Starting phenix.real_space_refine on Mon Nov 18 09:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/11_2024/8olu_16963.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/11_2024/8olu_16963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/11_2024/8olu_16963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/11_2024/8olu_16963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/11_2024/8olu_16963.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olu_16963/11_2024/8olu_16963.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 328 5.16 5 C 30760 2.51 5 N 8424 2.21 5 O 9418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 438 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 48930 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2150 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1840 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "F" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1819 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "G" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1714 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "H" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1705 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 8, 'TRANS': 219} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1732 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'VYW': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: O, W, b, a, Q, Z, V, Y, R, U, X, P, T, S Time building chain proxies: 27.06, per 1000 atoms: 0.55 Number of scatterers: 48930 At special positions: 0 Unit cell: (187.25, 189.39, 135.89, 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 328 16.00 O 9418 8.00 N 8424 7.00 C 30760 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: 12.30 Conformation dependent library (CDL) restraints added in 6.0 seconds 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11648 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 70 sheets defined 38.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.657A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (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 123 removed outlier: 3.617A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.819A pdb=" N SER A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.661A pdb=" N LEU A 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) 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: 3.670A 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 56 through 60 Processing helix chain 'B' and resid 77 through 100 Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.548A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 4.112A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.544A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (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 127 removed outlier: 3.972A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.555A pdb=" N LYS C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 250 through 267 Proline residue: C 256 - end of helix removed outlier: 3.778A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.570A pdb=" N GLN D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 181 through 204 removed outlier: 3.517A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.532A pdb=" N VAL E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 306 Processing helix chain 'E' and resid 331 through 340 Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.500A pdb=" N GLU F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 265 Processing helix chain 'F' and resid 269 through 283 Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.911A pdb=" N SER F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 348 through 362 Processing helix chain 'F' and resid 390 through 398 removed outlier: 3.709A pdb=" N ARG F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 103 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.753A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.832A pdb=" N LYS G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.731A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 Processing helix chain 'H' and resid 129 through 144 Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.846A 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: 3.607A 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 255 through 259 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.537A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 removed outlier: 3.539A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (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 176 Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 78 through 94 Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 163 through 182 Processing helix chain 'L' and resid 147 through 170 Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 230 through 242 removed outlier: 3.880A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 266 Processing helix chain 'L' and resid 291 through 299 Processing helix chain 'M' and resid 182 through 203 Processing helix chain 'M' and resid 210 through 225 removed outlier: 3.513A pdb=" N ARG M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 280 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 293 through 312 Processing helix chain 'N' and resid 53 through 74 Processing helix chain 'N' and resid 80 through 98 Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 142 through 153 Processing helix chain 'N' and resid 158 through 177 Processing helix chain 'N' and resid 208 through 211 Processing helix chain 'N' and resid 212 through 217 Processing helix chain 'O' and resid 19 through 31 removed outlier: 3.657A pdb=" N VAL O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR O 30 " --> pdb=" O PHE O 26 " (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 123 removed outlier: 3.613A pdb=" N ARG O 122 " --> pdb=" O LYS O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 188 removed outlier: 3.815A pdb=" N SER O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 removed outlier: 3.659A pdb=" N LEU O 193 " --> pdb=" O LEU O 190 " (cutoff:3.500A) 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: 3.665A 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 56 through 60 Processing helix chain 'P' and resid 77 through 100 Processing helix chain 'P' and resid 104 through 119 Processing helix chain 'P' and resid 164 through 176 removed outlier: 3.551A pdb=" N LYS P 174 " --> pdb=" O ALA P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 196 removed outlier: 4.112A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 229 removed outlier: 3.544A 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 127 removed outlier: 3.974A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 185 removed outlier: 3.557A pdb=" N LYS Q 183 " --> pdb=" O ALA Q 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP Q 184 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 206 Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 250 through 267 Proline residue: Q 256 - end of helix removed outlier: 3.772A pdb=" N ALA Q 264 " --> pdb=" O ARG Q 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'R' and resid 164 through 176 Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 218 through 231 removed outlier: 3.578A pdb=" N GLN R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'S' and resid 160 through 164 Processing helix chain 'S' and resid 181 through 204 removed outlier: 3.518A pdb=" N ILE S 187 " --> pdb=" O ALA S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 218 Processing helix chain 'S' and resid 273 through 285 removed outlier: 3.535A pdb=" N VAL S 280 " --> pdb=" O ALA S 276 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 306 Processing helix chain 'S' and resid 331 through 340 Processing helix chain 'T' and resid 183 through 195 removed outlier: 3.503A pdb=" N GLU T 191 " --> pdb=" O GLU T 187 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL T 193 " --> pdb=" O ALA T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 242 through 265 Processing helix chain 'T' and resid 269 through 283 Processing helix chain 'T' and resid 329 through 341 removed outlier: 3.909A pdb=" N SER T 333 " --> pdb=" O ARG T 329 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS T 340 " --> pdb=" O TYR T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 344 No H-bonds generated for 'chain 'T' and resid 342 through 344' Processing helix chain 'T' and resid 348 through 362 Processing helix chain 'T' and resid 390 through 398 removed outlier: 3.710A pdb=" N ARG T 395 " --> pdb=" O GLU T 391 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS T 396 " --> pdb=" O GLU T 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR T 397 " --> pdb=" O SER T 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 33 Processing helix chain 'U' and resid 81 through 103 Processing helix chain 'U' and resid 108 through 123 removed outlier: 3.754A pdb=" N TYR U 123 " --> pdb=" O PHE U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 178 removed outlier: 3.833A pdb=" N LYS U 178 " --> pdb=" O SER U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.738A pdb=" N GLY U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 125 Processing helix chain 'V' and resid 129 through 144 Processing helix chain 'V' and resid 183 through 188 removed outlier: 3.849A 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: 3.612A 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 255 through 259 Processing helix chain 'W' and resid 77 through 100 Processing helix chain 'W' and resid 104 through 119 Processing helix chain 'W' and resid 159 through 171 removed outlier: 3.537A pdb=" N GLN W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 195 removed outlier: 3.538A pdb=" N GLY W 191 " --> pdb=" O ALA W 187 " (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 176 Processing helix chain 'Y' and resid 50 through 71 Processing helix chain 'Y' and resid 78 through 94 Processing helix chain 'Y' and resid 146 through 158 Processing helix chain 'Y' and resid 163 through 182 Processing helix chain 'Z' and resid 147 through 170 Processing helix chain 'Z' and resid 174 through 189 Processing helix chain 'Z' and resid 230 through 242 removed outlier: 3.878A pdb=" N GLY Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL Z 237 " --> pdb=" O TYR Z 233 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR Z 240 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 266 Processing helix chain 'Z' and resid 291 through 299 Processing helix chain 'a' and resid 182 through 204 Processing helix chain 'a' and resid 210 through 225 removed outlier: 3.514A pdb=" N ARG a 225 " --> pdb=" O MET a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 280 Proline residue: a 273 - end of helix Processing helix chain 'a' and resid 293 through 312 Processing helix chain 'b' and resid 53 through 74 Processing helix chain 'b' and resid 80 through 98 Processing helix chain 'b' and resid 137 through 142 Processing helix chain 'b' and resid 142 through 153 Processing helix chain 'b' and resid 158 through 177 Processing helix chain 'b' and resid 208 through 211 Processing helix chain 'b' and resid 212 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.032A 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: 6.388A pdb=" N ILE A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.506A pdb=" N GLY B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.470A 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: 6.088A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 66 removed outlier: 6.520A pdb=" N ILE D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 267 through 270 removed outlier: 4.742A pdb=" N VAL E 317 " --> pdb=" O TYR E 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.144A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP E 247 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 323 through 326 removed outlier: 7.003A pdb=" N ILE F 377 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE F 388 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 379 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE F 386 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 228 through 232 removed outlier: 6.416A pdb=" N VAL F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU F 309 " --> pdb=" O TYR F 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.361A pdb=" N ALA G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 182 Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.488A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.555A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 153 through 156 removed outlier: 6.769A pdb=" N VAL I 202 " --> pdb=" O GLY I 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY I 217 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.411A pdb=" N GLU I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.530A pdb=" N ILE I 63 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR I 65 " --> pdb=" O CYS I 72 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS I 72 " --> pdb=" O TYR I 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 240 through 247 removed outlier: 3.604A pdb=" N LYS I 242 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS J 19 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.300A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.491A pdb=" N ILE J 49 " --> pdb=" O VAL J 45 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.207A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 21 through 24 removed outlier: 6.752A pdb=" N ASN K 22 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.409A pdb=" N GLN K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 224 through 227 removed outlier: 6.426A pdb=" N VAL L 273 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG L 288 " --> pdb=" O VAL L 273 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL L 275 " --> pdb=" O ILE L 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.534A pdb=" N ALA L 119 " --> pdb=" O ALA L 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR L 124 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 133 through 135 removed outlier: 3.845A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 263 through 265 removed outlier: 5.200A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AD5, first strand: chain 'M' and resid 168 through 172 removed outlier: 6.554A pdb=" N THR M 175 " --> pdb=" O LEU M 171 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN M 234 " --> pdb=" O TYR M 250 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER M 249 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU M 257 " --> pdb=" O SER M 249 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.462A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER N 45 " --> pdb=" O LEU N 41 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.462A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 132 through 135 Processing sheet with id=AD9, first strand: chain 'O' and resid 167 through 171 removed outlier: 6.052A pdb=" N LEU O 35 " --> pdb=" O GLN O 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 66 through 70 removed outlier: 6.387A pdb=" N ILE O 73 " --> pdb=" O VAL O 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 158 through 161 Processing sheet with id=AE3, first strand: chain 'P' and resid 63 through 67 removed outlier: 6.464A pdb=" N VAL P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 167 through 170 Processing sheet with id=AE5, first strand: chain 'Q' and resid 71 through 75 removed outlier: 6.089A pdb=" N ILE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE Q 140 " --> pdb=" O THR Q 156 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE7, first strand: chain 'R' and resid 63 through 66 removed outlier: 6.513A pdb=" N ILE R 69 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 267 through 270 removed outlier: 4.735A pdb=" N VAL S 317 " --> pdb=" O TYR S 330 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 171 removed outlier: 6.144A pdb=" N ILE S 174 " --> pdb=" O VAL S 170 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP S 247 " --> pdb=" O GLY S 250 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU S 253 " --> pdb=" O TYR S 265 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 323 through 326 removed outlier: 7.006A pdb=" N ILE T 377 " --> pdb=" O ILE T 388 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE T 388 " --> pdb=" O ILE T 377 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE T 379 " --> pdb=" O PHE T 386 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE T 386 " --> pdb=" O ILE T 379 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 228 through 232 removed outlier: 6.416A pdb=" N VAL T 235 " --> pdb=" O ILE T 231 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU T 309 " --> pdb=" O TYR T 321 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF4, first strand: chain 'U' and resid 67 through 71 removed outlier: 6.365A pdb=" N ALA U 74 " --> pdb=" O VAL U 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA U 142 " --> pdb=" O GLY U 145 