc_final: 0.6330 (p0) REVERT: R 175 SER cc_start: 0.6869 (m) cc_final: 0.6264 (p) REVERT: R 197 VAL cc_start: 0.6381 (OUTLIER) cc_final: 0.6025 (p) REVERT: R 211 ASN cc_start: 0.7719 (t0) cc_final: 0.7461 (t0) REVERT: R 219 ASP cc_start: 0.6018 (m-30) cc_final: 0.5529 (p0) REVERT: S 9 ASP cc_start: 0.5558 (t70) cc_final: 0.5325 (t0) REVERT: S 53 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6818 (ttt180) REVERT: S 132 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5027 (mp) REVERT: S 148 GLU cc_start: 0.7861 (pt0) cc_final: 0.7494 (pm20) REVERT: S 178 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6501 (mp10) REVERT: S 183 GLU cc_start: 0.6703 (tt0) cc_final: 0.6393 (tm-30) REVERT: S 226 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7063 (tptp) REVERT: S 232 GLN cc_start: 0.6155 (mt0) cc_final: 0.5736 (pm20) REVERT: T 119 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.7975 (mmt-90) REVERT: U 55 ARG cc_start: 0.7796 (ptm-80) cc_final: 0.7562 (ptm-80) REVERT: V 147 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7676 (m-40) REVERT: W 76 GLU cc_start: 0.8328 (mp0) cc_final: 0.7852 (pt0) REVERT: W 96 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: W 98 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7859 (mtmm) REVERT: X 85 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8624 (mttt) REVERT: Y 30 MET cc_start: 0.8456 (ptm) cc_final: 0.8113 (ptm) REVERT: Y 75 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7611 (mpt-90) REVERT: Y 201 ILE cc_start: 0.8575 (mt) cc_final: 0.8355 (tt) REVERT: Z 134 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: Z 216 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: a 64 PHE cc_start: 0.8369 (m-80) cc_final: 0.8063 (m-80) REVERT: a 131 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: b 1 MET cc_start: 0.6625 (mtm) cc_final: 0.6420 (mtp) REVERT: b 150 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7688 (mm-30) REVERT: b 157 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7876 (ttt-90) outliers start: 156 outliers final: 62 residues processed: 846 average time/residue: 1.5891 time to fit residues: 1613.8503 Evaluate side-chains 830 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 732 time to evaluate : 4.134 ------------------------------------------------------------------------------- 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 B residue 212 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain D residue 5 ARG 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 169 LEU Chi-restraints excluded: chain D residue 181 THR 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 53 ARG 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 196 THR Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 208 ILE 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 147 ASN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 183 ARG 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 O residue 40 ARG Chi-restraints excluded: chain O residue 113 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 49 LYS Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain Q residue 252 THR Chi-restraints excluded: chain R residue 5 ARG 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 169 LEU Chi-restraints excluded: chain R residue 181 THR 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 53 ARG Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 140 SER Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 204 ASP Chi-restraints excluded: chain V residue 143 MET Chi-restraints excluded: chain V residue 147 ASN Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 96 ARG Chi-restraints excluded: chain W residue 98 LYS Chi-restraints excluded: chain W residue 280 GLU Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 85 LYS 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 204 THR Chi-restraints excluded: chain Z residue 134 GLN 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 220 SER Chi-restraints excluded: chain Z residue 304 LYS Chi-restraints excluded: chain a residue 57 ASP 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 492 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 440 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 504 optimal weight: 3.9990 chunk 408 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 0.8980 chunk 530 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN C 94 ASN E 182 ASN ** I 266 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 O 207 GLN P 61 GLN P 223 GLN Q 60 ASN Q 94 ASN S 182 ASN ** W 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Z 302 GLN ** a 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.003 0.034 49428 Z= 0.186 Angle : 0.587 8.900 66880 Z= 0.326 Chirality : 0.045 0.171 7512 Planarity : 0.004 0.043 8644 Dihedral : 6.152 59.235 6922 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 2.18 % Allowed : 14.48 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.10), residues: 6200 helix: 2.20 (0.11), residues: 2348 sheet: 1.01 (0.13), residues: 1440 loop : -0.53 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 165 HIS 0.005 0.001 HIS b 90 PHE 0.016 0.002 PHE Q 140 TYR 0.018 0.002 TYR B 116 ARG 0.005 0.000 ARG a 133 *********************** 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 890 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 777 time to evaluate : 4.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7334 (tmm160) REVERT: A 197 ASP cc_start: 0.7787 (m-30) cc_final: 0.7478 (m-30) REVERT: B 173 GLU cc_start: 0.7522 (tt0) cc_final: 0.7119 (mt-10) REVERT: B 210 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.8291 (ttp-170) REVERT: B 217 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8101 (pm20) REVERT: C 15 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: C 148 HIS cc_start: 0.8446 (m-70) cc_final: 0.8231 (m-70) REVERT: C 156 THR cc_start: 0.8598 (m) cc_final: 0.8396 (p) REVERT: C 186 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6633 (pttm) REVERT: C 214 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6321 (tp30) REVERT: C 230 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.5136 (tp40) REVERT: C 250 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6792 (mmp80) REVERT: C 260 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6679 (tp30) REVERT: D 103 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7497 (t70) REVERT: D 138 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5858 (tm-30) REVERT: D 177 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6080 (mm-40) REVERT: D 197 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.5861 (p) REVERT: D 213 LYS cc_start: 0.6398 (mtmt) cc_final: 0.5887 (tttm) REVERT: E 9 ASP cc_start: 0.5509 (t70) cc_final: 0.5282 (t0) REVERT: E 41 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: E 148 GLU cc_start: 0.7832 (pt0) cc_final: 0.7518 (pm20) REVERT: E 178 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6433 (mp10) REVERT: E 183 GLU cc_start: 0.6680 (tt0) cc_final: 0.6344 (tm-30) REVERT: E 185 TYR cc_start: 0.6943 (t80) cc_final: 0.6687 (t80) REVERT: E 196 THR cc_start: 0.6228 (OUTLIER) cc_final: 0.5974 (p) REVERT: E 226 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7086 (tptp) REVERT: E 232 GLN cc_start: 0.6174 (mt0) cc_final: 0.5747 (pm20) REVERT: F 87 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: F 119 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7874 (mmt-90) REVERT: F 200 THR cc_start: 0.7312 (m) cc_final: 0.6931 (p) REVERT: G 84 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7989 (tpt90) REVERT: H 198 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7710 (mmtp) REVERT: I 76 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: I 96 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7977 (ttm170) REVERT: I 157 GLN cc_start: 0.8665 (mt0) cc_final: 0.8415 (mt0) REVERT: K 30 MET cc_start: 0.8417 (ptm) cc_final: 0.8046 (ptm) REVERT: M 64 PHE cc_start: 0.8345 (m-80) cc_final: 0.8008 (m-80) REVERT: N 1 MET cc_start: 0.6571 (mtm) cc_final: 0.6347 (mtp) REVERT: N 150 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7709 (mm-30) REVERT: N 157 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7816 (ttt-90) REVERT: O 40 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7332 (tmm160) REVERT: O 101 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7958 (tpt90) REVERT: O 197 ASP cc_start: 0.7786 (m-30) cc_final: 0.7476 (m-30) REVERT: P 173 GLU cc_start: 0.7519 (tt0) cc_final: 0.7150 (mt-10) REVERT: P 210 ARG cc_start: 0.8588 (ttp-170) cc_final: 0.8292 (ttp-170) REVERT: P 217 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8101 (pm20) REVERT: P 227 TYR cc_start: 0.8062 (m-80) cc_final: 0.7845 (m-80) REVERT: Q 15 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: Q 148 HIS cc_start: 0.8450 (m-70) cc_final: 0.8237 (m-70) REVERT: Q 186 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6626 (pttm) REVERT: Q 214 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6335 (tp30) REVERT: Q 230 GLN cc_start: 0.5477 (OUTLIER) cc_final: 0.5131 (tp40) REVERT: Q 250 ARG cc_start: 0.7068 (mtt180) cc_final: 0.6800 (mmp80) REVERT: Q 260 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6683 (tp30) REVERT: R 103 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7497 (t70) REVERT: R 138 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5959 (tm-30) REVERT: R 177 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6083 (mm-40) REVERT: R 197 VAL cc_start: 0.6288 (OUTLIER) cc_final: 0.5888 (p) REVERT: R 213 LYS cc_start: 0.6403 (mtmt) cc_final: 0.5885 (tttm) REVERT: S 9 ASP cc_start: 0.5505 (t70) cc_final: 0.5275 (t0) REVERT: S 41 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: S 148 GLU cc_start: 0.7840 (pt0) cc_final: 0.7519 (pm20) REVERT: S 178 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6425 (mp10) REVERT: S 183 GLU cc_start: 0.6693 (tt0) cc_final: 0.6342 (tm-30) REVERT: S 196 THR cc_start: 0.6225 (OUTLIER) cc_final: 0.5983 (p) REVERT: S 226 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7089 (tptp) REVERT: S 232 GLN cc_start: 0.6168 (mt0) cc_final: 0.5736 (pm20) REVERT: T 87 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8194 (ttt90) REVERT: T 119 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.7874 (mmt-90) REVERT: T 200 THR cc_start: 0.7314 (m) cc_final: 0.6928 (p) REVERT: U 55 ARG cc_start: 0.7782 (ptm-80) cc_final: 0.7538 (ptm-80) REVERT: U 84 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7988 (tpt90) REVERT: W 96 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7954 (ttm170) REVERT: W 98 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7767 (mtmm) REVERT: W 157 GLN cc_start: 0.8663 (mt0) cc_final: 0.8401 (mt0) REVERT: Y 30 MET cc_start: 0.8418 (ptm) cc_final: 0.8046 (ptm) REVERT: Y 75 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7542 (mpt-90) REVERT: Z 216 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: a 64 PHE cc_start: 0.8350 (m-80) cc_final: 0.8013 (m-80) REVERT: b 1 MET cc_start: 0.6573 (mtm) cc_final: 0.6347 (mtp) REVERT: b 150 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7707 (mm-30) REVERT: b 157 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7819 (ttt-90) outliers start: 113 outliers final: 47 residues processed: 852 average time/residue: 1.5799 time to fit residues: 1618.5769 Evaluate side-chains 822 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 744 time to evaluate : 4.192 ------------------------------------------------------------------------------- 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 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 186 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 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 169 LEU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 196 THR 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 84 ARG 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 76 GLU Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain K residue 63 CYS 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 M residue 57 ASP Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 190 ASP 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 P residue 212 SER Chi-restraints excluded: chain P residue 231 ILE 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 216 LEU Chi-restraints excluded: chain Q residue 230 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 169 LEU Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain S residue 41 GLN 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 S residue 196 