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 179 through 182 Processing sheet with id=AF6, first strand: chain 'V' and resid 74 through 76 removed outlier: 6.495A pdb=" N SER V 76 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL V 80 " --> pdb=" O SER V 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 88 through 92 removed outlier: 6.558A pdb=" N ILE V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 153 through 156 removed outlier: 6.764A pdb=" N VAL W 202 " --> pdb=" O GLY W 217 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY W 217 " --> pdb=" O VAL W 202 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 49 through 51 removed outlier: 6.411A pdb=" N GLU W 51 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL W 55 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.536A pdb=" N ILE W 63 " --> pdb=" O GLY W 74 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY W 74 " --> pdb=" O ILE W 63 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR W 65 " --> pdb=" O CYS W 72 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS W 72 " --> pdb=" O TYR W 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 240 through 247 removed outlier: 3.600A pdb=" N LYS W 242 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS X 19 " --> pdb=" O GLY X 16 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.291A pdb=" N GLU X 30 " --> pdb=" O THR X 34 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N THR X 34 " --> pdb=" O GLU X 30 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 42 through 46 removed outlier: 6.494A pdb=" N ILE X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 140 through 143 removed outlier: 4.212A pdb=" N VAL Y 191 " --> pdb=" O ILE Y 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 21 through 24 removed outlier: 6.752A pdb=" N ASN Y 22 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 36 through 40 removed outlier: 6.414A pdb=" N GLN Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 224 through 227 removed outlier: 6.419A pdb=" N VAL Z 273 " --> pdb=" O ARG Z 288 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG Z 288 " --> pdb=" O VAL Z 273 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL Z 275 " --> pdb=" O ILE Z 286 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 119 through 121 removed outlier: 6.538A pdb=" N ALA Z 119 " --> pdb=" O ALA Z 126 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR Z 124 " --> pdb=" O THR Z 121 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 133 through 135 removed outlier: 3.841A pdb=" N MET Z 199 " --> pdb=" O THR Z 143 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 263 through 265 removed outlier: 5.191A pdb=" N THR a 135 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 153 through 154 Processing sheet with id=AH4, first strand: chain 'a' and resid 168 through 172 removed outlier: 6.554A pdb=" N THR a 175 " --> pdb=" O LEU a 171 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN a 234 " --> pdb=" O TYR a 250 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER a 249 " --> pdb=" O GLU a 257 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU a 257 " --> pdb=" O SER a 249 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 29 through 32 removed outlier: 5.448A pdb=" N ALA b 30 " --> pdb=" O TYR b 26 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR b 26 " --> pdb=" O ALA b 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER b 45 " --> pdb=" O LEU b 41 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 29 through 32 removed outlier: 5.448A pdb=" N ALA b 30 " --> pdb=" O TYR b 26 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR b 26 " --> pdb=" O ALA b 30 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 132 through 135 2809 hydrogen bonds defined for protein. 8016 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: 23.47 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 10192 1.31 - 1.47: 17902 1.47 - 1.62: 21250 1.62 - 1.77: 25 1.77 - 1.92: 491 Bond restraints: 49860 Sorted by residual: bond pdb=" CE1 HIS b 44 " pdb=" NE2 HIS b 44 " ideal model delta sigma weight residual 1.321 1.434 -0.113 1.00e-02 1.00e+04 1.28e+02 bond pdb=" CE1 HIS N 44 " pdb=" NE2 HIS N 44 " ideal model delta sigma weight residual 1.321 1.433 -0.112 1.00e-02 1.00e+04 1.26e+02 bond pdb=" CE1 HIS I 145 " pdb=" NE2 HIS I 145 " ideal model delta sigma weight residual 1.321 1.410 -0.089 1.00e-02 1.00e+04 7.94e+01 bond pdb=" CE1 HIS W 145 " pdb=" NE2 HIS W 145 " ideal model delta sigma weight residual 1.321 1.410 -0.089 1.00e-02 1.00e+04 7.85e+01 bond pdb=" CE1 HIS X 147 " pdb=" NE2 HIS X 147 " ideal model delta sigma weight residual 1.321 1.406 -0.085 1.00e-02 1.00e+04 7.30e+01 ... (remaining 49855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 62963 3.91 - 7.82: 4239 7.82 - 11.73: 228 11.73 - 15.65: 24 15.65 - 19.56: 4 Bond angle restraints: 67458 Sorted by residual: angle pdb=" CA ASN L 137 " pdb=" CB ASN L 137 " pdb=" CG ASN L 137 " ideal model delta sigma weight residual 112.60 125.98 -13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA ASN Z 137 " pdb=" CB ASN Z 137 " pdb=" CG ASN Z 137 " ideal model delta sigma weight residual 112.60 125.93 -13.33 1.00e+00 1.00e+00 1.78e+02 angle pdb=" C PHE a 270 " pdb=" CA PHE a 270 " pdb=" CB PHE a 270 " ideal model delta sigma weight residual 109.56 90.00 19.56 1.65e+00 3.67e-01 1.40e+02 angle pdb=" C PHE M 270 " pdb=" CA PHE M 270 " pdb=" CB PHE M 270 " ideal model delta sigma weight residual 109.56 90.14 19.42 1.65e+00 3.67e-01 1.39e+02 angle pdb=" CA ASP U 144 " pdb=" CB ASP U 144 " pdb=" CG ASP U 144 " ideal model delta sigma weight residual 112.60 122.64 -10.04 1.00e+00 1.00e+00 1.01e+02 ... (remaining 67453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 26363 18.05 - 36.11: 2633 36.11 - 54.16: 632 54.16 - 72.21: 230 72.21 - 90.27: 102 Dihedral angle restraints: 29960 sinusoidal: 11728 harmonic: 18232 Sorted by residual: dihedral pdb=" C PHE a 270 " pdb=" N PHE a 270 " pdb=" CA PHE a 270 " pdb=" CB PHE a 270 " ideal model delta harmonic sigma weight residual -122.60 -101.15 -21.45 0 2.50e+00 1.60e-01 7.36e+01 dihedral pdb=" C PHE M 270 " pdb=" N PHE M 270 " pdb=" CA PHE M 270 " pdb=" CB PHE M 270 " ideal model delta harmonic sigma weight residual -122.60 -101.23 -21.37 0 2.50e+00 1.60e-01 7.31e+01 dihedral pdb=" CA GLY T 289 " pdb=" C GLY T 289 " pdb=" N LYS T 290 " pdb=" CA LYS T 290 " ideal model delta harmonic sigma weight residual 180.00 139.21 40.79 0 5.00e+00 4.00e-02 6.66e+01 ... (remaining 29957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4512 0.079 - 0.158: 2279 0.158 - 0.238: 591 0.238 - 0.317: 110 0.317 - 0.396: 24 Chirality restraints: 7516 Sorted by residual: chirality pdb=" CA ARG P 210 " pdb=" N ARG P 210 " pdb=" C ARG P 210 " pdb=" CB ARG P 210 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA SER S 196 " pdb=" N SER S 196 " pdb=" C SER S 196 " pdb=" CB SER S 196 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA SER E 196 " pdb=" N SER E 196 " pdb=" C SER E 196 " pdb=" CB SER E 196 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 7513 not shown) Planarity restraints: 8744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 106 " 0.926 9.50e-02 1.11e+02 4.15e-01 1.08e+02 pdb=" NE ARG L 106 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG L 106 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG L 106 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG L 106 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 106 " -0.920 9.50e-02 1.11e+02 4.13e-01 1.07e+02 pdb=" NE ARG Z 106 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG Z 106 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 106 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 106 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 225 " -0.764 9.50e-02 1.11e+02 3.42e-01 7.14e+01 pdb=" NE ARG M 225 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG M 225 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG M 225 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 225 " -0.024 2.00e-02 2.50e+03 ... (remaining 8741 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6530 2.72 - 3.27: 47873 3.27 - 3.81: 84650 3.81 - 4.36: 111814 4.36 - 4.90: 182526 Nonbonded interactions: 433393 Sorted by model distance: nonbonded pdb=" OG SER H 184 " pdb=" OD2 ASP H 221 " model vdw 2.180 3.040 nonbonded pdb=" OG SER V 184 " pdb=" OD2 ASP V 221 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP Z 150 " pdb=" OH TYR a 223 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP L 150 " pdb=" OH TYR M 223 " model vdw 2.231 3.040 nonbonded pdb=" NE2 GLN D 116 " pdb=" OD1 ASP E 184 " model vdw 2.233 3.120 ... (remaining 433388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.650 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 106.370 Find NCS groups from input model: 3.630 Set up NCS constraints: 0.310 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 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 : 0.018 0.122 49860 Z= 1.168 Angle : 2.109 19.557 67458 Z= 1.389 Chirality : 0.096 0.396 7516 Planarity : 0.032 0.415 8744 Dihedral : 17.272 90.267 18312 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.01 % Favored : 95.41 % Rotamer: Outliers : 5.92 % Allowed : 8.93 % Favored : 85.14 % Cbeta Deviations : 1.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.09), residues: 6256 helix: -2.40 (0.08), residues: 2330 sheet: -0.82 (0.12), residues: 1624 loop : -1.69 (0.11), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.017 TRP a 199 HIS 0.040 0.007 HIS P 69 PHE 0.078 0.015 PHE J 100 TYR 0.100 0.015 TYR P 116 ARG 0.049 0.005 ARG U 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 309 poor density : 1179 time to evaluate : 5.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7884 (tmm160) cc_final: 0.7439 (tmm160) REVERT: A 77 MET cc_start: 0.9013 (mmt) cc_final: 0.8618 (mmt) REVERT: A 141 ASP cc_start: 0.8943 (t70) cc_final: 0.8734 (t70) REVERT: A 150 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8387 (mmtt) REVERT: A 210 ILE cc_start: 0.8662 (pt) cc_final: 0.8393 (pt) REVERT: A 215 LYS cc_start: 0.8206 (mttt) cc_final: 0.7628 (ttpt) REVERT: A 228 ASN cc_start: 0.8130 (t0) cc_final: 0.7904 (t0) REVERT: B 16 LYS cc_start: 0.8798 (mttt) cc_final: 0.8410 (mmpt) REVERT: B 90 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8666 (mtmt) REVERT: B 100 ASN cc_start: 0.8950 (t0) cc_final: 0.8699 (t0) REVERT: B 140 ASN cc_start: 0.8561 (m-40) cc_final: 0.8315 (m110) REVERT: B 154 TRP cc_start: 0.8589 (m100) cc_final: 0.7929 (m-90) REVERT: B 169 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7614 (mtmm) REVERT: B 175 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7557 (mtp-110) REVERT: B 181 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7196 (pp20) REVERT: B 183 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7046 (tp30) REVERT: B 202 THR cc_start: 0.7812 (p) cc_final: 0.7381 (p) REVERT: B 204 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7957 (mp0) REVERT: B 205 ASN cc_start: 0.8534 (p0) cc_final: 0.7715 (p0) REVERT: B 214 ASN cc_start: 0.8567 (p0) cc_final: 0.8302 (m110) REVERT: C 17 ARG cc_start: 0.8264 (mtp180) cc_final: 0.8045 (mtm180) REVERT: C 26 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8099 (mt-10) REVERT: C 50 MET cc_start: 0.7411 (ptm) cc_final: 0.7156 (ppp) REVERT: C 71 MET cc_start: 0.8963 (mmt) cc_final: 0.8674 (mmt) REVERT: C 111 MET cc_start: 0.9192 (ttt) cc_final: 0.8779 (ttt) REVERT: C 180 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8555 (mt) REVERT: C 182 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7431 (mmtp) REVERT: C 183 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7510 (tttp) REVERT: C 192 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7449 (mp0) REVERT: C 204 LYS cc_start: 0.8185 (tptm) cc_final: 0.7706 (tttm) REVERT: C 206 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8152 (ptm) REVERT: C 221 MET cc_start: 0.9038 (tpp) cc_final: 0.8803 (tpp) REVERT: C 222 ARG cc_start: 0.8696 (ptt-90) cc_final: 0.8048 (ptp-170) REVERT: C 255 LYS cc_start: 0.7377 (tttt) cc_final: 0.7070 (tptp) REVERT: D 54 GLN cc_start: 0.8333 (pt0) cc_final: 0.7578 (mm-40) REVERT: D 59 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.5807 (pp) REVERT: D 103 ASP cc_start: 0.8791 (m-30) cc_final: 0.8558 (m-30) REVERT: D 141 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7805 (mmmt) REVERT: D 163 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8644 (ptt90) REVERT: D 172 MET cc_start: 0.8944 (mtm) cc_final: 0.8673 (mtm) REVERT: D 177 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7216 (mmpt) REVERT: D 180 MET cc_start: 0.8282 (mtm) cc_final: 0.7901 (mtm) REVERT: D 196 VAL cc_start: 0.8006 (m) cc_final: 0.7784 (m) REVERT: D 228 GLU cc_start: 0.6117 (tt0) cc_final: 0.5542 (tt0) REVERT: D 230 GLU cc_start: 0.5970 (tt0) cc_final: 0.5430 (tp30) REVERT: D 232 GLU cc_start: 0.6149 (tt0) cc_final: 0.5824 (tm-30) REVERT: E 110 ARG cc_start: 0.6222 (mtm-85) cc_final: 0.6003 (mtm180) REVERT: E 120 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8409 (mtm-85) REVERT: E 141 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7756 (ttp80) REVERT: E 144 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7462 (mt-10) REVERT: E 171 ASP cc_start: 0.8929 (t0) cc_final: 0.8727 (t0) REVERT: E 233 MET cc_start: 0.7231 (mmt) cc_final: 0.6849 (mmt) REVERT: E 248 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7221 (tt0) REVERT: E 264 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.8065 (ttm110) REVERT: E 278 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: E 282 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7582 (p) REVERT: E 289 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7650 (ptp) REVERT: E 290 THR cc_start: 0.8134 (p) cc_final: 0.7616 (t) REVERT: E 293 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6547 (mm-30) REVERT: E 313 GLU cc_start: 0.7573 (mp0) cc_final: 0.7238 (mp0) REVERT: E 316 GLU cc_start: 0.8577 (tt0) cc_final: 0.8367 (mt-10) REVERT: E 342 MET cc_start: 0.4126 (ttm) cc_final: 0.3760 (tpt) REVERT: F 169 GLU cc_start: 0.7180 (tt0) cc_final: 0.6943 (mp0) REVERT: F 190 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (m110) REVERT: F 304 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7949 (mtm-85) REVERT: G 29 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8408 (mttm) REVERT: G 33 ASN cc_start: 0.8580 (m-40) cc_final: 0.8339 (m-40) REVERT: G 43 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7551 (mmmm) REVERT: G 51 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: G 61 LYS cc_start: 0.7537 (mttt) cc_final: 0.7179 (mmtt) REVERT: G 180 ASP cc_start: 0.7895 (t0) cc_final: 0.7573 (t70) REVERT: G 184 LEU cc_start: 0.7796 (tp) cc_final: 0.7571 (tp) REVERT: H 123 ASP cc_start: 0.8843 (t70) cc_final: 0.8627 (t70) REVERT: H 137 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: H 203 LYS cc_start: 0.8684 (tttt) cc_final: 0.8432 (tttp) REVERT: I 59 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7856 (mtm-85) REVERT: I 71 MET cc_start: 0.8989 (mmm) cc_final: 0.8776 (mmm) REVERT: I 78 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8657 (t) REVERT: I 82 GLU cc_start: 0.8611 (tp30) cc_final: 0.8384 (tm-30) REVERT: I 120 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8222 (mm110) REVERT: I 175 MET cc_start: 0.9114 (mtm) cc_final: 0.8890 (mtm) REVERT: I 179 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8341 (mt-10) REVERT: I 213 GLU cc_start: 0.8439 (tt0) cc_final: 0.8195 (mp0) REVERT: I 244 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7086 (tm-30) REVERT: J 3 ILE cc_start: 0.8749 (mt) cc_final: 0.8232 (tp) REVERT: J 4 MET cc_start: 0.8579 (mmm) cc_final: 0.8337 (mmt) REVERT: J 12 MET cc_start: 0.8998 (tmm) cc_final: 0.8713 (tmm) REVERT: J 41 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8705 (mmtm) REVERT: J 66 LYS cc_start: 0.9234 (mtpp) cc_final: 0.9007 (mtpp) REVERT: J 68 GLN cc_start: 0.8874 (tt0) cc_final: 0.8615 (tt0) REVERT: J 92 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8908 (m) REVERT: J 97 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8624 (mt-10) REVERT: J 118 GLU cc_start: 0.8332 (tt0) cc_final: 0.7926 (mm-30) REVERT: J 158 MET cc_start: 0.8848 (mtp) cc_final: 0.8201 (mtm) REVERT: J 171 MET cc_start: 0.9081 (tpp) cc_final: 0.8771 (tpt) REVERT: J 188 MET cc_start: 0.9097 (mtp) cc_final: 0.8770 (mtp) REVERT: K 1 MET cc_start: 0.7162 (mmm) cc_final: 0.6713 (mtm) REVERT: K 3 GLU cc_start: 0.8114 (mp0) cc_final: 0.7829 (pt0) REVERT: K 31 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7755 (OUTLIER) REVERT: K 50 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8262 (mp0) REVERT: K 70 MET cc_start: 0.8648 (mmp) cc_final: 0.8370 (mmt) REVERT: K 125 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8667 (mm110) REVERT: K 159 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8412 (mtm-85) REVERT: K 173 LYS cc_start: 0.8845 (mttt) cc_final: 0.8640 (mttp) REVERT: K 180 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8327 (ttp-170) REVERT: K 206 HIS cc_start: 0.7938 (p90) cc_final: 0.7693 (p90) REVERT: L 123 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: L 131 MET cc_start: 0.8268 (mtp) cc_final: 0.8030 (tpt) REVERT: L 134 LEU cc_start: 0.8507 (tp) cc_final: 0.8248 (mt) REVERT: L 137 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6924 (t0) REVERT: L 139 TYR cc_start: 0.7776 (m-80) cc_final: 0.7284 (m-80) REVERT: L 160 MET cc_start: 0.9273 (ttp) cc_final: 0.9013 (ttp) REVERT: L 172 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8092 (mtm110) REVERT: L 205 GLN cc_start: 0.8154 (pm20) cc_final: 0.7795 (pm20) REVERT: L 244 LYS cc_start: 0.8385 (mttt) cc_final: 0.8109 (mmtp) REVERT: M 170 GLN cc_start: 0.8954 (tt0) cc_final: 0.8726 (tt0) REVERT: M 177 MET cc_start: 0.9120 (ptm) cc_final: 0.8649 (ptm) REVERT: M 201 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8264 (mmmt) REVERT: M 257 GLU cc_start: 0.8408 (pt0) cc_final: 0.8118 (pt0) REVERT: M 281 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8410 (mtp85) REVERT: M 292 MET cc_start: 0.8077 (mtm) cc_final: 0.7716 (ttm) REVERT: M 330 GLN cc_start: 0.8656 (mt0) cc_final: 0.8274 (mm-40) REVERT: M 332 GLU cc_start: 0.8457 (tt0) cc_final: 0.8152 (tt0) REVERT: N 1 MET cc_start: 0.7704 (mmm) cc_final: 0.7428 (mmm) REVERT: N 13 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8515 (mtpm) REVERT: N 39 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8261 (ttm170) REVERT: N 59 MET cc_start: 0.8982 (tpp) cc_final: 0.8768 (tpt) REVERT: N 64 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: N 106 MET cc_start: 0.8848 (mtt) cc_final: 0.8509 (mtt) REVERT: N 135 THR cc_start: 0.9291 (p) cc_final: 0.9024 (p) REVERT: N 151 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7659 (mt-10) REVERT: N 164 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (ttp80) REVERT: N 203 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8219 (mp0) REVERT: N 207 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8150 (mm-30) REVERT: O 56 ARG cc_start: 0.7881 (tmm160) cc_final: 0.7442 (tmm160) REVERT: O 77 MET cc_start: 0.9006 (mmt) cc_final: 0.8616 (mmt) REVERT: O 141 ASP cc_start: 0.8945 (t70) cc_final: 0.8735 (t70) REVERT: O 150 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8407 (mmtt) REVERT: O 210 ILE cc_start: 0.8653 (pt) cc_final: 0.8387 (pt) REVERT: O 214 VAL cc_start: 0.8352 (m) cc_final: 0.8141 (p) REVERT: O 215 LYS cc_start: 0.8200 (mttt) cc_final: 0.7602 (ttpt) REVERT: O 228 ASN cc_start: 0.8243 (t0) cc_final: 0.8016 (t0) REVERT: P 16 LYS cc_start: 0.8805 (mttt) cc_final: 0.8415 (mmpt) REVERT: P 61 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: P 90 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8724 (mtmt) REVERT: P 100 ASN cc_start: 0.8966 (t0) cc_final: 0.8717 (t0) REVERT: P 140 ASN cc_start: 0.8545 (m-40) cc_final: 0.8281 (m110) REVERT: P 154 TRP cc_start: 0.8598 (m100) cc_final: 0.7943 (m-90) REVERT: P 169 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7624 (mtmm) REVERT: P 175 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7586 (mtp-110) REVERT: P 180 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7218 (ttp) REVERT: P 181 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7396 (tm-30) REVERT: P 183 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7154 (tp30) REVERT: P 202 THR cc_start: 0.7812 (p) cc_final: 0.7374 (p) REVERT: P 204 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7948 (mp0) REVERT: P 205 ASN cc_start: 0.8564 (p0) cc_final: 0.7758 (p0) REVERT: P 214 ASN cc_start: 0.8558 (p0) cc_final: 0.8308 (m110) REVERT: Q 4 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.7967 (mtm110) REVERT: Q 17 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8043 (mtm180) REVERT: Q 26 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8089 (mt-10) REVERT: Q 50 MET cc_start: 0.7405 (ptm) cc_final: 0.7138 (ppp) REVERT: Q 71 MET cc_start: 0.8966 (mmt) cc_final: 0.8672 (mmt) REVERT: Q 111 MET cc_start: 0.9183 (ttt) cc_final: 0.8792 (ttt) REVERT: Q 180 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8558 (mt) REVERT: Q 182 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7552 (mmtp) REVERT: Q 183 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7473 (tttp) REVERT: Q 192 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7443 (mp0) REVERT: Q 204 LYS cc_start: 0.8183 (tptm) cc_final: 0.7705 (tttm) REVERT: Q 206 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8167 (ptm) REVERT: Q 221 MET cc_start: 0.9043 (tpp) cc_final: 0.8809 (tpp) REVERT: Q 222 ARG cc_start: 0.8701 (ptt-90) cc_final: 0.8048 (ptp-170) REVERT: Q 255 LYS cc_start: 0.7372 (tttt) cc_final: 0.7069 (tptp) REVERT: R 54 GLN cc_start: 0.8332 (pt0) cc_final: 0.7579 (mm-40) REVERT: R 59 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.5905 (pp) REVERT: R 103 ASP cc_start: 0.8802 (m-30) cc_final: 0.8560 (m-30) REVERT: R 141 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7795 (mmmt) REVERT: R 163 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8647 (ptt90) REVERT: R 172 MET cc_start: 0.8949 (mtm) cc_final: 0.8684 (mtm) REVERT: R 177 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (mmpt) REVERT: R 180 MET cc_start: 0.8264 (mtm) cc_final: 0.7864 (mtm) REVERT: R 196 VAL cc_start: 0.8024 (m) cc_final: 0.7792 (m) REVERT: R 228 GLU cc_start: 0.6147 (tt0) cc_final: 0.5583 (tt0) REVERT: R 230 GLU cc_start: 0.5974 (tt0) cc_final: 0.5496 (tp30) REVERT: R 232 GLU cc_start: 0.6132 (tt0) cc_final: 0.5824 (tm-30) REVERT: S 110 ARG cc_start: 0.6206 (mtm-85) cc_final: 0.5992 (mtm180) REVERT: S 120 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8408 (mtm-85) REVERT: S 141 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: S 144 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7466 (mt-10) REVERT: S 153 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7912 (ttm170) REVERT: S 171 ASP cc_start: 0.8933 (t0) cc_final: 0.8727 (t0) REVERT: S 233 MET cc_start: 0.7204 (mmt) cc_final: 0.6828 (mmt) REVERT: S 248 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7206 (tt0) REVERT: S 264 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8052 (ttm110) REVERT: S 278 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: S 282 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7582 (p) REVERT: S 289 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: S 290 THR cc_start: 0.8134 (p) cc_final: 0.7618 (t) REVERT: S 293 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6555 (mm-30) REVERT: S 313 GLU cc_start: 0.7573 (mp0) cc_final: 0.7292 (mp0) REVERT: S 342 MET cc_start: 0.4104 (ttm) cc_final: 0.3742 (tpt) REVERT: T 169 GLU cc_start: 0.7190 (tt0) cc_final: 0.6960 (mp0) REVERT: T 190 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8289 (m110) REVERT: T 304 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7947 (mtm-85) REVERT: T 371 ASN cc_start: 0.8526 (p0) cc_final: 0.8325 (p0) REVERT: U 29 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8408 (mttm) REVERT: U 33 ASN cc_start: 0.8576 (m-40) cc_final: 0.8329 (m-40) REVERT: U 43 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (mmmm) REVERT: U 51 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: U 61 LYS cc_start: 0.7545 (mttt) cc_final: 0.7193 (mmtt) REVERT: U 180 ASP cc_start: 0.7918 (t0) cc_final: 0.7543 (t70) REVERT: U 184 LEU cc_start: 0.7807 (tp) cc_final: 0.7581 (tp) REVERT: U 202 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7857 (t70) REVERT: U 221 ASP cc_start: 0.8280 (t0) cc_final: 0.8068 (t0) REVERT: V 123 ASP cc_start: 0.8842 (t70) cc_final: 0.8625 (t70) REVERT: V 137 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: V 203 LYS cc_start: 0.8679 (tttt) cc_final: 0.8438 (tttp) REVERT: V 280 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8550 (p) REVERT: W 58 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8267 (mtmt) REVERT: W 59 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: W 71 MET cc_start: 0.8979 (mmm) cc_final: 0.8758 (mmm) REVERT: W 78 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8644 (t) REVERT: W 82 GLU cc_start: 0.8606 (tp30) cc_final: 0.8390 (tm-30) REVERT: W 120 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8221 (mm110) REVERT: W 175 MET cc_start: 0.9127 (mtm) cc_final: 0.8900 (mtm) REVERT: W 179 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8367 (mt-10) REVERT: W 213 GLU cc_start: 0.8438 (tt0) cc_final: 0.8202 (mp0) REVERT: W 244 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7122 (tm-30) REVERT: X 3 ILE cc_start: 0.8723 (mt) cc_final: 0.8205 (tp) REVERT: X 12 MET cc_start: 0.8997 (tmm) cc_final: 0.8713 (tmm) REVERT: X 31 GLN cc_start: 0.8623 (mt0) cc_final: 0.8414 (mt0) REVERT: X 41 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8705 (mmtm) REVERT: X 66 LYS cc_start: 0.9229 (mtpp) cc_final: 0.9003 (mtpp) REVERT: X 68 GLN cc_start: 0.8877 (tt0) cc_final: 0.8616 (tt0) REVERT: X 92 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8888 (m) REVERT: X 97 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8622 (mt-10) REVERT: X 118 GLU cc_start: 0.8325 (tt0) cc_final: 0.7924 (mm-30) REVERT: X 158 MET cc_start: 0.8853 (mtp) cc_final: 0.8215 (mtm) REVERT: X 171 MET cc_start: 0.9079 (tpp) cc_final: 0.8769 (tpt) REVERT: X 188 MET cc_start: 0.9092 (mtp) cc_final: 0.8771 (mtp) REVERT: Y 1 MET cc_start: 0.7129 (mmm) cc_final: 0.6699 (mtm) REVERT: Y 3 GLU cc_start: 0.8107 (mp0) cc_final: 0.7826 (pt0) REVERT: Y 31 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: Y 50 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8271 (mp0) REVERT: Y 70 MET cc_start: 0.8656 (mmp) cc_final: 0.8382 (mmt) REVERT: Y 125 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8675 (mm110) REVERT: Y 159 ARG cc_start: 0.8677 (mtm110) cc_final: 0.8420 (mtm-85) REVERT: Y 164 GLN cc_start: 0.8484 (tp40) cc_final: 0.8279 (tp40) REVERT: Y 173 LYS cc_start: 0.8837 (mttt) cc_final: 0.8631 (mttp) REVERT: Y 180 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8327 (ttp-170) REVERT: Y 206 HIS cc_start: 0.7927 (p90) cc_final: 0.7685 (p90) REVERT: Z 123 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: Z 131 MET cc_start: 0.8265 (mtp) cc_final: 0.8027 (tpt) REVERT: Z 134 LEU cc_start: 0.8506 (tp) cc_final: 0.8247 (mt) REVERT: Z 137 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6928 (t0) REVERT: Z 139 TYR cc_start: 0.7760 (m-80) cc_final: 0.7267 (m-80) REVERT: Z 172 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8101 (mtm110) REVERT: Z 205 GLN cc_start: 0.8117 (pm20) cc_final: 0.7774 (pm20) REVERT: Z 244 LYS cc_start: 0.8411 (mttt) cc_final: 0.8130 (mmtp) REVERT: a 167 LYS cc_start: 0.8851 (mttp) cc_final: 0.8592 (mttm) REVERT: a 177 MET cc_start: 0.9122 (ptm) cc_final: 0.8646 (ptm) REVERT: a 201 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8254 (mmmt) REVERT: a 257 GLU cc_start: 0.8434 (pt0) cc_final: 0.8138 (pt0) REVERT: a 281 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8410 (mtp85) REVERT: a 292 MET cc_start: 0.8058 (mtm) cc_final: 0.7648 (ttm) REVERT: a 317 ASP cc_start: 0.8170 (m-30) cc_final: 0.7937 (m-30) REVERT: a 330 GLN cc_start: 0.8644 (mt0) cc_final: 0.8260 (mm-40) REVERT: a 331 GLN cc_start: 0.8093 (mt0) cc_final: 0.7745 (mt0) REVERT: a 332 GLU cc_start: 0.8457 (tt0) cc_final: 0.8134 (tt0) REVERT: b 1 MET cc_start: 0.7721 (mmm) cc_final: 0.7431 (mmm) REVERT: b 13 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8516 (mtpm) REVERT: b 39 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8262 (ttm170) REVERT: b 59 MET cc_start: 0.8985 (tpp) cc_final: 0.8784 (tpt) REVERT: b 64 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: b 106 MET cc_start: 0.8853 (mtt) cc_final: 0.8508 (mtt) REVERT: b 135 THR cc_start: 0.9303 (p) cc_final: 0.9050 (p) REVERT: b 164 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8452 (ttp80) REVERT: b 203 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8216 (mp0) REVERT: b 207 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8247 (mm-30) outliers start: 309 outliers final: 81 residues processed: 1382 average time/residue: 1.8325 time to fit residues: 3075.6073 Evaluate side-chains 983 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 847 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain D residue 12 PRO Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain M residue 219 SER Chi-restraints excluded: chain M residue 333 SER Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 144 PRO Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 180 MET Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 206 MET Chi-restraints excluded: chain Q residue 233 LEU Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain R residue 12 PRO Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain S residue 141 ARG Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 278 GLN Chi-restraints excluded: chain S residue 282 THR Chi-restraints excluded: chain S residue 289 MET Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 362 SER Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 51 GLU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 195 SER Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain V residue 173 SER Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 224 SER Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 280 SER Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 116 THR Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 137 ASN Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 284 THR Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 219 SER Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 64 GLU Chi-restraints excluded: chain b residue 144 PRO Chi-restraints excluded: chain b residue 164 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 521 optimal weight: 0.9980 chunk 468 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 484 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 561 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 207 GLN A 228 ASN A 232 GLN A 236 ASN B 107 GLN B 200 GLN C 152 GLN C 239 HIS C 257 HIS D 23 GLN E 222 GLN E 255 GLN E 262 HIS E 288 ASN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS I 201 GLN J 31 GLN J 65 ASN K 72 GLN K 102 GLN K 186 ASN L 108 ASN L 291 GLN N 148 GLN N 205 HIS O 89 GLN O 207 GLN O 228 ASN O 232 GLN P 93 GLN P 107 GLN P 200 GLN Q 152 GLN Q 239 HIS Q 257 HIS R 23 GLN S 222 GLN S 255 GLN S 262 HIS S 288 ASN T 331 GLN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 115 HIS W 201 GLN X 65 ASN Y 72 GLN Y 102 GLN Y 164 GLN Y 186 ASN Z 108 ASN Z 291 GLN a 280 ASN b 148 GLN b 205 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 49860 Z= 0.204 Angle : 0.627 7.669 67458 Z= 0.339 Chirality : 0.045 0.169 7516 Planarity : 0.004 0.056 8744 Dihedral : 7.889 60.466 7261 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.27 % Rotamer: Outliers : 2.99 % Allowed : 14.42 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -0.13 (0.10), residues: 6256 helix: 0.56 (0.10), residues: 2332 sheet: 0.11 (0.12), residues: 1572 loop : -0.74 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 185 HIS 0.007 0.001 HIS U 198 PHE 0.019 0.002 PHE B 64 TYR 0.022 0.002 TYR V 190 ARG 0.009 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1007 time to evaluate : 5.538 Fit side-chains REVERT: A 62 SER cc_start: 0.8874 (p) cc_final: 0.8577 (p) REVERT: A 140 MET cc_start: 0.8970 (mmm) cc_final: 0.8559 (mmt) REVERT: A 150 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8162 (mmtp) REVERT: A 215 LYS cc_start: 0.8023 (mttt) cc_final: 0.7495 (ttpt) REVERT: B 82 ARG cc_start: 0.8367 (tpt-90) cc_final: 0.8064 (ttm-80) REVERT: B 90 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8623 (tptt) REVERT: B 140 ASN cc_start: 0.8428 (m-40) cc_final: 0.8192 (m110) REVERT: B 169 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7552 (mtmm) REVERT: B 175 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7558 (mtp-110) REVERT: B 183 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7046 (tp30) REVERT: B 215 ARG cc_start: 0.8487 (ptt-90) cc_final: 0.8199 (ptt-90) REVERT: C 50 MET cc_start: 0.7449 (ptm) cc_final: 0.7191 (ppp) REVERT: C 180 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8380 (mt) REVERT: C 204 LYS cc_start: 0.8287 (tptm) cc_final: 0.7849 (tttm) REVERT: C 214 ASP cc_start: 0.7567 (m-30) cc_final: 0.7305 (m-30) REVERT: C 245 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8139 (ttt90) REVERT: C 263 GLN cc_start: 0.6609 (mt0) cc_final: 0.6370 (mm110) REVERT: D 54 GLN cc_start: 0.8237 (pt0) cc_final: 0.7520 (mm-40) REVERT: D 57 ARG cc_start: 0.5324 (ptt90) cc_final: 0.5034 (ptt-90) REVERT: D 141 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7733 (mmmt) REVERT: D 170 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: D 172 MET cc_start: 0.8700 (mtm) cc_final: 0.8475 (mtm) REVERT: D 180 MET cc_start: 0.8063 (mtm) cc_final: 0.7862 (mtm) REVERT: D 228 GLU cc_start: 0.6135 (tt0) cc_final: 0.5875 (tt0) REVERT: D 232 GLU cc_start: 0.6198 (tt0) cc_final: 0.5909 (tm-30) REVERT: E 233 MET cc_start: 0.6625 (mmt) cc_final: 0.6267 (mmt) REVERT: E 282 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7589 (p) REVERT: E 289 MET cc_start: 0.8005 (ptm) cc_final: 0.7610 (ptp) REVERT: E 313 GLU cc_start: 0.7798 (mp0) cc_final: 0.7438 (mp0) REVERT: E 339 MET cc_start: 0.6290 (mtm) cc_final: 0.6004 (mmm) REVERT: E 342 MET cc_start: 0.4016 (ttm) cc_final: 0.3366 (tmt) REVERT: F 304 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7773 (mtm-85) REVERT: G 33 ASN cc_start: 0.8436 (m-40) cc_final: 0.8203 (m-40) REVERT: G 43 LYS cc_start: 0.7690 (pttt) cc_final: 0.7454 (mmmt) REVERT: G 61 LYS cc_start: 0.7568 (mttt) cc_final: 0.7278 (mmtt) REVERT: G 180 ASP cc_start: 0.7818 (t0) cc_final: 0.7401 (t70) REVERT: H 137 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: H 139 LYS cc_start: 0.8554 (tppp) cc_final: 0.8288 (tptp) REVERT: I 61 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7793 (mmm-85) REVERT: I 78 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8365 (t) REVERT: I 82 GLU cc_start: 0.8379 (tp30) cc_final: 0.8101 (tt0) REVERT: I 120 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8121 (mm110) REVERT: I 179 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8509 (mt-10) REVERT: I 213 GLU cc_start: 0.8385 (tt0) cc_final: 0.8180 (mp0) REVERT: I 244 GLU cc_start: 0.8055 (mt-10) cc_final: 0.6760 (tm-30) REVERT: I 246 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: J 4 MET cc_start: 0.8701 (mmm) cc_final: 0.8403 (mmt) REVERT: J 12 MET cc_start: 0.8936 (tmm) cc_final: 0.8593 (tmm) REVERT: J 31 GLN cc_start: 0.8531 (mt0) cc_final: 0.8173 (mt0) REVERT: J 66 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8872 (mtpp) REVERT: J 75 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8944 (tmtm) REVERT: J 118 GLU cc_start: 0.8264 (tt0) cc_final: 0.7773 (mm-30) REVERT: J 171 MET cc_start: 0.8999 (tpp) cc_final: 0.8691 (tpp) REVERT: K 1 MET cc_start: 0.7240 (mmm) cc_final: 0.6859 (mmm) REVERT: K 50 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8092 (mp0) REVERT: K 76 HIS cc_start: 0.7391 (m-70) cc_final: 0.6709 (p-80) REVERT: K 116 GLU cc_start: 0.7327 (pm20) cc_final: 0.6987 (pp20) REVERT: K 125 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8443 (mm110) REVERT: K 180 ARG cc_start: 0.8581 (ttm110) cc_final: 0.8241 (ttp-170) REVERT: L 205 GLN cc_start: 0.7974 (pm20) cc_final: 0.7553 (pm20) REVERT: L 240 THR cc_start: 0.8050 (m) cc_final: 0.7841 (m) REVERT: L 244 LYS cc_start: 0.8140 (mttt) cc_final: 0.7842 (mmtp) REVERT: L 249 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7715 (mp0) REVERT: L 281 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8280 (mttp) REVERT: M 170 GLN cc_start: 0.8832 (tt0) cc_final: 0.8485 (tt0) REVERT: M 177 MET cc_start: 0.8706 (ptm) cc_final: 0.8474 (ptm) REVERT: M 201 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8061 (ttmm) REVERT: M 257 GLU cc_start: 0.8187 (pt0) cc_final: 0.7981 (pt0) REVERT: M 326 LYS cc_start: 0.7680 (pttp) cc_final: 0.7270 (ptmt) REVERT: M 331 GLN cc_start: 0.7877 (tt0) cc_final: 0.7443 (mt0) REVERT: M 332 GLU cc_start: 0.8362 (tt0) cc_final: 0.8057 (tt0) REVERT: N 39 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8647 (tpp80) REVERT: N 64 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7935 (tp30) REVERT: N 157 LEU cc_start: 0.8844 (mt) cc_final: 0.8640 (mp) REVERT: N 163 MET cc_start: 0.8675 (tpp) cc_final: 0.8387 (tpp) REVERT: N 195 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.8253 (mtp85) REVERT: N 203 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8336 (mm-30) REVERT: O 62 SER cc_start: 0.8872 (p) cc_final: 0.8579 (p) REVERT: O 140 MET cc_start: 0.8967 (mmm) cc_final: 0.8551 (mmt) REVERT: O 150 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8167 (mmtp) REVERT: O 215 LYS cc_start: 0.8024 (mttt) cc_final: 0.7484 (ttpt) REVERT: P 90 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8548 (mtmt) REVERT: P 140 ASN cc_start: 0.8418 (m-40) cc_final: 0.8175 (m110) REVERT: P 166 PRO cc_start: 0.8485 (Cg_exo) cc_final: 0.8274 (Cg_endo) REVERT: P 169 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7529 (mtmm) REVERT: P 175 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7091 (mmt180) REVERT: P 183 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7052 (tp30) REVERT: P 215 ARG cc_start: 0.8548 (ptt-90) cc_final: 0.8265 (ptt-90) REVERT: Q 50 MET cc_start: 0.7444 (ptm) cc_final: 0.7168 (ppp) REVERT: Q 180 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8373 (mt) REVERT: Q 204 LYS cc_start: 0.8280 (tptm) cc_final: 0.7846 (tttm) REVERT: Q 214 ASP cc_start: 0.7567 (m-30) cc_final: 0.7307 (m-30) REVERT: Q 245 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8139 (ttt90) REVERT: Q 263 GLN cc_start: 0.6645 (mt0) cc_final: 0.6338 (mm110) REVERT: R 54 GLN cc_start: 0.8238 (pt0) cc_final: 0.7520 (mm-40) REVERT: R 57 ARG cc_start: 0.5347 (ptt90) cc_final: 0.5052 (ptt-90) REVERT: R 170 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: R 172 MET cc_start: 0.8706 (mtm) cc_final: 0.8473 (mtm) REVERT: R 180 MET cc_start: 0.8082 (mtm) cc_final: 0.7880 (mtm) REVERT: R 228 GLU cc_start: 0.6152 (tt0) cc_final: 0.5894 (tt0) REVERT: R 232 GLU cc_start: 0.6201 (tt0) cc_final: 0.5936 (tm-30) REVERT: S 164 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7867 (mmm) REVERT: S 233 MET cc_start: 0.6617 (mmt) cc_final: 0.6262 (mmt) REVERT: S 248 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7100 (tt0) REVERT: S 282 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7584 (p) REVERT: S 289 MET cc_start: 0.8005 (ptm) cc_final: 0.7650 (ptp) REVERT: S 313 GLU cc_start: 0.7857 (mp0) cc_final: 0.7464 (mp0) REVERT: S 339 MET cc_start: 0.6297 (mtm) cc_final: 0.6019 (mmm) REVERT: S 342 MET cc_start: 0.3980 (ttm) cc_final: 0.3336 (tmt) REVERT: T 304 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7762 (mtm-85) REVERT: U 33 ASN cc_start: 0.8424 (m-40) cc_final: 0.8161 (m-40) REVERT: U 43 LYS cc_start: 0.7665 (pttt) cc_final: 0.7452 (mmmt) REVERT: U 61 LYS cc_start: 0.7570 (mttt) cc_final: 0.7288 (mmtt) REVERT: U 180 ASP cc_start: 0.7843 (t0) cc_final: 0.7408 (t70) REVERT: V 137 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: V 139 LYS cc_start: 0.8521 (tppp) cc_final: 0.8256 (tptp) REVERT: V 239 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8249 (mm-30) REVERT: W 61 ARG cc_start: 0.8052 (mmt180) cc_final: 0.7794 (mmm-85) REVERT: W 78 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8318 (t) REVERT: W 82 GLU cc_start: 0.8373 (tp30) cc_final: 0.8096 (tt0) REVERT: W 120 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8132 (mm110) REVERT: W 179 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8497 (mt-10) REVERT: W 213 GLU cc_start: 0.8390 (tt0) cc_final: 0.8185 (mp0) REVERT: W 244 GLU cc_start: 0.8055 (mt-10) cc_final: 0.6767 (tm-30) REVERT: W 246 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: X 12 MET cc_start: 0.8937 (tmm) cc_final: 0.8597 (tmm) REVERT: X 66 LYS cc_start: 0.9102 (mtpp) cc_final: 0.8868 (mtpp) REVERT: X 75 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8952 (tmtm) REVERT: X 118 GLU cc_start: 0.8259 (tt0) cc_final: 0.7773 (mm-30) REVERT: X 171 MET cc_start: 0.9003 (tpp) cc_final: 0.8694 (tpp) REVERT: Y 1 MET cc_start: 0.7222 (mmm) cc_final: 0.6851 (mmm) REVERT: Y 76 HIS cc_start: 0.7390 (m-70) cc_final: 0.6749 (p-80) REVERT: Y 111 ASP cc_start: 0.8617 (m-30) cc_final: 0.8404 (m-30) REVERT: Y 116 GLU cc_start: 0.7329 (pm20) cc_final: 0.6991 (pp20) REVERT: Y 180 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8242 (ttp-170) REVERT: Z 205 GLN cc_start: 0.7972 (pm20) cc_final: 0.7544 (pm20) REVERT: Z 240 THR cc_start: 0.8017 (m) cc_final: 0.7799 (m) REVERT: Z 244 LYS cc_start: 0.8182 (mttt) cc_final: 0.7880 (mmtp) REVERT: Z 249 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7727 (mp0) REVERT: a 170 GLN cc_start: 0.8758 (tt0) cc_final: 0.8490 (tt0) REVERT: a 177 MET cc_start: 0.8718 (ptm) cc_final: 0.8492 (ptm) REVERT: a 201 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8065 (ttmm) REVERT: a 257 GLU cc_start: 0.8178 (pt0) cc_final: 0.7970 (pt0) REVERT: a 326 LYS cc_start: 0.7686 (pttp) cc_final: 0.7282 (ptmt) REVERT: a 331 GLN cc_start: 0.7770 (mt0) cc_final: 0.7445 (mt0) REVERT: a 332 GLU cc_start: 0.8305 (tt0) cc_final: 0.8082 (tt0) REVERT: b 39 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8660 (tpp80) REVERT: b 64 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7941 (tp30) REVERT: b 157 LEU cc_start: 0.8879 (mt) cc_final: 0.8678 (mp) REVERT: b 163 MET cc_start: 0.8683 (tpp) cc_final: 0.8417 (tpp) REVERT: b 203 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8347 (mm-30) outliers start: 156 outliers final: 45 residues processed: 1107 average time/residue: 1.8947 time to fit residues: 2540.1496 Evaluate side-chains 895 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 826 time to evaluate : 5.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 246 ARG Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 164 MET Chi-restraints excluded: chain S residue 165 SER Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 278 GLN Chi-restraints excluded: chain S residue 282 THR Chi-restraints excluded: chain S residue 307 GLU Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 246 ARG Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 187 SER Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain Z residue 284 THR Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain b residue 39 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 0.9990 chunk 174 optimal weight: 0.2980 chunk 467 optimal weight: 9.9990 chunk 382 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 562 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 500 optimal weight: 4.9990 chunk 557 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 451 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN D 23 GLN D 223 GLN F 190 ASN F 206 ASN F 225 GLN F 311 GLN F 331 GLN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN I 166 GLN K 72 GLN L 291 GLN M 244 HIS M 280 ASN N 205 HIS O 228 ASN P 94 GLN R 23 GLN R 223 GLN T 190 ASN T 206 ASN T 225 GLN T 311 GLN V 211 GLN V 266 GLN W 166 GLN Y 72 GLN Z 291 GLN a 244 HIS a 280 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 49860 Z= 0.247 Angle : 0.582 7.595 67458 Z= 0.314 Chirality : 0.044 0.164 7516 Planarity : 0.004 0.045 8744 Dihedral : 6.454 59.926 7074 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Rotamer: Outliers : 2.84 % Allowed : 16.05 % Favored : 81.12 % 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: 0.69 (0.10), residues: 6256 helix: 1.48 (0.11), residues: 2334 sheet: 0.23 (0.12), residues: 1572 loop : -0.33 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP V 245 HIS 0.004 0.001 HIS L 261 PHE 0.017 0.002 PHE L 260 TYR 0.021 0.002 TYR W 119 ARG 0.005 0.001 ARG M 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 869 time to evaluate : 5.769 Fit side-chains REVERT: A 62 SER cc_start: 0.8905 (p) cc_final: 0.8515 (p) REVERT: A 140 MET cc_start: 0.8983 (mmm) cc_final: 0.8662 (mmt) REVERT: A 150 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8131 (mmtp) REVERT: A 215 LYS cc_start: 0.8026 (mttt) cc_final: 0.7650 (mmtt) REVERT: B 90 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8642 (tptt) REVERT: B 140 ASN cc_start: 0.8372 (m-40) cc_final: 0.8128 (m110) REVERT: B 163 THR cc_start: 0.8260 (p) cc_final: 0.8003 (m) REVERT: B 169 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7583 (mtmm) REVERT: B 183 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7332 (tp30) REVERT: B 202 THR cc_start: 0.7758 (p) cc_final: 0.7394 (p) REVERT: B 204 GLU cc_start: 0.7903 (mp0) cc_final: 0.7484 (mp0) REVERT: B 205 ASN cc_start: 0.8087 (p0) cc_final: 0.7174 (p0) REVERT: B 215 ARG cc_start: 0.8436 (ptt-90) cc_final: 0.8146 (ptt-90) REVERT: C 50 MET cc_start: 0.7417 (ptm) cc_final: 0.7101 (ppp) REVERT: C 61 MET cc_start: 0.8517 (mmm) cc_final: 0.8241 (mmm) REVERT: C 161 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: C 180 LEU cc_start: 0.8789 (mt) cc_final: 0.8448 (mt) REVERT: C 204 LYS cc_start: 0.8359 (tptm) cc_final: 0.7823 (tttm) REVERT: C 214 ASP cc_start: 0.7654 (m-30) cc_final: 0.7373 (m-30) REVERT: C 259 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6593 (mm-30) REVERT: C 266 GLU cc_start: 0.5749 (mt-10) cc_final: 0.5444 (mm-30) REVERT: D 54 GLN cc_start: 0.8050 (pt0) cc_final: 0.7512 (mm-40) REVERT: D 61 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7971 (tppt) REVERT: D 141 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7727 (mmmt) REVERT: D 210 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: D 228 GLU cc_start: 0.6272 (tt0) cc_final: 0.5950 (tt0) REVERT: D 232 GLU cc_start: 0.6264 (tt0) cc_final: 0.5987 (tm-30) REVERT: E 233 MET cc_start: 0.6555 (mmt) cc_final: 0.6207 (mmt) REVERT: E 278 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: E 282 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7620 (p) REVERT: E 289 MET cc_start: 0.7968 (ptm) cc_final: 0.7554 (ptp) REVERT: E 307 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.5001 (pt0) REVERT: E 313 GLU cc_start: 0.7857 (mp0) cc_final: 0.7549 (mp0) REVERT: E 327 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8029 (tp) REVERT: F 205 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7799 (tttm) REVERT: F 304 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7825 (mtm-85) REVERT: F 390 GLU cc_start: 0.3890 (OUTLIER) cc_final: 0.3495 (mm-30) REVERT: G 33 ASN cc_start: 0.8334 (m-40) cc_final: 0.8025 (m110) REVERT: G 43 LYS cc_start: 0.7891 (pttt) cc_final: 0.7685 (mttm) REVERT: G 61 LYS cc_start: 0.7673 (mttt) cc_final: 0.7325 (mmtt) REVERT: G 180 ASP cc_start: 0.7711 (t0) cc_final: 0.7284 (t70) REVERT: H 137 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8761 (m-80) REVERT: H 139 LYS cc_start: 0.8584 (tppp) cc_final: 0.8178 (ttpt) REVERT: H 201 MET cc_start: 0.8839 (mtm) cc_final: 0.8447 (mtm) REVERT: I 82 GLU cc_start: 0.8387 (tp30) cc_final: 0.8132 (tm-30) REVERT: I 120 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8049 (mm110) REVERT: I 244 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7091 (tm-30) REVERT: I 246 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7039 (ttm170) REVERT: J 12 MET cc_start: 0.8936 (tmm) cc_final: 0.8616 (tmm) REVERT: J 66 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8829 (mtpp) REVERT: J 75 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8968 (tmtm) REVERT: J 118 GLU cc_start: 0.8424 (tt0) cc_final: 0.8113 (tp30) REVERT: J 171 MET cc_start: 0.8967 (tpp) cc_final: 0.8646 (tpp) REVERT: K 1 MET cc_start: 0.7433 (mmm) cc_final: 0.6957 (mmm) REVERT: K 50 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7926 (mp0) REVERT: K 76 HIS cc_start: 0.7356 (m-70) cc_final: 0.6633 (p-80) REVERT: K 116 GLU cc_start: 0.7498 (pm20) cc_final: 0.7098 (pp20) REVERT: K 125 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8450 (mm110) REVERT: L 205 GLN cc_start: 0.8001 (pm20) cc_final: 0.7519 (pm20) REVERT: L 244 LYS cc_start: 0.8154 (mttt) cc_final: 0.7848 (mmtp) REVERT: L 249 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7858 (mp0) REVERT: L 281 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: M 201 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7992 (mtpt) REVERT: M 326 LYS cc_start: 0.7738 (pttp) cc_final: 0.7460 (ptmt) REVERT: M 331 GLN cc_start: 0.7893 (tt0) cc_final: 0.7510 (mt0) REVERT: M 332 GLU cc_start: 0.8378 (tt0) cc_final: 0.8130 (tt0) REVERT: N 39 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (tpp80) REVERT: N 64 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7998 (tp30) REVERT: N 71 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8249 (ptmm) REVERT: N 151 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7741 (mt-10) REVERT: O 62 SER cc_start: 0.8908 (p) cc_final: 0.8514 (p) REVERT: O 140 MET cc_start: 0.8980 (mmm) cc_final: 0.8648 (mmt) REVERT: O 150 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8152 (mmtp) REVERT: O 183 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8061 (tptp) REVERT: O 215 LYS cc_start: 0.7939 (mttt) cc_final: 0.7347 (ttpt) REVERT: P 90 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8474 (mtmt) REVERT: P 140 ASN cc_start: 0.8363 (m-40) cc_final: 0.8113 (m110) REVERT: P 169 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7551 (mtmm) REVERT: P 173 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7566 (tp30) REVERT: P 175 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7173 (mmt180) REVERT: P 183 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7282 (tp30) REVERT: P 204 GLU cc_start: 0.7888 (mp0) cc_final: 0.7451 (mp0) REVERT: P 205 ASN cc_start: 0.8076 (p0) cc_final: 0.7358 (p0) REVERT: P 215 ARG cc_start: 0.8456 (ptt-90) cc_final: 0.8160 (ptt-90) REVERT: Q 61 MET cc_start: 0.8515 (mmm) cc_final: 0.8241 (mmm) REVERT: Q 161 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: Q 204 LYS cc_start: 0.8350 (tptm) cc_final: 0.7819 (tttm) REVERT: Q 214 ASP cc_start: 0.7621 (m-30) cc_final: 0.7164 (m-30) REVERT: Q 266 GLU cc_start: 0.5848 (mt-10) cc_final: 0.5567 (mm-30) REVERT: R 54 GLN cc_start: 0.8037 (pt0) cc_final: 0.7498 (mm-40) REVERT: R 61 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7959 (tppt) REVERT: R 210 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8431 (mt0) REVERT: R 228 GLU cc_start: 