THR Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 84 ARG 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 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 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 57 ASP Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 0.9980 chunk 532 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 347 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 592 optimal weight: 9.9990 chunk 491 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN D 54 GLN E 155 GLN E 182 ASN K 22 ASN L 251 GLN L 302 GLN O 93 GLN P 61 GLN P 223 GLN Q 60 ASN R 54 GLN S 155 GLN S 182 ASN Y 22 ASN Z 251 GLN Z 302 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 49428 Z= 0.171 Angle : 0.560 8.968 66880 Z= 0.311 Chirality : 0.044 0.168 7512 Planarity : 0.004 0.041 8644 Dihedral : 5.933 59.173 6922 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Rotamer: Outliers : 2.11 % Allowed : 14.77 % 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: 1.48 (0.10), residues: 6200 helix: 2.37 (0.11), residues: 2350 sheet: 1.06 (0.13), residues: 1446 loop : -0.48 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 154 HIS 0.004 0.001 HIS X 147 PHE 0.015 0.002 PHE Q 140 TYR 0.017 0.002 TYR B 116 ARG 0.005 0.000 ARG O 56 *********************** 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 876 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 767 time to evaluate : 4.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7340 (tmm160) REVERT: A 197 ASP cc_start: 0.7773 (m-30) cc_final: 0.7464 (m-30) REVERT: B 173 GLU cc_start: 0.7472 (tt0) cc_final: 0.7118 (mt-10) REVERT: B 210 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8287 (ttp-170) REVERT: B 217 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8121 (pm20) REVERT: C 15 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: C 186 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6619 (pttm) REVERT: C 250 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6786 (mmp80) REVERT: D 103 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7423 (t70) REVERT: D 138 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5844 (tm-30) REVERT: D 177 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6015 (mm-40) REVERT: E 9 ASP cc_start: 0.5413 (t70) cc_final: 0.5190 (t0) REVERT: E 132 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.5042 (mp) REVERT: E 148 GLU cc_start: 0.7840 (pt0) cc_final: 0.7561 (pm20) REVERT: E 178 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6289 (mp10) REVERT: E 183 GLU cc_start: 0.6664 (tt0) cc_final: 0.6283 (tm-30) REVERT: E 185 TYR cc_start: 0.6924 (t80) cc_final: 0.6657 (t80) REVERT: E 196 THR cc_start: 0.6270 (m) cc_final: 0.6033 (p) REVERT: E 226 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7097 (tptp) REVERT: E 232 GLN cc_start: 0.6185 (mt0) cc_final: 0.5757 (pm20) REVERT: F 87 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8178 (ttt90) REVERT: F 119 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7857 (mmt-90) REVERT: F 200 THR cc_start: 0.7293 (m) cc_final: 0.6914 (p) REVERT: H 198 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7699 (mmtp) REVERT: H 260 ASP cc_start: 0.8452 (m-30) cc_final: 0.8050 (p0) REVERT: I 96 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7963 (ttm170) REVERT: I 157 GLN cc_start: 0.8627 (mt0) cc_final: 0.8386 (mt0) REVERT: K 30 MET cc_start: 0.8406 (ptm) cc_final: 0.8036 (ptm) REVERT: M 64 PHE cc_start: 0.8375 (m-80) cc_final: 0.7980 (m-80) REVERT: N 1 MET cc_start: 0.6482 (mtm) cc_final: 0.6257 (mtp) REVERT: N 150 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7704 (mm-30) REVERT: N 157 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7821 (ttt-90) REVERT: O 40 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7336 (tmm160) REVERT: O 197 ASP cc_start: 0.7773 (m-30) cc_final: 0.7464 (m-30) REVERT: P 210 ARG cc_start: 0.8588 (ttp-170) cc_final: 0.8286 (ttp-170) REVERT: P 217 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8116 (pm20) REVERT: Q 15 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: Q 186 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6620 (pttm) REVERT: Q 250 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6797 (mmp80) REVERT: R 103 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7425 (t70) REVERT: R 138 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: R 177 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6016 (mm-40) REVERT: S 9 ASP cc_start: 0.5412 (t70) cc_final: 0.5189 (t0) REVERT: S 132 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5077 (mp) REVERT: S 148 GLU cc_start: 0.7840 (pt0) cc_final: 0.7555 (pm20) REVERT: S 178 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: S 183 GLU cc_start: 0.6632 (tt0) cc_final: 0.6272 (tm-30) REVERT: S 196 THR cc_start: 0.6263 (m) cc_final: 0.6036 (p) REVERT: S 226 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7095 (tptp) REVERT: S 232 GLN cc_start: 0.6193 (mt0) cc_final: 0.5770 (pm20) REVERT: T 87 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8186 (ttt90) REVERT: T 119 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7854 (mmt-90) REVERT: T 200 THR cc_start: 0.7293 (m) cc_final: 0.6909 (p) REVERT: U 55 ARG cc_start: 0.7778 (ptm-80) cc_final: 0.7552 (ptm-80) REVERT: V 260 ASP cc_start: 0.8458 (m-30) cc_final: 0.8063 (p0) REVERT: W 96 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7967 (ttm170) REVERT: W 157 GLN cc_start: 0.8626 (mt0) cc_final: 0.8375 (mt0) REVERT: Y 30 MET cc_start: 0.8401 (ptm) cc_final: 0.8031 (ptm) REVERT: Y 75 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7566 (mpt-90) REVERT: Z 216 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: a 64 PHE cc_start: 0.8378 (m-80) cc_final: 0.7984 (m-80) REVERT: b 1 MET cc_start: 0.6483 (mtm) cc_final: 0.6257 (mtp) REVERT: b 150 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7685 (mm-30) REVERT: b 157 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7823 (ttt-90) outliers start: 109 outliers final: 44 residues processed: 839 average time/residue: 1.6233 time to fit residues: 1632.2286 Evaluate side-chains 802 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 736 time to evaluate : 4.211 ------------------------------------------------------------------------------- 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 212 SER Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 242 THR 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 169 LEU Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 132 LEU 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 F residue 208 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 96 ARG 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 77 ILE 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 P residue 212 SER Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain Q residue 242 THR 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 169 LEU Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain S residue 42 THR 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 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 96 ARG 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 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 Chi-restraints excluded: chain a residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 337 optimal weight: 5.9990 chunk 432 optimal weight: 1.9990 chunk 335 optimal weight: 0.6980 chunk 498 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 589 optimal weight: 7.9990 chunk 369 optimal weight: 0.0570 chunk 359 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN D 54 GLN E 155 GLN E 182 ASN F 207 ASN I 266 GLN L 251 GLN O 93 GLN P 61 GLN P 223 GLN Q 60 ASN Q 161 ASN R 54 GLN S 155 GLN S 182 ASN W 266 GLN Z 251 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 49428 Z= 0.125 Angle : 0.491 8.631 66880 Z= 0.272 Chirality : 0.042 0.162 7512 Planarity : 0.004 0.044 8644 Dihedral : 5.514 58.134 6916 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.47 % Favored : 98.50 % Rotamer: Outliers : 1.62 % Allowed : 15.02 % Favored : 83.35 % 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: 1.73 (0.11), residues: 6200 helix: 2.62 (0.11), residues: 2356 sheet: 1.00 (0.13), residues: 1500 loop : -0.29 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 165 HIS 0.004 0.001 HIS U 119 PHE 0.012 0.001 PHE C 140 TYR 0.015 0.001 TYR I 102 ARG 0.006 0.000 ARG O 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 866 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 782 time to evaluate : 4.208 Fit side-chains REVERT: A 40 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7357 (tmm160) REVERT: A 197 ASP cc_start: 0.7697 (m-30) cc_final: 0.7350 (m-30) REVERT: B 173 GLU cc_start: 0.7432 (tt0) cc_final: 0.7071 (mt-10) REVERT: B 210 ARG cc_start: 0.8595 (ttp-170) cc_final: 0.8382 (ttp-170) REVERT: B 213 GLU cc_start: 0.8654 (mp0) cc_final: 0.8342 (mp0) REVERT: B 217 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8102 (pm20) REVERT: C 186 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6641 (pttm) REVERT: C 214 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6348 (mm-30) REVERT: C 250 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6780 (mmp80) REVERT: D 103 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7218 (t70) REVERT: D 138 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5743 (tm-30) REVERT: D 177 GLN cc_start: 0.6705 (mt0) cc_final: 0.5935 (mm-40) REVERT: E 41 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: E 53 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6827 (ttt180) REVERT: E 148 GLU cc_start: 0.7831 (pt0) cc_final: 0.7568 (pm20) REVERT: E 178 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6273 (mp10) REVERT: E 183 GLU cc_start: 0.6624 (tt0) cc_final: 0.6242 (tm-30) REVERT: E 185 TYR cc_start: 0.6910 (t80) cc_final: 0.6658 (t80) REVERT: E 196 THR cc_start: 0.6272 (m) cc_final: 0.6046 (p) REVERT: E 226 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7101 (tptp) REVERT: E 232 GLN cc_start: 0.6284 (mt0) cc_final: 0.5848 (pm20) REVERT: F 87 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: F 119 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7761 (mmt-90) REVERT: F 200 THR cc_start: 0.7325 (m) cc_final: 0.6997 (p) REVERT: H 139 LYS cc_start: 0.8547 (tppp) cc_final: 0.8231 (tttt) REVERT: H 198 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7736 (mmtp) REVERT: H 260 ASP cc_start: 0.8469 (m-30) cc_final: 0.8049 (p0) REVERT: I 96 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8041 (mtm180) REVERT: K 30 MET cc_start: 0.8337 (ptm) cc_final: 0.7990 (ptm) REVERT: M 64 PHE cc_start: 0.8355 (m-80) cc_final: 0.7975 (m-80) REVERT: N 1 MET cc_start: 0.6449 (mtm) cc_final: 0.6231 (mtp) REVERT: N 157 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7737 (ttt-90) REVERT: O 40 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7354 (tmm160) REVERT: O 197 ASP cc_start: 0.7700 (m-30) cc_final: 0.7351 (m-30) REVERT: P 173 GLU cc_start: 0.7421 (tt0) cc_final: 0.7065 (mt-10) REVERT: P 210 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8384 (ttp-170) REVERT: P 213 GLU cc_start: 0.8641 (mp0) cc_final: 0.8345 (mp0) REVERT: P 217 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8101 (pm20) REVERT: Q 186 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6643 (pttm) REVERT: Q 214 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6261 (tp30) REVERT: Q 250 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6792 (mmp80) REVERT: R 103 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7224 (t70) REVERT: R 138 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.5660 (tm-30) REVERT: R 177 GLN cc_start: 0.6702 (mt0) cc_final: 0.5930 (mm-40) REVERT: S 41 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: S 53 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6823 (ttt180) REVERT: S 148 GLU cc_start: 0.7831 (pt0) cc_final: 0.7564 (pm20) REVERT: S 178 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6272 (mp10) REVERT: S 183 GLU cc_start: 0.6623 (tt0) cc_final: 0.6246 (tm-30) REVERT: S 196 THR cc_start: 0.6220 (m) cc_final: 0.6018 (p) REVERT: S 226 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7101 (tptp) REVERT: S 232 GLN cc_start: 0.6254 (mt0) cc_final: 0.5809 (pm20) REVERT: T 87 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8224 (ttt90) REVERT: T 119 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7722 (mmt-90) REVERT: T 200 THR cc_start: 0.7303 (m) cc_final: 0.6969 (p) REVERT: U 55 ARG cc_start: 0.7761 (ptm-80) cc_final: 0.7437 (pmm-80) REVERT: V 139 LYS cc_start: 0.8547 (tppp) cc_final: 0.8229 (tttt) REVERT: V 260 ASP cc_start: 0.8464 (m-30) cc_final: 0.8041 (p0) REVERT: W 96 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8041 (mtm180) REVERT: Y 30 MET cc_start: 0.8338 (ptm) cc_final: 0.7989 (ptm) REVERT: Z 216 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: Z 304 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8100 (mttt) REVERT: a 64 PHE cc_start: 0.8357 (m-80) cc_final: 0.7977 (m-80) REVERT: b 1 MET cc_start: 0.6458 (mtm) cc_final: 0.6242 (mtp) REVERT: b 157 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7740 (ttt-90) outliers start: 84 outliers final: 27 residues processed: 832 average time/residue: 1.5825 time to fit residues: 1585.1854 Evaluate side-chains 794 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 746 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 53 ARG 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 F residue 208 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain K residue 77 ILE 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 P residue 231 ILE Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain Q residue 242 THR Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain R residue 220 ASP Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN 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 96 ARG Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Z residue 216 GLN Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 375 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 463 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN C 161 ASN C 163 ASN E 155 GLN E 182 ASN ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 251 GLN L 302 GLN N 70 GLN O 93 GLN P 61 GLN Q 60 ASN Q 163 ASN S 155 GLN S 182 ASN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Z 302 GLN b 70 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49428 Z= 0.191 Angle : 0.572 8.992 66880 Z= 0.317 Chirality : 0.045 0.166 7512 Planarity : 0.004 0.040 8644 Dihedral : 5.705 59.654 6910 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 1.55 % Allowed : 15.53 % Favored : 82.93 % 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: 1.62 (0.10), residues: 6200 helix: 2.50 (0.11), residues: 2344 sheet: 1.12 (0.13), residues: 1470 loop : -0.41 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 161 HIS 0.005 0.001 HIS b 90 PHE 0.017 0.002 PHE J 20 TYR 0.018 0.002 TYR P 116 ARG 0.005 0.000 ARG Z 183 *********************** 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 848 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 768 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7336 (tmm160) REVERT: A 197 ASP cc_start: 0.7761 (m-30) cc_final: 0.7460 (m-30) REVERT: B 173 GLU cc_start: 0.7504 (tt0) cc_final: 0.7160 (mt-10) REVERT: B 210 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8410 (ttp-170) REVERT: B 217 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8100 (pm20) REVERT: C 186 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6663 (pttm) REVERT: C 214 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6447 (mm-30) REVERT: C 250 ARG cc_start: 0.7077 (mtt180) cc_final: 0.6797 (mmp80) REVERT: D 103 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7436 (t70) REVERT: D 138 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5799 (tm-30) REVERT: D 177 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5962 (mm-40) REVERT: E 10 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6521 (ptm160) REVERT: E 41 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: E 53 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6814 (ttt180) REVERT: E 60 ASP cc_start: 0.7406 (m-30) cc_final: 0.7132 (m-30) REVERT: E 148 GLU cc_start: 0.7840 (pt0) cc_final: 0.7569 (pm20) REVERT: E 178 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6223 (mp10) REVERT: E 183 GLU cc_start: 0.6640 (tt0) cc_final: 0.6260 (tm-30) REVERT: E 226 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7089 (tptp) REVERT: E 232 GLN cc_start: 0.6276 (mt0) cc_final: 0.5840 (pm20) REVERT: F 87 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8197 (ttt90) REVERT: F 119 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7808 (mmt-90) REVERT: F 200 THR cc_start: 0.7300 (m) cc_final: 0.6916 (p) REVERT: G 79 MET cc_start: 0.8258 (mmm) cc_final: 0.7935 (mtp) REVERT: G 204 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6358 (m-30) REVERT: H 198 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7724 (mmtp) REVERT: H 260 ASP cc_start: 0.8473 (m-30) cc_final: 0.8044 (p0) REVERT: I 96 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8047 (ttm170) REVERT: I 157 GLN cc_start: 0.8632 (mt0) cc_final: 0.8383 (mt0) REVERT: K 30 MET cc_start: 0.8391 (ptm) cc_final: 0.8023 (ptm) REVERT: M 64 PHE cc_start: 0.8383 (m-80) cc_final: 0.7990 (m-80) REVERT: N 1 MET cc_start: 0.6435 (mtm) cc_final: 0.6218 (mtp) REVERT: N 150 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7692 (mm-30) REVERT: N 157 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7780 (ttt-90) REVERT: O 40 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7338 (tmm160) REVERT: O 197 ASP cc_start: 0.7761 (m-30) cc_final: 0.7459 (m-30) REVERT: P 173 GLU cc_start: 0.7480 (tt0) cc_final: 0.7139 (mt-10) REVERT: P 210 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8407 (ttp-170) REVERT: P 217 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8097 (pm20) REVERT: Q 186 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6655 (pttm) REVERT: Q 250 ARG cc_start: 0.7077 (mtt180) cc_final: 0.6811 (mmp80) REVERT: R 103 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7433 (t70) REVERT: R 138 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5763 (tm-30) REVERT: R 177 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5963 (mm-40) REVERT: R 213 LYS cc_start: 0.6131 (mtmt) cc_final: 0.5665 (tttm) REVERT: S 10 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6526 (ptm160) REVERT: S 41 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: S 53 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6822 (ttt180) REVERT: S 60 ASP cc_start: 0.7413 (m-30) cc_final: 0.7124 (m-30) REVERT: S 148 GLU cc_start: 0.7849 (pt0) cc_final: 0.7572 (pm20) REVERT: S 178 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6298 (mp10) REVERT: S 183 GLU cc_start: 0.6604 (tt0) cc_final: 0.6213 (tm-30) REVERT: S 196 THR cc_start: 0.6291 (m) cc_final: 0.6049 (p) REVERT: S 226 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7089 (tptp) REVERT: S 232 GLN cc_start: 0.6293 (mt0) cc_final: 0.5847 (pm20) REVERT: T 87 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8205 (ttt90) REVERT: T 119 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7808 (mmt-90) REVERT: T 200 THR cc_start: 0.7296 (m) cc_final: 0.6911 (p) REVERT: U 55 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.7599 (ptm-80) REVERT: U 79 MET cc_start: 0.8263 (mmm) cc_final: 0.7952 (mtp) REVERT: U 204 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6424 (m-30) REVERT: U 229 MET cc_start: 0.5858 (mtm) cc_final: 0.5332 (mmm) REVERT: V 260 ASP cc_start: 0.8480 (m-30) cc_final: 0.8066 (p0) REVERT: W 96 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8047 (ttm170) REVERT: W 157 GLN cc_start: 0.8638 (mt0) cc_final: 0.8391 (mt0) REVERT: Y 30 MET cc_start: 0.8389 (ptm) cc_final: 0.8021 (ptm) REVERT: Z 216 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: a 64 PHE cc_start: 0.8383 (m-80) cc_final: 0.7990 (m-80) REVERT: b 1 MET cc_start: 0.6438 (mtm) cc_final: 0.6219 (mtp) REVERT: b 150 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7689 (mm-30) REVERT: b 157 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7783 (ttt-90) outliers start: 80 outliers final: 37 residues processed: 823 average time/residue: 1.5975 time to fit residues: 1576.7399 Evaluate side-chains 807 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 744 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 242 THR 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 219 ASP Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain F residue 208 ILE 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 96 ARG Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 220 SER 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 P residue 231 ILE Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain Q residue 242 THR 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 219 ASP Chi-restraints excluded: chain R residue 220 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 227 LEU 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 96 ARG Chi-restraints excluded: chain W residue 282 ILE 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 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 6.9990 chunk 565 optimal weight: 5.9990 chunk 515 optimal weight: 6.9990 chunk 549 optimal weight: 1.9990 chunk 564 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 496 optimal weight: 0.6980 chunk 519 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN C 163 ASN E 155 GLN E 182 ASN ** L 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN N 70 GLN O 93 GLN P 61 GLN P 223 GLN Q 60 ASN Q 163 ASN S 155 GLN S 182 ASN ** Z 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 302 GLN b 70 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.005 0.041 49428 Z= 0.301 Angle : 0.691 9.483 66880 Z= 0.382 Chirality : 0.049 0.190 7512 Planarity : 0.005 0.061 8644 Dihedral : 6.060 58.341 6910 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.90 % Rotamer: Outliers : 1.72 % Allowed : 15.45 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.10), residues: 6200 helix: 2.10 (0.11), residues: 2344 sheet: 1.07 (0.13), residues: 1426 loop : -0.58 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 154 HIS 0.008 0.002 HIS b 90 PHE 0.021 0.003 PHE B 171 TYR 0.023 0.002 TYR A 9 ARG 0.006 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 844 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 755 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7359 (tmm160) REVERT: A 227 GLU cc_start: 0.7835 (tt0) cc_final: 0.7628 (tp30) REVERT: B 173 GLU cc_start: 0.7588 (tt0) cc_final: 0.7234 (mt-10) REVERT: B 181 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7195 (pm20) REVERT: B 210 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8325 (ttp-170) REVERT: B 217 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8097 (pm20) REVERT: C 186 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6619 (pttm) REVERT: C 214 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6307 (tp30) REVERT: C 250 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6830 (mmp80) REVERT: D 103 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7576 (t0) REVERT: D 138 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5906 (tm-30) REVERT: D 177 GLN cc_start: 0.6780 (mt0) cc_final: 0.6021 (mm-40) REVERT: E 10 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6623 (ptm160) REVERT: E 41 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: E 53 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6508 (ttp-170) REVERT: E 60 ASP cc_start: 0.7472 (m-30) cc_final: 0.7201 (m-30) REVERT: E 148 GLU cc_start: 0.7852 (pt0) cc_final: 0.7553 (pm20) REVERT: E 178 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6293 (mp10) REVERT: E 183 GLU cc_start: 0.6653 (tt0) cc_final: 0.6262 (tm-30) REVERT: E 226 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7075 (tptp) REVERT: E 232 GLN cc_start: 0.6270 (mt0) cc_final: 0.5837 (pm20) REVERT: F 87 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8285 (ttt90) REVERT: F 119 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7884 (mmt-90) REVERT: G 79 MET cc_start: 0.8347 (mmm) cc_final: 0.8038 (mtp) REVERT: G 204 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: G 229 MET cc_start: 0.5844 (mtm) cc_final: 0.5349 (mmm) REVERT: H 198 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7691 (mmtp) REVERT: I 96 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8061 (ttm170) REVERT: I 157 GLN cc_start: 0.8649 (mt0) cc_final: 0.8402 (mt0) REVERT: K 30 MET cc_start: 0.8458 (ptm) cc_final: 0.8093 (ptm) REVERT: M 64 PHE cc_start: 0.8386 (m-80) cc_final: 0.7970 (m-80) REVERT: N 1 MET cc_start: 0.6483 (mtm) cc_final: 0.6252 (mtp) REVERT: N 150 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7718 (mm-30) REVERT: N 157 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7878 (ttt-90) REVERT: O 40 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7370 (tmm160) REVERT: P 173 GLU cc_start: 0.7583 (tt0) cc_final: 0.7232 (mt-10) REVERT: P 181 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7202 (pm20) REVERT: P 210 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8325 (ttp-170) REVERT: P 217 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8096 (pm20) REVERT: Q 186 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6617 (pttm) REVERT: Q 214 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6477 (tp30) REVERT: Q 250 ARG cc_start: 0.7130 (mtt180) cc_final: 0.6856 (mmp80) REVERT: R 103 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7573 (t0) REVERT: R 138 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: R 177 GLN cc_start: 0.6783 (mt0) cc_final: 0.6018 (mm-40) REVERT: R 213 LYS cc_start: 0.6434 (mtmt) cc_final: 0.5877 (tttm) REVERT: S 10 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6628 (ptm160) REVERT: S 41 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: S 53 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6510 (ttp-170) REVERT: S 60 ASP cc_start: 0.7475 (m-30) cc_final: 0.7202 (m-30) REVERT: S 132 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5077 (mp) REVERT: S 148 GLU cc_start: 0.7835 (pt0) cc_final: 0.7533 (pm20) REVERT: S 178 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6266 (mp10) REVERT: S 183 GLU cc_start: 0.6643 (tt0) cc_final: 0.6251 (tm-30) REVERT: S 226 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7075 (tptp) REVERT: S 232 GLN cc_start: 0.6258 (mt0) cc_final: 0.5833 (pm20) REVERT: T 87 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8281 (ttt90) REVERT: T 119 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7880 (mmt-90) REVERT: U 55 ARG cc_start: 0.7820 (ptm-80) cc_final: 0.7613 (ptm160) REVERT: U 79 MET cc_start: 0.8345 (mmm) cc_final: 0.8014 (mtp) REVERT: U 204 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: U 229 MET cc_start: 0.5885 (mtm) cc_final: 0.5325 (mmm) REVERT: W 96 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8057 (ttm170) REVERT: W 157 GLN cc_start: 0.8657 (mt0) cc_final: 0.8411 (mt0) REVERT: Y 30 MET cc_start: 0.8459 (ptm) cc_final: 0.8094 (ptm) REVERT: Z 216 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: a 64 PHE cc_start: 0.8387 (m-80) cc_final: 0.7970 (m-80) REVERT: b 1 MET cc_start: 0.6486 (mtm) cc_final: 0.6256 (mtp) REVERT: b 157 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7878 (ttt-90) outliers start: 89 outliers final: 43 residues processed: 819 average time/residue: 1.6261 time to fit residues: 1598.3989 Evaluate side-chains 807 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 739 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 242 THR 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 219 ASP Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 227 LEU 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 I residue 96 ARG Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain K residue 77 ILE 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 O residue 40 ARG Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain Q residue 242 THR 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 219 ASP Chi-restraints excluded: chain R residue 220 ASP Chi-restraints excluded: chain S residue 10 ARG Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 54 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 227 LEU 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 96 ARG Chi-restraints excluded: chain W residue 282 ILE 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 a residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 581 optimal weight: 0.7980 chunk 354 optimal weight: 0.8980 chunk 275 optimal weight: 0.9980 chunk 404 optimal weight: 0.9980 chunk 609 optimal weight: 5.9990 chunk 561 optimal weight: 2.9990 chunk 485 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 375 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN C 163 ASN E 155 GLN E 182 ASN J 71 ASN ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 251 GLN O 93 GLN P 61 GLN P 223 GLN Q 60 ASN Q 163 ASN S 155 GLN S 182 ASN X 71 ASN Z 251 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 49428 Z= 0.147 Angle : 0.528 8.419 66880 Z= 0.293 Chirality : 0.043 0.183 7512 Planarity : 0.004 0.043 8644 Dihedral : 5.617 59.631 6910 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.35 % Rotamer: Outliers : 1.12 % Allowed : 16.16 % Favored : 82.71 % 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: 1.58 (0.10), residues: 6200 helix: 2.47 (0.11), residues: 2356 sheet: 0.96 (0.12), residues: 1522 loop : -0.38 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 161 HIS 0.004 0.001 HIS L 117 PHE 0.027 0.001 PHE P 171 TYR 0.016 0.001 TYR O 9 ARG 0.008 0.000 ARG R 5 ********************** 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 809 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 751 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7346 (tmm160) REVERT: A 197 ASP cc_start: 0.7725 (m-30) cc_final: 0.7402 (m-30) REVERT: B 173 GLU cc_start: 0.7498 (tt0) cc_final: 0.7145 (mt-10) REVERT: B 181 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7075 (pm20) REVERT: B 210 ARG cc_start: 0.8598 (ttp-170) cc_final: 0.8294 (ttp-170) REVERT: B 217 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8110 (pm20) REVERT: C 186 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6615 (pttm) REVERT: C 214 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6268 (tp30) REVERT: C 250 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6806 (mmp80) REVERT: D 103 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7363 (t70) REVERT: D 138 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5843 (tm-30) REVERT: D 177 GLN cc_start: 0.6730 (mt0) cc_final: 0.5990 (mm-40) REVERT: E 41 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: E 53 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6813 (ttt180) REVERT: E 60 ASP cc_start: 0.7404 (m-30) cc_final: 0.7112 (m-30) REVERT: E 148 GLU cc_start: 0.7838 (pt0) cc_final: 0.7556 (pm20) REVERT: E 178 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6222 (mp10) REVERT: E 183 GLU cc_start: 0.6643 (tt0) cc_final: 0.6238 (tm-30) REVERT: E 226 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7129 (tptp) REVERT: E 232 GLN cc_start: 0.6266 (mt0) cc_final: 0.5829 (pm20) REVERT: F 87 