0.6286 (tt0) cc_final: 0.5968 (tt0) REVERT: R 232 GLU cc_start: 0.6270 (tt0) cc_final: 0.6008 (tm-30) REVERT: S 144 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7765 (mt-10) REVERT: S 233 MET cc_start: 0.6548 (mmt) cc_final: 0.6203 (mmt) REVERT: S 278 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: S 282 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7619 (p) REVERT: S 289 MET cc_start: 0.7971 (ptm) cc_final: 0.7577 (ptp) REVERT: S 313 GLU cc_start: 0.7850 (mp0) cc_final: 0.7535 (mp0) REVERT: T 205 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7800 (tttm) REVERT: T 304 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7839 (mtm-85) REVERT: T 390 GLU cc_start: 0.3886 (OUTLIER) cc_final: 0.3498 (mm-30) REVERT: U 33 ASN cc_start: 0.8327 (m-40) cc_final: 0.8047 (m110) REVERT: U 43 LYS cc_start: 0.7881 (pttt) cc_final: 0.7675 (mttm) REVERT: U 61 LYS cc_start: 0.7675 (mttt) cc_final: 0.7335 (mmtt) REVERT: U 180 ASP cc_start: 0.7700 (t0) cc_final: 0.7444 (t70) REVERT: V 137 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8763 (m-80) REVERT: V 139 LYS cc_start: 0.8583 (tppp) cc_final: 0.8181 (ttpt) REVERT: V 201 MET cc_start: 0.8842 (mtm) cc_final: 0.8550 (mtm) REVERT: V 239 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8193 (mm-30) REVERT: W 82 GLU cc_start: 0.8383 (tp30) cc_final: 0.8130 (tm-30) REVERT: W 120 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8055 (mm110) REVERT: W 244 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7082 (tm-30) REVERT: W 246 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7051 (ttm170) REVERT: X 12 MET cc_start: 0.8940 (tmm) cc_final: 0.8617 (tmm) REVERT: X 66 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8796 (mtpp) REVERT: X 75 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8965 (tmtm) REVERT: X 118 GLU cc_start: 0.8419 (tt0) cc_final: 0.8112 (tp30) REVERT: X 171 MET cc_start: 0.8968 (tpp) cc_final: 0.8647 (tpp) REVERT: Y 1 MET cc_start: 0.7431 (mmm) cc_final: 0.6961 (mmm) REVERT: Y 76 HIS cc_start: 0.7370 (m-70) cc_final: 0.6646 (p-80) REVERT: Y 116 GLU cc_start: 0.7492 (pm20) cc_final: 0.7071 (pp20) REVERT: Z 205 GLN cc_start: 0.7998 (pm20) cc_final: 0.7507 (pm20) REVERT: Z 244 LYS cc_start: 0.8170 (mttt) cc_final: 0.7862 (mmtp) REVERT: Z 249 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7824 (mp0) REVERT: Z 281 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8405 (mttp) REVERT: a 201 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7992 (mtpt) REVERT: a 326 LYS cc_start: 0.7739 (pttp) cc_final: 0.7464 (ptmt) REVERT: a 331 GLN cc_start: 0.7691 (mt0) cc_final: 0.7471 (mt0) REVERT: a 332 GLU cc_start: 0.8335 (tt0) cc_final: 0.8123 (tt0) REVERT: b 39 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8617 (tpp80) REVERT: b 64 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8002 (tp30) REVERT: b 71 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8238 (ptmm) outliers start: 148 outliers final: 46 residues processed: 957 average time/residue: 1.8944 time to fit residues: 2199.1340 Evaluate side-chains 867 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 791 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 246 ARG Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 278 GLN Chi-restraints excluded: chain S residue 282 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain W residue 246 ARG Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 116 THR Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain b residue 39 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 0.9980 chunk 422 optimal weight: 5.9990 chunk 291 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 377 optimal weight: 0.8980 chunk 564 optimal weight: 2.9990 chunk 597 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 534 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 232 GLN D 23 GLN D 223 GLN E 255 GLN E 278 GLN F 190 ASN F 225 GLN F 311 GLN H 211 GLN H 266 GLN K 72 GLN L 192 HIS L 291 GLN M 244 HIS M 280 ASN N 89 HIS N 205 HIS O 228 ASN O 232 GLN R 23 GLN R 223 GLN S 255 GLN S 278 GLN T 190 ASN T 225 GLN T 311 GLN V 266 GLN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 192 HIS Z 291 GLN a 244 HIS a 280 ASN b 89 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 49860 Z= 0.176 Angle : 0.521 7.361 67458 Z= 0.280 Chirality : 0.042 0.156 7516 Planarity : 0.004 0.048 8744 Dihedral : 5.695 58.475 7048 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.48 % Rotamer: Outliers : 2.24 % Allowed : 16.74 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 6256 helix: 1.88 (0.11), residues: 2328 sheet: 0.25 (0.12), residues: 1584 loop : -0.11 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 154 HIS 0.004 0.001 HIS M 160 PHE 0.012 0.001 PHE U 15 TYR 0.018 0.001 TYR Y 128 ARG 0.004 0.000 ARG S 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 895 time to evaluate : 5.484 Fit side-chains REVERT: A 62 SER cc_start: 0.8907 (p) cc_final: 0.8516 (p) REVERT: A 140 MET cc_start: 0.8940 (mmm) cc_final: 0.8658 (mmt) REVERT: A 150 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8083 (mmtp) REVERT: A 215 LYS cc_start: 0.8011 (mttt) cc_final: 0.7471 (ttpt) REVERT: B 90 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8673 (tptt) REVERT: B 140 ASN cc_start: 0.8340 (m-40) cc_final: 0.8062 (m110) REVERT: B 169 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7497 (mtmm) REVERT: B 183 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7304 (tp30) REVERT: B 202 THR cc_start: 0.7712 (p) cc_final: 0.7349 (p) REVERT: B 204 GLU cc_start: 0.7871 (mp0) cc_final: 0.7462 (mp0) REVERT: B 205 ASN cc_start: 0.8001 (p0) cc_final: 0.7091 (p0) REVERT: C 187 GLU cc_start: 0.7760 (tt0) cc_final: 0.7464 (mp0) REVERT: C 189 MET cc_start: 0.7441 (mtp) cc_final: 0.6958 (ttm) REVERT: C 204 LYS cc_start: 0.8359 (tptm) cc_final: 0.7849 (tttm) REVERT: C 233 LEU cc_start: 0.7981 (mt) cc_final: 0.7719 (mm) REVERT: C 259 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6659 (mm-30) REVERT: C 266 GLU cc_start: 0.5767 (mt-10) cc_final: 0.5452 (mm-30) REVERT: D 54 GLN cc_start: 0.7924 (pt0) cc_final: 0.7465 (mm-40) REVERT: D 141 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7826 (mmmt) REVERT: D 192 SER cc_start: 0.8453 (m) cc_final: 0.8195 (p) REVERT: D 210 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: D 232 GLU cc_start: 0.6236 (tt0) cc_final: 0.5996 (tm-30) REVERT: E 144 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7719 (mt-10) REVERT: E 233 MET cc_start: 0.6566 (mmt) cc_final: 0.6208 (mmt) REVERT: E 265 TYR cc_start: 0.8424 (m-80) cc_final: 0.8076 (m-80) REVERT: E 282 THR cc_start: 0.7834 (m) cc_final: 0.7585 (p) REVERT: E 289 MET cc_start: 0.7895 (ptm) cc_final: 0.7514 (ptp) REVERT: E 313 GLU cc_start: 0.7796 (mp0) cc_final: 0.7516 (mp0) REVERT: F 205 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7717 (tttm) REVERT: F 304 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.7842 (mtm-85) REVERT: F 390 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.3592 (mm-30) REVERT: G 33 ASN cc_start: 0.8324 (m-40) cc_final: 0.8064 (m110) REVERT: G 43 LYS cc_start: 0.7883 (pttt) cc_final: 0.7652 (mmmt) REVERT: G 61 LYS cc_start: 0.7671 (mttt) cc_final: 0.7327 (mmtt) REVERT: G 143 ASP cc_start: 0.8141 (m-30) cc_final: 0.7920 (m-30) REVERT: G 180 ASP cc_start: 0.7713 (t0) cc_final: 0.7452 (t70) REVERT: H 137 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8763 (m-80) REVERT: H 139 LYS cc_start: 0.8551 (tppp) cc_final: 0.8178 (tttt) REVERT: I 82 GLU cc_start: 0.8360 (tp30) cc_final: 0.8132 (tm-30) REVERT: I 120 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8024 (mm110) REVERT: I 133 ASP cc_start: 0.8441 (p0) cc_final: 0.8126 (p0) REVERT: I 244 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7099 (tm-30) REVERT: J 12 MET cc_start: 0.8922 (tmm) cc_final: 0.8655 (tmm) REVERT: J 66 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8748 (mtpp) REVERT: J 118 GLU cc_start: 0.8409 (tt0) cc_final: 0.8123 (tp30) REVERT: J 171 MET cc_start: 0.8956 (tpp) cc_final: 0.8659 (tpp) REVERT: K 1 MET cc_start: 0.7356 (mmm) cc_final: 0.6852 (mmm) REVERT: K 50 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7930 (mp0) REVERT: K 76 HIS cc_start: 0.7355 (m-70) cc_final: 0.6732 (p-80) REVERT: K 180 ARG cc_start: 0.8367 (ttm110) cc_final: 0.8043 (ttp-110) REVERT: L 205 GLN cc_start: 0.7957 (pm20) cc_final: 0.7477 (pm20) REVERT: L 244 LYS cc_start: 0.8122 (mttt) cc_final: 0.7806 (mmtp) REVERT: L 249 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7836 (mp0) REVERT: L 281 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8357 (mttp) REVERT: M 201 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7983 (mtpt) REVERT: M 326 LYS cc_start: 0.7676 (pttp) cc_final: 0.7409 (ptmt) REVERT: N 1 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7112 (ptm) REVERT: N 39 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8547 (ttp-170) REVERT: N 64 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7803 (tp30) REVERT: N 71 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8406 (ptmm) REVERT: O 62 SER cc_start: 0.8925 (p) cc_final: 0.8556 (p) REVERT: O 140 MET cc_start: 0.8940 (mmm) cc_final: 0.8663 (mmt) REVERT: O 150 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8085 (mmtp) REVERT: O 215 LYS cc_start: 0.7978 (mttt) cc_final: 0.7568 (mptt) REVERT: P 90 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8434 (mtmt) REVERT: P 140 ASN cc_start: 0.8328 (m-40) cc_final: 0.8060 (m110) REVERT: P 169 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7571 (mtmm) REVERT: P 175 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7115 (mmt180) REVERT: P 183 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7332 (tp30) REVERT: P 204 GLU cc_start: 0.7818 (mp0) cc_final: 0.7420 (mp0) REVERT: P 205 ASN cc_start: 0.7961 (p0) cc_final: 0.7280 (p0) REVERT: P 215 ARG cc_start: 0.8406 (ptt-90) cc_final: 0.8157 (ptt-90) REVERT: Q 2 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.7112 (m) REVERT: Q 161 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: Q 187 GLU cc_start: 0.7762 (tt0) cc_final: 0.7443 (mp0) REVERT: Q 189 MET cc_start: 0.7423 (mtp) cc_final: 0.6925 (ttm) REVERT: Q 204 LYS cc_start: 0.8224 (tptm) cc_final: 0.7838 (ttmt) REVERT: Q 214 ASP cc_start: 0.7584 (m-30) cc_final: 0.7284 (m-30) REVERT: Q 233 LEU cc_start: 0.8060 (mt) cc_final: 0.7791 (mm) REVERT: Q 259 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6655 (mm-30) REVERT: Q 266 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5513 (mm-30) REVERT: R 54 GLN cc_start: 0.7891 (pt0) cc_final: 0.7435 (mm-40) REVERT: R 141 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7895 (mmtt) REVERT: R 192 SER cc_start: 0.8457 (m) cc_final: 0.8202 (p) REVERT: R 210 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: R 213 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: R 232 GLU cc_start: 0.6383 (tt0) cc_final: 0.6123 (tm-30) REVERT: S 144 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7720 (mt-10) REVERT: S 233 MET cc_start: 0.6556 (mmt) cc_final: 0.6201 (mmt) REVERT: S 282 THR cc_start: 0.7834 (m) cc_final: 0.7583 (p) REVERT: S 289 MET cc_start: 0.7906 (ptm) cc_final: 0.7496 (ptp) REVERT: S 313 GLU cc_start: 0.7783 (mp0) cc_final: 0.7493 (mp0) REVERT: T 205 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7707 (tttm) REVERT: T 304 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7856 (mtm-85) REVERT: T 390 GLU cc_start: 0.4133 (OUTLIER) cc_final: 0.3615 (mm-30) REVERT: U 33 ASN cc_start: 0.8293 (m-40) cc_final: 0.8019 (m110) REVERT: U 43 LYS cc_start: 0.7874 (pttt) cc_final: 0.7654 (mmmt) REVERT: U 61 LYS cc_start: 0.7626 (mttt) cc_final: 0.7291 (mmtt) REVERT: U 180 ASP cc_start: 0.7707 (t0) cc_final: 0.7439 (t70) REVERT: V 137 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8760 (m-80) REVERT: V 139 LYS cc_start: 0.8550 (tppp) cc_final: 0.8181 (tttt) REVERT: W 82 GLU cc_start: 0.8344 (tp30) cc_final: 0.8126 (tm-30) REVERT: W 120 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8014 (mm110) REVERT: W 244 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7100 (tm-30) REVERT: X 12 MET cc_start: 0.8921 (tmm) cc_final: 0.8654 (tmm) REVERT: X 66 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8744 (mtpp) REVERT: X 118 GLU cc_start: 0.8410 (tt0) cc_final: 0.8054 (tp30) REVERT: X 171 MET cc_start: 0.8959 (tpp) cc_final: 0.8661 (tpp) REVERT: Y 1 MET cc_start: 0.7355 (mmm) cc_final: 0.6848 (mmm) REVERT: Y 76 HIS cc_start: 0.7363 (m-70) cc_final: 0.6741 (p-80) REVERT: Y 111 ASP cc_start: 0.8667 (m-30) cc_final: 0.8462 (m-30) REVERT: Y 116 GLU cc_start: 0.7539 (pm20) cc_final: 0.7153 (pp20) REVERT: Y 180 ARG cc_start: 0.8358 (ttm110) cc_final: 0.8036 (ttp-110) REVERT: Z 205 GLN cc_start: 0.7953 (pm20) cc_final: 0.7469 (pm20) REVERT: Z 244 LYS cc_start: 0.8150 (mttt) cc_final: 0.7833 (mmtp) REVERT: Z 249 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7815 (mp0) REVERT: Z 281 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: a 201 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7972 (mtpt) REVERT: a 326 LYS cc_start: 0.7679 (pttp) cc_final: 0.7411 (ptmt) REVERT: a 331 GLN cc_start: 0.7653 (mt0) cc_final: 0.7429 (mt0) REVERT: b 1 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7103 (ptm) REVERT: b 39 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8547 (ttp-170) REVERT: b 64 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7848 (tp30) REVERT: b 71 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8393 (ptmm) outliers start: 117 outliers final: 49 residues processed: 971 average time/residue: 1.9010 time to fit residues: 2239.7637 Evaluate side-chains 888 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 819 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain S residue 107 GLU Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 379 ILE Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 116 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 202 ILE Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 39 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 444 optimal weight: 0.2980 chunk 246 optimal weight: 0.9990 chunk 509 optimal weight: 6.9990 chunk 412 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 536 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 93 GLN D 23 GLN D 164 HIS E 255 GLN E 328 HIS F 190 ASN F 225 GLN F 311 GLN H 246 ASN H 266 GLN K 72 GLN K 125 GLN L 192 HIS L 291 GLN M 280 ASN M 330 GLN O 232 GLN P 94 GLN R 23 GLN R 164 HIS S 255 GLN S 328 HIS T 190 ASN T 225 GLN T 311 GLN V 246 ASN V 266 GLN Y 72 GLN Z 192 HIS Z 291 GLN a 280 ASN a 330 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 49860 Z= 0.320 Angle : 0.597 8.805 67458 Z= 0.320 Chirality : 0.045 0.165 7516 Planarity : 0.005 0.047 8744 Dihedral : 5.908 57.471 7034 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 2.70 % Allowed : 17.06 % Favored : 80.23 % 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: 0.94 (0.10), residues: 6256 helix: 1.73 (0.11), residues: 2340 sheet: 0.18 (0.12), residues: 1602 loop : -0.07 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 245 HIS 0.006 0.001 HIS U 68 PHE 0.019 0.002 PHE L 260 TYR 0.022 0.002 TYR W 119 ARG 0.007 0.001 ARG M 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 790 time to evaluate : 5.323 Fit side-chains REVERT: A 56 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7492 (ptt90) REVERT: A 115 MET cc_start: 0.9081 (mmm) cc_final: 0.8881 (mmp) REVERT: A 150 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8136 (mmtt) REVERT: A 215 LYS cc_start: 0.7944 (mttt) cc_final: 0.7553 (mptt) REVERT: B 90 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8574 (mtmt) REVERT: B 140 ASN cc_start: 0.8250 (m-40) cc_final: 0.7934 (m110) REVERT: B 169 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7564 (mtmm) REVERT: B 173 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: B 183 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 197 PHE cc_start: 0.6264 (t80) cc_final: 0.5933 (t80) REVERT: B 202 THR cc_start: 0.7674 (p) cc_final: 0.7439 (p) REVERT: B 204 GLU cc_start: 0.7883 (mp0) cc_final: 0.7511 (mp0) REVERT: B 205 ASN cc_start: 0.8069 (p0) cc_final: 0.7698 (p0) REVERT: C 204 LYS cc_start: 0.8250 (tptm) cc_final: 0.7872 (ttmt) REVERT: C 259 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6576 (mm-30) REVERT: D 54 GLN cc_start: 0.7904 (pt0) cc_final: 0.7492 (mm-40) REVERT: D 210 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: E 144 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7571 (mt-10) REVERT: E 233 MET cc_start: 0.6753 (mmt) cc_final: 0.6421 (mmt) REVERT: E 282 THR cc_start: 0.7815 (m) cc_final: 0.7552 (p) REVERT: E 313 GLU cc_start: 0.7783 (mp0) cc_final: 0.7537 (mp0) REVERT: E 327 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8021 (tp) REVERT: F 205 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7783 (tttm) REVERT: F 390 GLU cc_start: 0.4209 (OUTLIER) cc_final: 0.3651 (mm-30) REVERT: G 43 LYS cc_start: 0.7787 (pttt) cc_final: 0.7571 (mmmt) REVERT: G 61 LYS cc_start: 0.7630 (mttt) cc_final: 0.7273 (mmtt) REVERT: G 180 ASP cc_start: 0.7743 (t0) cc_final: 0.7475 (t70) REVERT: G 204 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5123 (tm-30) REVERT: H 137 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: H 139 LYS cc_start: 0.8615 (tppp) cc_final: 0.8224 (ttpt) REVERT: I 82 GLU cc_start: 0.8408 (tp30) cc_final: 0.8150 (tm-30) REVERT: I 120 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8036 (mm110) REVERT: I 244 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7189 (tm-30) REVERT: J 12 MET cc_start: 0.8922 (tmm) cc_final: 0.8606 (tmm) REVERT: J 66 LYS cc_start: 0.9091 (mtpp) cc_final: 0.8819 (mtpp) REVERT: J 75 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8741 (tmtm) REVERT: J 118 GLU cc_start: 0.8448 (tt0) cc_final: 0.8080 (tp30) REVERT: J 171 MET cc_start: 0.8977 (tpp) cc_final: 0.8670 (tpp) REVERT: K 1 MET cc_start: 0.7421 (mmm) cc_final: 0.6616 (mmm) REVERT: K 50 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7963 (mp0) REVERT: K 76 HIS cc_start: 0.7352 (m-70) cc_final: 0.6616 (p-80) REVERT: K 116 GLU cc_start: 0.7548 (pm20) cc_final: 0.7206 (pp20) REVERT: K 180 ARG cc_start: 0.8375 (ttm110) cc_final: 0.7978 (ttp-110) REVERT: L 205 GLN cc_start: 0.7977 (pm20) cc_final: 0.7558 (pm20) REVERT: L 244 LYS cc_start: 0.8191 (mttt) cc_final: 0.7863 (mmtp) REVERT: L 249 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7831 (mp0) REVERT: L 281 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: M 152 ARG cc_start: 0.8407 (tpp80) cc_final: 0.8174 (tpp80) REVERT: M 201 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7997 (mtpt) REVERT: M 326 LYS cc_start: 0.7765 (pttp) cc_final: 0.7452 (ptmt) REVERT: M 331 GLN cc_start: 0.8040 (tt0) cc_final: 0.7634 (mt0) REVERT: N 64 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7915 (tp30) REVERT: N 71 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8296 (ptmm) REVERT: O 56 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7488 (ptt90) REVERT: O 115 MET cc_start: 0.9069 (mmm) cc_final: 0.8860 (mmp) REVERT: O 150 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8139 (mmtt) REVERT: O 215 LYS cc_start: 0.7923 (mttt) cc_final: 0.7523 (mptt) REVERT: O 248 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5297 (tp30) REVERT: P 90 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8539 (mtmt) REVERT: P 140 ASN cc_start: 0.8248 (m-40) cc_final: 0.7946 (m110) REVERT: P 163 THR cc_start: 0.8244 (p) cc_final: 0.7982 (m) REVERT: P 169 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7524 (mtmm) REVERT: P 173 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: P 175 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7335 (mmt180) REVERT: P 183 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7317 (tp30) REVERT: P 197 PHE cc_start: 0.6243 (t80) cc_final: 0.6005 (t80) REVERT: P 204 GLU cc_start: 0.7833 (mp0) cc_final: 0.7459 (mp0) REVERT: P 205 ASN cc_start: 0.8065 (p0) cc_final: 0.7313 (p0) REVERT: Q 204 LYS cc_start: 0.8259 (tptm) cc_final: 0.7880 (ttmt) REVERT: Q 210 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5869 (mppt) REVERT: Q 214 ASP cc_start: 0.7596 (m-30) cc_final: 0.7282 (m-30) REVERT: R 54 GLN cc_start: 0.7884 (pt0) cc_final: 0.7474 (mm-40) REVERT: R 210 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: R 213 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: R 231 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5271 (pttt) REVERT: S 144 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7601 (mt-10) REVERT: S 233 MET cc_start: 0.6747 (mmt) cc_final: 0.6397 (mmt) REVERT: S 282 THR cc_start: 0.7829 (m) cc_final: 0.7551 (p) REVERT: S 313 GLU cc_start: 0.7746 (mp0) cc_final: 0.7502 (mp0) REVERT: S 327 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8025 (tp) REVERT: T 205 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7777 (tttm) REVERT: T 390 GLU cc_start: 0.4216 (OUTLIER) cc_final: 0.3652 (mm-30) REVERT: U 43 LYS cc_start: 0.7836 (pttt) cc_final: 0.7594 (mmmt) REVERT: U 61 LYS cc_start: 0.7606 (mttt) cc_final: 0.7264 (mmtt) REVERT: U 180 ASP cc_start: 0.7729 (t0) cc_final: 0.7471 (t70) REVERT: U 204 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5079 (tm130) REVERT: V 137 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: V 139 LYS cc_start: 0.8611 (tppp) cc_final: 0.8222 (ttpt) REVERT: W 82 GLU cc_start: 0.8397 (tp30) cc_final: 0.8149 (tm-30) REVERT: W 120 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8040 (mm110) REVERT: W 244 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7147 (tm-30) REVERT: X 12 MET cc_start: 0.8923 (tmm) cc_final: 0.8607 (tmm) REVERT: X 66 LYS cc_start: 0.9080 (mtpp) cc_final: 0.8808 (mtpp) REVERT: X 75 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8744 (tmtm) REVERT: X 118 GLU cc_start: 0.8444 (tt0) cc_final: 0.8087 (tp30) REVERT: X 171 MET cc_start: 0.8984 (tpp) cc_final: 0.8679 (tpp) REVERT: Y 1 MET cc_start: 0.7405 (mmm) cc_final: 0.6605 (mmm) REVERT: Y 76 HIS cc_start: 0.7363 (m-70) cc_final: 0.6629 (p-80) REVERT: Y 180 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7975 (ttp-110) REVERT: Z 205 GLN cc_start: 0.7954 (pm20) cc_final: 0.7522 (pm20) REVERT: Z 242 TYR cc_start: 0.8551 (t80) cc_final: 0.8247 (t80) REVERT: Z 244 LYS cc_start: 0.8209 (mttt) cc_final: 0.7871 (mmtp) REVERT: Z 249 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7826 (mp0) REVERT: Z 281 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: a 326 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7452 (ptmt) REVERT: a 331 GLN cc_start: 0.7817 (mt0) cc_final: 0.7600 (mt0) REVERT: b 64 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7920 (tp30) REVERT: b 71 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8286 (ptmm) outliers start: 141 outliers final: 59 residues processed: 878 average time/residue: 1.9393 time to fit residues: 2060.9864 Evaluate side-chains 856 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 774 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 201 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain R residue 231 LYS Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 379 ILE Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 0.6980 chunk 537 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 350 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 597 optimal weight: 3.9990 chunk 496 optimal weight: 7.9990 chunk 276 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 313 optimal weight: 8.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN D 23 GLN E 328 HIS F 190 ASN F 225 GLN F 311 GLN H 266 GLN K 72 GLN L 192 HIS L 291 GLN M 280 ASN M 330 GLN ** O 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 223 GLN Q 186 HIS R 23 GLN S 328 HIS T 190 ASN T 225 GLN T 311 GLN T 331 GLN V 266 GLN Y 72 GLN ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 192 HIS Z 291 GLN a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 49860 Z= 0.160 Angle : 0.506 7.841 67458 Z= 0.271 Chirality : 0.042 0.152 7516 Planarity : 0.004 0.048 8744 Dihedral : 5.298 57.246 7018 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 17.98 % Favored : 80.00 % 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: 1.19 (0.10), residues: 6256 helix: 2.03 (0.11), residues: 2336 sheet: 0.24 (0.12), residues: 1576 loop : 0.02 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 154 HIS 0.003 0.001 HIS a 160 PHE 0.011 0.001 PHE J 20 TYR 0.019 0.001 TYR K 128 ARG 0.008 0.000 ARG a 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 855 time to evaluate : 5.593 Fit side-chains REVERT: A 215 LYS cc_start: 0.7930 (mttt) cc_final: 0.7563 (mptt) REVERT: A 248 GLU cc_start: 0.6399 (mt-10) cc_final: 0.5257 (tp30) REVERT: B 90 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8415 (tptt) REVERT: B 140 ASN cc_start: 0.8251 (m-40) cc_final: 0.7919 (m110) REVERT: B 169 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7477 (mtmm) REVERT: B 183 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7418 (tp30) REVERT: B 197 PHE cc_start: 0.6211 (t80) cc_final: 0.5953 (t80) REVERT: B 202 THR cc_start: 0.7694 (p) cc_final: 0.7443 (p) REVERT: B 204 GLU cc_start: 0.7871 (mp0) cc_final: 0.7506 (mp0) REVERT: B 205 ASN cc_start: 0.8010 (p0) cc_final: 0.7594 (p0) REVERT: C 187 GLU cc_start: 0.7734 (tt0) cc_final: 0.7419 (mp0) REVERT: C 204 LYS cc_start: 0.8227 (tptm) cc_final: 0.7802 (mttm) REVERT: C 233 LEU cc_start: 0.7856 (mt) cc_final: 0.7585 (mm) REVERT: D 54 GLN cc_start: 0.7789 (pt0) cc_final: 0.7449 (mm-40) REVERT: D 192 SER cc_start: 0.8550 (m) cc_final: 0.8268 (p) REVERT: D 210 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: D 231 LYS cc_start: 0.5866 (OUTLIER) cc_final: 0.5134 (pttt) REVERT: E 144 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7693 (mt-10) REVERT: E 233 MET cc_start: 0.6750 (mmt) cc_final: 0.6408 (mmt) REVERT: E 313 GLU cc_start: 0.7730 (mp0) cc_final: 0.7507 (mp0) REVERT: F 205 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7677 (tttm) REVERT: F 390 GLU cc_start: 0.4323 (OUTLIER) cc_final: 0.3785 (mm-30) REVERT: G 33 ASN cc_start: 0.8238 (m-40) cc_final: 0.7947 (m110) REVERT: G 61 LYS cc_start: 0.7607 (mttt) cc_final: 0.7287 (mmtt) REVERT: G 180 ASP cc_start: 0.7719 (t0) cc_final: 0.7470 (t70) REVERT: H 137 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8742 (m-80) REVERT: H 139 LYS cc_start: 0.8604 (tppp) cc_final: 0.8201 (ttpt) REVERT: I 82 GLU cc_start: 0.8376 (tp30) cc_final: 0.8142 (tm-30) REVERT: I 120 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8014 (mm110) REVERT: I 133 ASP cc_start: 0.8417 (p0) cc_final: 0.8125 (p0) REVERT: I 244 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7185 (tm-30) REVERT: J 12 MET cc_start: 0.8908 (tmm) cc_final: 0.8658 (tmm) REVERT: J 66 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8771 (mtpp) REVERT: J 75 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8931 (tmtm) REVERT: J 118 GLU cc_start: 0.8433 (tt0) cc_final: 0.8040 (tp30) REVERT: J 171 MET cc_start: 0.8949 (tpp) cc_final: 0.8686 (tpp) REVERT: K 1 MET cc_start: 0.7389 (mmm) cc_final: 0.6602 (mmm) REVERT: K 50 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7878 (mp0) REVERT: K 76 HIS cc_start: 0.7366 (m-70) cc_final: 0.6731 (p-80) REVERT: K 80 GLU cc_start: 0.8638 (mp0) cc_final: 0.8433 (mm-30) REVERT: K 98 GLU cc_start: 0.7905 (mp0) cc_final: 0.7643 (pm20) REVERT: K 116 GLU cc_start: 0.7623 (pm20) cc_final: 0.7198 (pp20) REVERT: K 180 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8041 (ttp-110) REVERT: L 138 ASP cc_start: 0.7726 (m-30) cc_final: 0.7377 (m-30) REVERT: L 205 GLN cc_start: 0.7949 (pm20) cc_final: 0.7451 (pm20) REVERT: L 244 LYS cc_start: 0.8110 (mttt) cc_final: 0.7772 (mmtp) REVERT: L 249 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7829 (mp0) REVERT: L 281 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8284 (mttp) REVERT: M 326 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7486 (ptmt) REVERT: M 331 GLN cc_start: 0.7817 (tt0) cc_final: 0.7528 (mt0) REVERT: N 1 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7060 (ptm) REVERT: N 64 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7828 (tp30) REVERT: N 71 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8411 (ptmm) REVERT: O 215 LYS cc_start: 0.7913 (mttt) cc_final: 0.7534 (mptt) REVERT: O 248 GLU cc_start: 0.6441 (mt-10) cc_final: 0.5257 (tp30) REVERT: P 61 GLN cc_start: 0.8449 (tt0) cc_final: 0.8246 (tt0) REVERT: P 90 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8399 (mtmt) REVERT: P 140 ASN cc_start: 0.8237 (m-40) cc_final: 0.7904 (m110) REVERT: P 169 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7565 (mtmm) REVERT: P 175 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7222 (mmt180) REVERT: P 183 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7446 (tp30) REVERT: P 197 PHE cc_start: 0.6211 (t80) cc_final: 0.5965 (t80) REVERT: P 204 GLU cc_start: 0.7833 (mp0) cc_final: 0.7440 (mp0) REVERT: P 205 ASN cc_start: 0.7979 (p0) cc_final: 0.7254 (p0) REVERT: Q 161 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: Q 187 GLU cc_start: 0.7755 (tt0) cc_final: 0.7455 (mp0) REVERT: Q 189 MET cc_start: 0.7393 (mtp) cc_final: 0.7190 (ttm) REVERT: Q 204 LYS cc_start: 0.8236 (tptm) cc_final: 0.7811 (mttm) REVERT: Q 210 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5775 (mppt) REVERT: Q 214 ASP cc_start: 0.7569 (m-30) cc_final: 0.7291 (m-30) REVERT: Q 233 LEU cc_start: 0.7840 (mt) cc_final: 0.7571 (mm) REVERT: R 54 GLN cc_start: 0.7778 (pt0) cc_final: 0.7448 (mm-40) REVERT: R 173 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7811 (mt-10) REVERT: R 192 SER cc_start: 0.8561 (m) cc_final: 0.8281 (p) REVERT: R 210 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: S 144 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7717 (mt-10) REVERT: S 233 MET cc_start: 0.6742 (mmt) cc_final: 0.6401 (mmt) REVERT: S 313 GLU cc_start: 0.7716 (mp0) cc_final: 0.7496 (mp0) REVERT: T 205 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7668 (tttm) REVERT: T 390 GLU cc_start: 0.4325 (OUTLIER) cc_final: 0.3782 (mm-30) REVERT: U 33 ASN cc_start: 0.8233 (m-40) cc_final: 0.7935 (m110) REVERT: U 61 LYS cc_start: 0.7603 (mttt) cc_final: 0.7293 (mmtt) REVERT: V 137 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: V 139 LYS cc_start: 0.8601 (tppp) cc_final: 0.8202 (ttpt) REVERT: W 82 GLU cc_start: 0.8366 (tp30) cc_final: 0.8141 (tm-30) REVERT: W 120 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8024 (mm110) REVERT: W 133 ASP cc_start: 0.8404 (p0) cc_final: 0.8104 (p0) REVERT: W 244 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7158 (tm-30) REVERT: X 12 MET cc_start: 0.8907 (tmm) cc_final: 0.8657 (tmm) REVERT: X 66 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8757 (mtpp) REVERT: X 75 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8936 (tmtm) REVERT: X 118 GLU cc_start: 0.8430 (tt0) cc_final: 0.8044 (tp30) REVERT: X 171 MET cc_start: 0.8955 (tpp) cc_final: 0.8696 (tpp) REVERT: Y 1 MET cc_start: 0.7393 (mmm) cc_final: 0.6607 (mmm) REVERT: Y 76 HIS cc_start: 0.7400 (m-70) cc_final: 0.6754 (p-80) REVERT: Y 116 GLU cc_start: 0.7597 (pm20) cc_final: 0.7180 (pp20) REVERT: Y 180 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8044 (ttp-110) REVERT: Z 138 ASP cc_start: 0.7730 (m-30) cc_final: 0.7374 (m-30) REVERT: Z 205 GLN cc_start: 0.7938 (pm20) cc_final: 0.7435 (pm20) REVERT: Z 244 LYS cc_start: 0.8113 (mttt) cc_final: 0.7771 (mmtp) REVERT: Z 249 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7847 (mp0) REVERT: Z 281 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8305 (mttp) REVERT: a 326 LYS cc_start: 0.7752 (pttp) cc_final: 0.7488 (ptmt) REVERT: b 1 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7072 (ptm) REVERT: b 64 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7831 (tp30) REVERT: b 71 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8391 (ptmm) outliers start: 105 outliers final: 50 residues processed: 920 average time/residue: 1.8525 time to fit residues: 2077.7794 Evaluate side-chains 859 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 793 time to evaluate : 5.