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8166 (ttt90) REVERT: F 119 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7782 (mmt-90) REVERT: F 200 THR cc_start: 0.7328 (m) cc_final: 0.6965 (p) REVERT: G 79 MET cc_start: 0.8206 (mmm) cc_final: 0.7837 (mtp) REVERT: G 84 ARG cc_start: 0.8332 (tpt-90) cc_final: 0.7931 (tpt90) REVERT: G 204 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6344 (m-30) REVERT: G 229 MET cc_start: 0.5903 (mtm) cc_final: 0.5400 (mmm) REVERT: H 198 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7712 (mmtp) REVERT: H 260 ASP cc_start: 0.8460 (m-30) cc_final: 0.8054 (p0) REVERT: I 96 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8066 (mtm180) REVERT: I 157 GLN cc_start: 0.8618 (mt0) cc_final: 0.8357 (mt0) REVERT: K 30 MET cc_start: 0.8353 (ptm) cc_final: 0.7919 (ptm) REVERT: L 216 GLN cc_start: 0.8107 (pm20) cc_final: 0.7899 (pm20) REVERT: M 64 PHE cc_start: 0.8361 (m-80) cc_final: 0.7966 (m-80) REVERT: N 1 MET cc_start: 0.6416 (mtm) cc_final: 0.6194 (mtp) REVERT: N 150 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7684 (mm-30) REVERT: N 157 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7787 (ttt-90) REVERT: O 40 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7345 (tmm160) REVERT: O 197 ASP cc_start: 0.7722 (m-30) cc_final: 0.7400 (m-30) REVERT: P 173 GLU cc_start: 0.7477 (tt0) cc_final: 0.7126 (mt-10) REVERT: P 210 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8291 (ttp-170) REVERT: Q 186 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6597 (pttm) REVERT: Q 214 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6380 (tp30) REVERT: Q 250 ARG cc_start: 0.7081 (mtt180) cc_final: 0.6816 (mmp80) REVERT: R 103 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7358 (t70) REVERT: R 138 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5783 (tm-30) REVERT: R 177 GLN cc_start: 0.6701 (mt0) cc_final: 0.5957 (mm-40) REVERT: S 41 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: S 53 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6810 (ttt180) REVERT: S 60 ASP cc_start: 0.7411 (m-30) cc_final: 0.7119 (m-30) REVERT: S 148 GLU cc_start: 0.7815 (pt0) cc_final: 0.7553 (pm20) REVERT: S 178 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6305 (mp10) REVERT: S 183 GLU cc_start: 0.6646 (tt0) cc_final: 0.6243 (tm-30) REVERT: S 226 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7125 (tptp) REVERT: S 232 GLN cc_start: 0.6288 (mt0) cc_final: 0.5829 (pm20) REVERT: T 87 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8167 (ttt90) REVERT: T 119 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7788 (mmt-90) REVERT: T 200 THR cc_start: 0.7323 (m) cc_final: 0.6965 (p) REVERT: U 55 ARG cc_start: 0.7756 (ptm-80) cc_final: 0.7434 (pmm-80) REVERT: U 79 MET cc_start: 0.8209 (mmm) cc_final: 0.7845 (mtp) REVERT: U 84 ARG cc_start: 0.8330 (tpt-90) cc_final: 0.7926 (tpt90) REVERT: U 204 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6367 (m-30) REVERT: U 229 MET cc_start: 0.5884 (mtm) cc_final: 0.5330 (mmm) REVERT: V 260 ASP cc_start: 0.8455 (m-30) cc_final: 0.8051 (p0) REVERT: W 96 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8064 (mtm180) REVERT: W 157 GLN cc_start: 0.8617 (mt0) cc_final: 0.8357 (mt0) REVERT: Y 30 MET cc_start: 0.8352 (ptm) cc_final: 0.7917 (ptm) REVERT: Z 216 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: a 64 PHE cc_start: 0.8359 (m-80) cc_final: 0.7967 (m-80) REVERT: b 1 MET cc_start: 0.6418 (mtm) cc_final: 0.6196 (mtp) REVERT: b 157 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7791 (ttt-90) outliers start: 58 outliers final: 29 residues processed: 792 average time/residue: 1.6522 time to fit residues: 1578.3557 Evaluate side-chains 777 residues out of total 5172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 726 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 227 LEU 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 I residue 96 ARG Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 220 SER 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 P residue 231 ILE Chi-restraints excluded: chain Q residue 186 LYS Chi-restraints excluded: chain Q residue 242 THR Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 138 GLU Chi-restraints excluded: chain R residue 219 ASP Chi-restraints excluded: chain R residue 220 ASP Chi-restraints excluded: chain S residue 41 GLN Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 53 ARG Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 227 LEU 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 96 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 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 0.5980 chunk 385 optimal weight: 5.9990 chunk 517 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 447 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 486 optimal weight: 0.0060 chunk 203 optimal weight: 6.9990 chunk 499 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.1202 ------------------------------------------------------------------------------- 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 B 223 GLN C 60 ASN C 163 ASN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN K 22 ASN K 165 GLN ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 251 GLN L 302 GLN O 93 GLN P 61 GLN P 223 GLN Q 60 ASN Q 163 ASN S 182 ASN Y 22 ASN ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Z 302 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105894 restraints weight = 50176.085| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.16 r_work: 0.3081 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 49428 Z= 0.212 Angle : 0.603 8.937 66880 Z= 0.333 Chirality : 0.046 0.185 7512 Planarity : 0.005 0.044 8644 Dihedral : 5.783 58.680 6910 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.33 % Allowed : 16.11 % Favored : 82.56 % 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: 1.47 (0.10), residues: 6200 helix: 2.32 (0.11), residues: 2354 sheet: 1.10 (0.13), residues: 1448 loop : -0.48 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 154 HIS 0.005 0.001 HIS b 90 PHE 0.027 0.002 PHE P 171 TYR 0.024 0.002 TYR A 9 ARG 0.011 0.001 ARG R 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21826.22 seconds wall clock time: 375 minutes 37.53 seconds (22537.53 seconds total)