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 210 ARG Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 436 optimal weight: 0.5980 chunk 338 optimal weight: 10.0000 chunk 503 optimal weight: 8.9990 chunk 333 optimal weight: 0.4980 chunk 595 optimal weight: 0.0770 chunk 372 optimal weight: 6.9990 chunk 363 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN C 186 HIS D 23 GLN D 164 HIS E 113 ASN E 255 GLN E 328 HIS F 190 ASN F 225 GLN F 311 GLN F 331 GLN H 266 GLN K 72 GLN L 192 HIS L 291 GLN M 280 ASN M 330 GLN P 94 GLN P 223 GLN Q 186 HIS R 23 GLN R 164 HIS S 113 ASN S 255 GLN S 328 HIS T 190 ASN T 225 GLN T 311 GLN V 266 GLN Y 72 GLN Z 192 HIS Z 291 GLN a 154 ASN a 280 ASN a 330 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 49860 Z= 0.223 Angle : 0.534 7.590 67458 Z= 0.286 Chirality : 0.043 0.156 7516 Planarity : 0.004 0.048 8744 Dihedral : 5.369 57.107 7006 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 2.13 % Allowed : 18.08 % Favored : 79.79 % 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: 1.16 (0.10), residues: 6256 helix: 1.99 (0.11), residues: 2344 sheet: 0.21 (0.12), residues: 1594 loop : 0.01 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 185 HIS 0.003 0.001 HIS Z 261 PHE 0.015 0.002 PHE L 260 TYR 0.021 0.001 TYR K 128 ARG 0.008 0.000 ARG M 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 793 time to evaluate : 5.615 Fit side-chains REVERT: A 215 LYS cc_start: 0.7912 (mttt) cc_final: 0.7545 (mptt) REVERT: A 248 GLU cc_start: 0.6467 (mt-10) cc_final: 0.5337 (tp30) REVERT: B 90 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8466 (mtmt) REVERT: B 140 ASN cc_start: 0.8203 (m-40) cc_final: 0.7892 (m110) REVERT: B 169 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7595 (mtmm) REVERT: B 183 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7340 (tp30) REVERT: B 197 PHE cc_start: 0.6298 (t80) cc_final: 0.5942 (t80) REVERT: B 202 THR cc_start: 0.7702 (p) cc_final: 0.7467 (p) REVERT: B 204 GLU cc_start: 0.7897 (mp0) cc_final: 0.7535 (mp0) REVERT: B 205 ASN cc_start: 0.8016 (p0) cc_final: 0.7606 (p0) REVERT: C 187 GLU cc_start: 0.7820 (tt0) cc_final: 0.7429 (mp0) REVERT: C 204 LYS cc_start: 0.8243 (tptm) cc_final: 0.7907 (tptt) REVERT: D 61 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7827 (mmtm) REVERT: D 210 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: D 231 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5079 (pttt) REVERT: E 144 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7639 (mt-10) REVERT: E 233 MET cc_start: 0.6793 (mmt) cc_final: 0.6448 (mmt) REVERT: E 257 ASP cc_start: 0.8103 (m-30) cc_final: 0.7812 (m-30) REVERT: E 313 GLU cc_start: 0.7691 (mp0) cc_final: 0.7475 (mp0) REVERT: E 327 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8021 (tp) REVERT: E 329 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: F 205 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7708 (tttm) REVERT: F 276 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8357 (ptt) REVERT: F 390 GLU cc_start: 0.4423 (OUTLIER) cc_final: 0.3907 (mm-30) REVERT: G 33 ASN cc_start: 0.8306 (m-40) cc_final: 0.8043 (m110) REVERT: G 61 LYS cc_start: 0.7621 (mttt) cc_final: 0.7282 (mmtt) REVERT: G 180 ASP cc_start: 0.7723 (t0) cc_final: 0.7444 (t70) REVERT: G 204 GLN cc_start: 0.6098 (OUTLIER) cc_final: 0.5180 (tm-30) REVERT: H 137 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: H 139 LYS cc_start: 0.8688 (tppp) cc_final: 0.8270 (ttpt) REVERT: I 82 GLU cc_start: 0.8388 (tp30) cc_final: 0.8158 (tm-30) REVERT: I 120 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8029 (mm110) REVERT: I 133 ASP cc_start: 0.8474 (p0) cc_final: 0.8188 (p0) REVERT: I 244 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7174 (tm-30) REVERT: J 12 MET cc_start: 0.8914 (tmm) cc_final: 0.8644 (tmm) REVERT: J 66 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8817 (mtpp) REVERT: J 75 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8716 (tmtm) REVERT: J 118 GLU cc_start: 0.8439 (tt0) cc_final: 0.8043 (tp30) REVERT: J 171 MET cc_start: 0.8950 (tpp) cc_final: 0.8666 (tpp) REVERT: K 1 MET cc_start: 0.7384 (mmm) cc_final: 0.6600 (mmm) REVERT: K 21 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8857 (tp) REVERT: K 50 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7940 (mp0) REVERT: K 76 HIS cc_start: 0.7408 (m-70) cc_final: 0.6746 (p-80) REVERT: K 98 GLU cc_start: 0.7941 (mp0) cc_final: 0.7674 (pm20) REVERT: K 116 GLU cc_start: 0.7588 (pm20) cc_final: 0.7155 (pp20) REVERT: K 180 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8054 (ttp-110) REVERT: L 138 ASP cc_start: 0.7746 (m-30) cc_final: 0.7391 (m-30) REVERT: L 205 GLN cc_start: 0.7938 (pm20) cc_final: 0.7422 (pm20) REVERT: L 244 LYS cc_start: 0.8123 (mttt) cc_final: 0.7779 (mmtp) REVERT: L 249 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7847 (mp0) REVERT: L 281 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8278 (mttp) REVERT: M 292 MET cc_start: 0.7708 (ttt) cc_final: 0.7501 (ttp) REVERT: M 326 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7518 (ptmt) REVERT: N 64 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7853 (tp30) REVERT: O 215 LYS cc_start: 0.7905 (mttt) cc_final: 0.7528 (mptt) REVERT: O 248 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5299 (tp30) REVERT: P 90 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8460 (mtmt) REVERT: P 140 ASN cc_start: 0.8222 (m-40) cc_final: 0.7903 (m110) REVERT: P 169 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7547 (mtmm) REVERT: P 175 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7275 (mmt180) REVERT: P 183 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7363 (tp30) REVERT: P 197 PHE cc_start: 0.6278 (t80) cc_final: 0.5892 (t80) REVERT: P 204 GLU cc_start: 0.7852 (mp0) cc_final: 0.7489 (mp0) REVERT: P 205 ASN cc_start: 0.8003 (p0) cc_final: 0.7579 (p0) REVERT: Q 187 GLU cc_start: 0.7792 (tt0) cc_final: 0.7458 (mp0) REVERT: Q 204 LYS cc_start: 0.8248 (tptm) cc_final: 0.7919 (tptt) REVERT: Q 210 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5728 (mppt) REVERT: Q 214 ASP cc_start: 0.7653 (m-30) cc_final: 0.7381 (m-30) REVERT: R 61 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7813 (tppt) REVERT: R 192 SER cc_start: 0.8595 (m) cc_final: 0.8302 (p) REVERT: R 210 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: S 144 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7681 (mt-10) REVERT: S 233 MET cc_start: 0.6784 (mmt) cc_final: 0.6436 (mmt) REVERT: S 327 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8020 (tp) REVERT: S 329 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8061 (mmm) REVERT: T 205 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7718 (tttm) REVERT: T 390 GLU cc_start: 0.4419 (OUTLIER) cc_final: 0.3905 (mm-30) REVERT: U 33 ASN cc_start: 0.8298 (m-40) cc_final: 0.7999 (m-40) REVERT: U 61 LYS cc_start: 0.7597 (mttt) cc_final: 0.7276 (mmtt) REVERT: V 137 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: V 139 LYS cc_start: 0.8687 (tppp) cc_final: 0.8272 (ttpt) REVERT: W 82 GLU cc_start: 0.8379 (tp30) cc_final: 0.8156 (tm-30) REVERT: W 120 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8037 (mm110) REVERT: W 133 ASP cc_start: 0.8531 (p0) cc_final: 0.8212 (p0) REVERT: W 244 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7169 (tm-30) REVERT: X 12 MET cc_start: 0.8917 (tmm) cc_final: 0.8646 (tmm) REVERT: X 66 LYS cc_start: 0.9080 (mtpp) cc_final: 0.8810 (mtpp) REVERT: X 75 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8720 (tmtm) REVERT: X 118 GLU cc_start: 0.8458 (tt0) cc_final: 0.8061 (tp30) REVERT: X 171 MET cc_start: 0.8956 (tpp) cc_final: 0.8677 (tpp) REVERT: Y 1 MET cc_start: 0.7383 (mmm) cc_final: 0.6596 (mmm) REVERT: Y 76 HIS cc_start: 0.7432 (m-70) cc_final: 0.6764 (p-80) REVERT: Y 116 GLU cc_start: 0.7580 (pm20) cc_final: 0.7145 (pp20) REVERT: Y 180 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8039 (ttp-110) REVERT: Z 138 ASP cc_start: 0.7749 (m-30) cc_final: 0.7390 (m-30) REVERT: Z 205 GLN cc_start: 0.7968 (pm20) cc_final: 0.7537 (pm20) REVERT: Z 244 LYS cc_start: 0.8168 (mttt) cc_final: 0.7807 (mmtp) REVERT: Z 249 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7830 (mp0) REVERT: Z 281 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8318 (mttp) REVERT: a 292 MET cc_start: 0.7645 (ttt) cc_final: 0.7436 (ttp) REVERT: a 326 LYS cc_start: 0.7775 (pttp) cc_final: 0.7526 (ptmt) REVERT: b 64 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7854 (tp30) outliers start: 111 outliers final: 59 residues processed: 866 average time/residue: 1.9294 time to fit residues: 2029.0831 Evaluate side-chains 850 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 771 time to evaluate : 5.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 210 ARG Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 235 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 378 optimal weight: 7.9990 chunk 405 optimal weight: 0.7980 chunk 294 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 468 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN D 164 HIS E 113 ASN E 328 HIS F 190 ASN F 225 GLN F 311 GLN F 331 GLN H 266 GLN K 72 GLN L 192 HIS L 291 GLN M 280 ASN M 303 ASN M 330 GLN P 94 GLN P 223 GLN Q 186 HIS R 23 GLN R 164 HIS S 113 ASN S 328 HIS T 190 ASN T 225 GLN T 331 GLN V 266 GLN Y 72 GLN Z 192 HIS Z 291 GLN a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 49860 Z= 0.288 Angle : 0.574 7.720 67458 Z= 0.307 Chirality : 0.044 0.160 7516 Planarity : 0.004 0.048 8744 Dihedral : 5.585 58.388 7006 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.11 % Rotamer: Outliers : 2.24 % Allowed : 17.81 % Favored : 79.95 % 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: 1.06 (0.10), residues: 6256 helix: 1.88 (0.11), residues: 2346 sheet: 0.13 (0.12), residues: 1598 loop : 0.03 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 185 HIS 0.005 0.001 HIS U 68 PHE 0.018 0.002 PHE Z 260 TYR 0.022 0.002 TYR Y 128 ARG 0.008 0.001 ARG M 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 757 time to evaluate : 5.558 Fit side-chains REVERT: A 215 LYS cc_start: 0.7879 (mttt) cc_final: 0.7511 (mptt) REVERT: A 248 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5345 (tp30) REVERT: B 90 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8502 (mtmt) REVERT: B 140 ASN cc_start: 0.8232 (m-40) cc_final: 0.7926 (m110) REVERT: B 169 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7634 (mtmm) REVERT: B 173 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: B 183 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7341 (tp30) REVERT: B 197 PHE cc_start: 0.6314 (t80) cc_final: 0.5952 (t80) REVERT: B 202 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7450 (p) REVERT: B 204 GLU cc_start: 0.7882 (mp0) cc_final: 0.7512 (mp0) REVERT: B 205 ASN cc_start: 0.8068 (p0) cc_final: 0.7626 (p0) REVERT: C 187 GLU cc_start: 0.7799 (tt0) cc_final: 0.7419 (mp0) REVERT: C 204 LYS cc_start: 0.8301 (tptm) cc_final: 0.7929 (ttmt) REVERT: D 61 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7890 (tppt) REVERT: D 210 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: D 231 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5052 (pttt) REVERT: E 144 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7650 (mt-10) REVERT: E 233 MET cc_start: 0.6615 (mmt) cc_final: 0.6298 (mmt) REVERT: E 313 GLU cc_start: 0.7686 (mp0) cc_final: 0.7479 (mp0) REVERT: E 327 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8045 (tp) REVERT: E 329 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8071 (mmm) REVERT: F 205 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7759 (tttm) REVERT: F 221 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6381 (mt) REVERT: F 276 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8460 (ptt) REVERT: F 390 GLU cc_start: 0.4430 (OUTLIER) cc_final: 0.3895 (mm-30) REVERT: G 61 LYS cc_start: 0.7726 (mttt) cc_final: 0.7359 (mmtt) REVERT: G 180 ASP cc_start: 0.7877 (t0) cc_final: 0.7581 (t70) REVERT: G 204 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5250 (tm130) REVERT: H 137 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: H 139 LYS cc_start: 0.8692 (tppp) cc_final: 0.8429 (ttmm) REVERT: I 82 GLU cc_start: 0.8415 (tp30) cc_final: 0.8177 (tm-30) REVERT: I 120 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8045 (mm110) REVERT: I 133 ASP cc_start: 0.8508 (p0) cc_final: 0.8224 (p0) REVERT: I 244 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7170 (tm-30) REVERT: J 12 MET cc_start: 0.8911 (tmm) cc_final: 0.8633 (tmm) REVERT: J 66 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8839 (mtpp) REVERT: J 75 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8718 (tmtm) REVERT: J 118 GLU cc_start: 0.8476 (tt0) cc_final: 0.8133 (tp30) REVERT: K 1 MET cc_start: 0.7296 (mmm) cc_final: 0.6549 (mmm) REVERT: K 50 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7964 (mp0) REVERT: K 76 HIS cc_start: 0.7331 (m-70) cc_final: 0.6671 (p-80) REVERT: K 80 GLU cc_start: 0.8729 (mp0) cc_final: 0.8501 (mm-30) REVERT: K 116 GLU cc_start: 0.7569 (pm20) cc_final: 0.7116 (pp20) REVERT: K 125 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: K 180 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7971 (ttp-110) REVERT: L 138 ASP cc_start: 0.7636 (m-30) cc_final: 0.7283 (m-30) REVERT: L 205 GLN cc_start: 0.7975 (pm20) cc_final: 0.7499 (pm20) REVERT: L 244 LYS cc_start: 0.8190 (mttt) cc_final: 0.7841 (mmtp) REVERT: L 249 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7839 (mp0) REVERT: L 281 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8298 (mttp) REVERT: M 292 MET cc_start: 0.7749 (ttt) cc_final: 0.7441 (ttp) REVERT: M 326 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7554 (ptmt) REVERT: N 64 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7909 (tp30) REVERT: N 71 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8310 (ptmm) REVERT: O 215 LYS cc_start: 0.7869 (mttt) cc_final: 0.7419 (mptt) REVERT: O 248 GLU cc_start: 0.6477 (mt-10) cc_final: 0.5333 (tp30) REVERT: P 90 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8505 (mtmt) REVERT: P 140 ASN cc_start: 0.8223 (m-40) cc_final: 0.7914 (m110) REVERT: P 169 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7640 (mtmm) REVERT: P 173 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: P 175 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7256 (mmt180) REVERT: P 183 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7466 (tp30) REVERT: P 197 PHE cc_start: 0.6256 (t80) cc_final: 0.5860 (t80) REVERT: P 204 GLU cc_start: 0.7831 (mp0) cc_final: 0.7488 (mp0) REVERT: P 205 ASN cc_start: 0.8056 (p0) cc_final: 0.7641 (p0) REVERT: Q 204 LYS cc_start: 0.8301 (tptm) cc_final: 0.7975 (tptt) REVERT: Q 210 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5803 (mppt) REVERT: Q 214 ASP cc_start: 0.7654 (m-30) cc_final: 0.7371 (m-30) REVERT: R 61 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7891 (tppt) REVERT: R 210 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: R 213 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7454 (pt0) REVERT: R 231 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5143 (pttt) REVERT: S 144 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7606 (mt-10) REVERT: S 233 MET cc_start: 0.6610 (mmt) cc_final: 0.6289 (mmt) REVERT: S 327 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8043 (tp) REVERT: S 329 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: T 205 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7755 (tttm) REVERT: T 390 GLU cc_start: 0.4437 (OUTLIER) cc_final: 0.3893 (mm-30) REVERT: U 33 ASN cc_start: 0.8323 (m-40) cc_final: 0.8042 (m110) REVERT: U 61 LYS cc_start: 0.7641 (mttt) cc_final: 0.7291 (mmtt) REVERT: U 204 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5255 (tm130) REVERT: V 137 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: V 139 LYS cc_start: 0.8691 (tppp) cc_final: 0.8428 (ttmm) REVERT: W 82 GLU cc_start: 0.8403 (tp30) cc_final: 0.8171 (tm-30) REVERT: W 120 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8044 (mm110) REVERT: W 133 ASP cc_start: 0.8565 (p0) cc_final: 0.8234 (p0) REVERT: W 244 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7169 (tm-30) REVERT: X 12 MET cc_start: 0.8913 (tmm) cc_final: 0.8632 (tmm) REVERT: X 66 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8810 (mtpp) REVERT: X 75 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8719 (tmtm) REVERT: X 118 GLU cc_start: 0.8473 (tt0) cc_final: 0.8133 (tp30) REVERT: Y 1 MET cc_start: 0.7283 (mmm) cc_final: 0.6526 (mmm) REVERT: Y 76 HIS cc_start: 0.7366 (m-70) cc_final: 0.6691 (p-80) REVERT: Y 116 GLU cc_start: 0.7559 (pm20) cc_final: 0.7111 (pp20) REVERT: Y 180 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7965 (ttp-110) REVERT: Z 138 ASP cc_start: 0.7644 (m-30) cc_final: 0.7290 (m-30) REVERT: Z 205 GLN cc_start: 0.7968 (pm20) cc_final: 0.7505 (pm20) REVERT: Z 244 LYS cc_start: 0.8201 (mttt) cc_final: 0.7854 (mmtp) REVERT: Z 249 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7806 (mp0) REVERT: Z 281 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8308 (mttp) REVERT: a 292 MET cc_start: 0.7674 (ttt) cc_final: 0.7369 (ttp) REVERT: a 326 LYS cc_start: 0.7779 (pttp) cc_final: 0.7498 (ptmt) REVERT: b 64 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7912 (tp30) REVERT: b 71 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8300 (ptmm) outliers start: 117 outliers final: 64 residues processed: 832 average time/residue: 1.9509 time to fit residues: 1990.9347 Evaluate side-chains 835 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 745 time to evaluate : 5.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 210 ARG Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 231 LYS Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 201 LYS Chi-restraints excluded: chain a residue 235 MET Chi-restraints excluded: chain a residue 331 GLN Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 4.9990 chunk 570 optimal weight: 0.8980 chunk 520 optimal weight: 4.9990 chunk 555 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 435 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 501 optimal weight: 5.9990 chunk 524 optimal weight: 1.9990 chunk 553 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN D 164 HIS E 113 ASN E 255 GLN E 328 HIS F 190 ASN F 225 GLN F 311 GLN H 266 GLN J 31 GLN K 72 GLN L 192 HIS L 291 GLN M 280 ASN M 303 ASN M 330 GLN P 223 GLN Q 186 HIS R 23 GLN R 164 HIS S 113 ASN S 255 GLN S 328 HIS T 190 ASN T 225 GLN V 266 GLN Y 72 GLN Y 125 GLN Z 192 HIS Z 291 GLN a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 49860 Z= 0.237 Angle : 0.546 7.584 67458 Z= 0.292 Chirality : 0.043 0.156 7516 Planarity : 0.004 0.048 8744 Dihedral : 5.460 57.767 7006 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 2.09 % Allowed : 18.06 % Favored : 79.85 % 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: 1.10 (0.10), residues: 6256 helix: 1.92 (0.11), residues: 2346 sheet: 0.16 (0.12), residues: 1590 loop : 0.02 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 185 HIS 0.004 0.001 HIS Z 261 PHE 0.016 0.002 PHE L 260 TYR 0.022 0.001 TYR K 128 ARG 0.007 0.001 ARG M 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 761 time to evaluate : 5.533 Fit side-chains REVERT: A 215 LYS cc_start: 0.7868 (mttt) cc_final: 0.7300 (ttpt) REVERT: A 248 GLU cc_start: 0.6484 (mt-10) cc_final: 0.5335 (tp30) REVERT: B 90 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8454 (mtmt) REVERT: B 140 ASN cc_start: 0.8223 (m-40) cc_final: 0.7884 (m110) REVERT: B 169 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7630 (mtmm) REVERT: B 183 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7361 (tp30) REVERT: B 197 PHE cc_start: 0.6196 (t80) cc_final: 0.5846 (t80) REVERT: B 202 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7463 (p) REVERT: B 204 GLU cc_start: 0.7896 (mp0) cc_final: 0.7534 (mp0) REVERT: B 205 ASN cc_start: 0.8048 (p0) cc_final: 0.7620 (p0) REVERT: C 187 GLU cc_start: 0.7893 (tt0) cc_final: 0.7464 (mp0) REVERT: C 204 LYS cc_start: 0.8275 (tptm) cc_final: 0.7916 (ttmt) REVERT: D 61 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7930 (tppt) REVERT: D 210 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: D 231 LYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5042 (pttt) REVERT: E 144 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7624 (mt-10) REVERT: E 233 MET cc_start: 0.6621 (mmt) cc_final: 0.6289 (mmt) REVERT: E 327 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8039 (tp) REVERT: E 329 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8069 (mmm) REVERT: F 205 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7748 (tttm) REVERT: F 276 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8442 (ptt) REVERT: F 390 GLU cc_start: 0.4525 (OUTLIER) cc_final: 0.3998 (mm-30) REVERT: G 33 ASN cc_start: 0.8322 (m-40) cc_final: 0.8065 (m110) REVERT: G 61 LYS cc_start: 0.7643 (mttt) cc_final: 0.7274 (mmtt) REVERT: G 180 ASP cc_start: 0.7875 (t0) cc_final: 0.7600 (t70) REVERT: G 204 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5234 (tm130) REVERT: H 137 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: H 139 LYS cc_start: 0.8729 (tppp) cc_final: 0.8305 (ttpt) REVERT: I 82 GLU cc_start: 0.8388 (tp30) cc_final: 0.8158 (tm-30) REVERT: I 120 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8036 (mm110) REVERT: I 133 ASP cc_start: 0.8496 (p0) cc_final: 0.8193 (p0) REVERT: I 244 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7169 (tm-30) REVERT: J 12 MET cc_start: 0.8905 (tmm) cc_final: 0.8615 (tmm) REVERT: J 66 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8823 (mtpp) REVERT: J 75 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8950 (tmtm) REVERT: J 118 GLU cc_start: 0.8463 (tt0) cc_final: 0.8044 (tp30) REVERT: K 1 MET cc_start: 0.7420 (mmm) cc_final: 0.6713 (mmm) REVERT: K 50 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7933 (mp0) REVERT: K 76 HIS cc_start: 0.7352 (m-70) cc_final: 0.6763 (p-80) REVERT: K 116 GLU cc_start: 0.7576 (pm20) cc_final: 0.7125 (pp20) REVERT: K 180 ARG cc_start: 0.8361 (ttm110) cc_final: 0.7969 (ttp-110) REVERT: L 138 ASP cc_start: 0.7609 (m-30) cc_final: 0.7278 (m-30) REVERT: L 205 GLN cc_start: 0.7930 (pm20) cc_final: 0.7401 (pm20) REVERT: L 244 LYS cc_start: 0.8164 (mttt) cc_final: 0.7786 (mmtp) REVERT: L 249 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7841 (mp0) REVERT: L 281 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: M 326 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7535 (ptmt) REVERT: N 64 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7850 (tp30) REVERT: N 71 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8332 (ptmm) REVERT: O 215 LYS cc_start: 0.7891 (mttt) cc_final: 0.7548 (mmtt) REVERT: O 248 GLU cc_start: 0.6480 (mt-10) cc_final: 0.5327 (tp30) REVERT: P 90 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8469 (mtmt) REVERT: P 140 ASN cc_start: 0.8228 (m-40) cc_final: 0.7871 (m110) REVERT: P 169 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7606 (mtmm) REVERT: P 175 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7199 (mmt180) REVERT: P 183 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7367 (tp30) REVERT: P 197 PHE cc_start: 0.6158 (t80) cc_final: 0.5775 (t80) REVERT: P 204 GLU cc_start: 0.7847 (mp0) cc_final: 0.7501 (mp0) REVERT: P 205 ASN cc_start: 0.8016 (p0) cc_final: 0.7650 (p0) REVERT: Q 187 GLU cc_start: 0.7878 (tt0) cc_final: 0.7465 (mp0) REVERT: Q 204 LYS cc_start: 0.8276 (tptm) cc_final: 0.7962 (tptt) REVERT: Q 210 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5706 (mppt) REVERT: Q 214 ASP cc_start: 0.7656 (m-30) cc_final: 0.7363 (m-30) REVERT: R 61 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7930 (tppt) REVERT: R 210 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: R 213 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7519 (pt0) REVERT: R 231 LYS cc_start: 0.5818 (OUTLIER) cc_final: 0.5083 (pttt) REVERT: S 144 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7625 (mt-10) REVERT: S 233 MET cc_start: 0.6597 (mmt) cc_final: 0.6284 (mmt) REVERT: S 257 ASP cc_start: 0.8133 (m-30) cc_final: 0.7835 (m-30) REVERT: S 327 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8029 (tp) REVERT: S 329 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8057 (mmm) REVERT: T 205 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7758 (tttm) REVERT: T 221 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6439 (mt) REVERT: T 390 GLU cc_start: 0.4519 (OUTLIER) cc_final: 0.3992 (mm-30) REVERT: U 33 ASN cc_start: 0.8311 (m-40) cc_final: 0.8047 (m110) REVERT: U 61 LYS cc_start: 0.7629 (mttt) cc_final: 0.7276 (mmtt) REVERT: U 204 GLN cc_start: 0.6109 (OUTLIER) cc_final: 0.5268 (tm130) REVERT: V 137 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8670 (m-80) REVERT: V 139 LYS cc_start: 0.8731 (tppp) cc_final: 0.8308 (ttpt) REVERT: W 82 GLU cc_start: 0.8382 (tp30) cc_final: 0.8157 (tm-30) REVERT: W 120 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8031 (mm110) REVERT: W 133 ASP cc_start: 0.8519 (p0) cc_final: 0.8203 (p0) REVERT: W 244 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7165 (tm-30) REVERT: X 12 MET cc_start: 0.8905 (tmm) cc_final: 0.8616 (tmm) REVERT: X 66 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8827 (mtpp) REVERT: X 75 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8945 (tmtm) REVERT: X 118 GLU cc_start: 0.8466 (tt0) cc_final: 0.8012 (tp30) REVERT: Y 1 MET cc_start: 0.7426 (mmm) cc_final: 0.6712 (mmm) REVERT: Y 76 HIS cc_start: 0.7411 (m-70) cc_final: 0.6742 (p-80) REVERT: Y 116 GLU cc_start: 0.7578 (pm20) cc_final: 0.7131 (pp20) REVERT: Y 180 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7989 (ttp-110) REVERT: Z 138 ASP cc_start: 0.7662 (m-30) cc_final: 0.7320 (m-30) REVERT: Z 205 GLN cc_start: 0.7922 (pm20) cc_final: 0.7419 (pm20) REVERT: Z 244 LYS cc_start: 0.8174 (mttt) cc_final: 0.7789 (mmtp) REVERT: Z 249 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7830 (mp0) REVERT: Z 281 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8322 (mttp) REVERT: a 292 MET cc_start: 0.7478 (ttt) cc_final: 0.7277 (ttp) REVERT: a 326 LYS cc_start: 0.7788 (pttp) cc_final: 0.7538 (ptmt) REVERT: b 64 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7853 (tp30) REVERT: b 71 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8321 (ptmm) outliers start: 109 outliers final: 67 residues processed: 827 average time/residue: 1.8182 time to fit residues: 1830.6059 Evaluate side-chains 827 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 737 time to evaluate : 5.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain L residue 291 GLN Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 210 ARG Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 231 LYS Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain Z residue 291 GLN Chi-restraints excluded: chain a residue 235 MET Chi-restraints excluded: chain a residue 331 GLN Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 5.9990 chunk 586 optimal weight: 9.9990 chunk 358 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 408 optimal weight: 7.9990 chunk 615 optimal weight: 0.0770 chunk 566 optimal weight: 0.9990 chunk 490 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN D 164 HIS E 113 ASN E 328 HIS F 190 ASN F 225 GLN F 311 GLN H 266 GLN J 31 GLN K 72 GLN L 192 HIS M 280 ASN M 330 GLN Q 186 HIS R 23 GLN R 164 HIS S 113 ASN S 328 HIS T 190 ASN T 225 GLN T 331 GLN V 266 GLN Y 72 GLN Z 192 HIS a 280 ASN a 303 ASN a 330 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 49860 Z= 0.223 Angle : 0.543 7.579 67458 Z= 0.290 Chirality : 0.043 0.156 7516 Planarity : 0.004 0.048 8744 Dihedral : 5.413 57.314 7006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.96 % Allowed : 18.35 % Favored : 79.70 % 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: 1.12 (0.10), residues: 6256 helix: 1.93 (0.11), residues: 2346 sheet: 0.15 (0.12), residues: 1592 loop : 0.06 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 185 HIS 0.003 0.001 HIS U 68 PHE 0.017 0.002 PHE T 389 TYR 0.023 0.001 TYR K 128 ARG 0.011 0.001 ARG M 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12512 Ramachandran restraints generated. 6256 Oldfield, 0 Emsley, 6256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 763 time to evaluate : 5.607 Fit side-chains REVERT: A 215 LYS cc_start: 0.7885 (mttt) cc_final: 0.7311 (ttpt) REVERT: A 248 GLU cc_start: 0.6484 (mt-10) cc_final: 0.5338 (tp30) REVERT: B 90 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8448 (mtmt) REVERT: B 140 ASN cc_start: 0.8233 (m-40) cc_final: 0.7878 (m110) REVERT: B 169 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7634 (mtmm) REVERT: B 183 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7355 (tp30) REVERT: B 197 PHE cc_start: 0.6103 (t80) cc_final: 0.5759 (t80) REVERT: B 202 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7470 (p) REVERT: B 204 GLU cc_start: 0.7895 (mp0) cc_final: 0.7526 (mp0) REVERT: B 205 ASN cc_start: 0.8038 (p0) cc_final: 0.7610 (p0) REVERT: C 187 GLU cc_start: 0.7896 (tt0) cc_final: 0.7460 (mp0) REVERT: C 204 LYS cc_start: 0.8265 (tptm) cc_final: 0.7910 (ttmt) REVERT: D 61 LYS cc_start: 0.8255 (mmmm) cc_final: 0.7929 (tppt) REVERT: D 210 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: D 231 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5048 (pttt) REVERT: E 144 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7620 (mt-10) REVERT: E 233 MET cc_start: 0.6647 (mmt) cc_final: 0.6352 (mmt) REVERT: E 257 ASP cc_start: 0.8112 (m-30) cc_final: 0.7828 (m-30) REVERT: E 304 GLN cc_start: 0.6913 (tt0) cc_final: 0.6482 (tm-30) REVERT: E 327 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8051 (tp) REVERT: E 329 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8073 (mmm) REVERT: F 205 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7757 (tttm) REVERT: F 221 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6432 (mt) REVERT: F 276 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8441 (ptt) REVERT: F 390 GLU cc_start: 0.4518 (OUTLIER) cc_final: 0.3986 (mm-30) REVERT: G 33 ASN cc_start: 0.8324 (m-40) cc_final: 0.8041 (m110) REVERT: G 61 LYS cc_start: 0.7631 (mttt) cc_final: 0.7280 (mmtt) REVERT: G 180 ASP cc_start: 0.7866 (t0) cc_final: 0.7580 (t70) REVERT: G 204 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5268 (tm-30) REVERT: H 137 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: H 139 LYS cc_start: 0.8730 (tppp) cc_final: 0.8308 (ttpt) REVERT: I 120 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8032 (mm110) REVERT: I 133 ASP cc_start: 0.8488 (p0) cc_final: 0.8183 (p0) REVERT: I 213 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: I 244 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7164 (tm-30) REVERT: J 12 MET cc_start: 0.8923 (tmm) cc_final: 0.8643 (tmm) REVERT: J 66 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8819 (mtpp) REVERT: J 75 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8945 (tmtm) REVERT: J 118 GLU cc_start: 0.8468 (tt0) cc_final: 0.8052 (tp30) REVERT: K 1 MET cc_start: 0.7418 (mmm) cc_final: 0.6712 (mmm) REVERT: K 50 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7908 (mp0) REVERT: K 76 HIS cc_start: 0.7352 (m-70) cc_final: 0.6754 (p-80) REVERT: K 116 GLU cc_start: 0.7573 (pm20) cc_final: 0.7122 (pp20) REVERT: K 180 ARG cc_start: 0.8358 (ttm110) cc_final: 0.7971 (ttp-110) REVERT: L 138 ASP cc_start: 0.7644 (m-30) cc_final: 0.7317 (m-30) REVERT: L 205 GLN cc_start: 0.7928 (pm20) cc_final: 0.7399 (pm20) REVERT: L 244 LYS cc_start: 0.8134 (mttt) cc_final: 0.7781 (mmtp) REVERT: L 249 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7843 (mp0) REVERT: L 281 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8277 (mttp) REVERT: M 326 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7526 (ptmt) REVERT: N 64 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7852 (tp30) REVERT: O 215 LYS cc_start: 0.7883 (mttt) cc_final: 0.7542 (mmtt) REVERT: O 248 GLU cc_start: 0.6478 (mt-10) cc_final: 0.5326 (tp30) REVERT: P 90 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8466 (mtmt) REVERT: P 140 ASN cc_start: 0.8210 (m-40) cc_final: 0.7849 (m110) REVERT: P 169 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7583 (mtmm) REVERT: P 175 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7203 (mmt180) REVERT: P 183 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7370 (tp30) REVERT: P 204 GLU cc_start: 0.7845 (mp0) cc_final: 0.7475 (mp0) REVERT: P 205 ASN cc_start: 0.8012 (p0) cc_final: 0.7310 (p0) REVERT: Q 187 GLU cc_start: 0.7896 (tt0) cc_final: 0.7471 (mp0) REVERT: Q 204 LYS cc_start: 0.8269 (tptm) cc_final: 0.7914 (ttmt) REVERT: Q 210 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5666 (mppt) REVERT: Q 214 ASP cc_start: 0.7672 (m-30) cc_final: 0.7391 (m-30) REVERT: R 61 LYS cc_start: 0.8258 (mmmm) cc_final: 0.7930 (tppt) REVERT: R 192 SER cc_start: 0.8619 (m) cc_final: 0.8306 (p) REVERT: R 210 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: R 213 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7533 (pt0) REVERT: R 231 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5075 (pttt) REVERT: S 144 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7652 (mt-10) REVERT: S 233 MET cc_start: 0.6644 (mmt) cc_final: 0.6344 (mmt) REVERT: S 257 ASP cc_start: 0.8125 (m-30) cc_final: 0.7828 (m-30) REVERT: S 304 GLN cc_start: 0.6917 (tt0) cc_final: 0.6489 (tm-30) REVERT: S 329 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8059 (mmm) REVERT: T 205 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7742 (tttm) REVERT: T 221 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6444 (mt) REVERT: T 376 THR cc_start: 0.8661 (m) cc_final: 0.8318 (p) REVERT: T 390 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.3986 (mm-30) REVERT: U 33 ASN cc_start: 0.8309 (m-40) cc_final: 0.8046 (m110) REVERT: U 61 LYS cc_start: 0.7645 (mttt) cc_final: 0.7313 (mmtt) REVERT: U 204 GLN cc_start: 0.6090 (OUTLIER) cc_final: 0.5262 (tm130) REVERT: V 137 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: V 139 LYS cc_start: 0.8730 (tppp) cc_final: 0.8311 (ttpt) REVERT: W 120 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8044 (mm110) REVERT: W 133 ASP cc_start: 0.8514 (p0) cc_final: 0.8200 (p0) REVERT: W 244 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7166 (tm-30) REVERT: X 12 MET cc_start: 0.8923 (tmm) cc_final: 0.8645 (tmm) REVERT: X 66 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8805 (mtpp) REVERT: X 75 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8947 (tmtm) REVERT: X 118 GLU cc_start: 0.8470 (tt0) cc_final: 0.8018 (tp30) REVERT: Y 1 MET cc_start: 0.7422 (mmm) cc_final: 0.6711 (mmm) REVERT: Y 76 HIS cc_start: 0.7410 (m-70) cc_final: 0.6744 (p-80) REVERT: Y 116 GLU cc_start: 0.7599 (pm20) cc_final: 0.7146 (pp20) REVERT: Y 180 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7994 (ttp-110) REVERT: Z 138 ASP cc_start: 0.7651 (m-30) cc_final: 0.7318 (m-30) REVERT: Z 205 GLN cc_start: 0.7921 (pm20) cc_final: 0.7417 (pm20) REVERT: Z 244 LYS cc_start: 0.8146 (mttt) cc_final: 0.7762 (mmtp) REVERT: Z 249 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7831 (mp0) REVERT: Z 281 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8321 (mttp) REVERT: a 326 LYS cc_start: 0.7769 (pttp) cc_final: 0.7522 (ptmt) REVERT: b 64 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7855 (tp30) outliers start: 102 outliers final: 65 residues processed: 825 average time/residue: 1.8768 time to fit residues: 1888.3809 Evaluate side-chains 834 residues out of total 5216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 745 time to evaluate : 5.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 210 ARG Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 231 LYS Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 329 MET Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 287 CYS Chi-restraints excluded: chain T residue 312 THR Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 390 GLU Chi-restraints excluded: chain U residue 204 GLN Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Z residue 130 VAL Chi-restraints excluded: chain Z residue 215 ASP Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 281 LYS Chi-restraints excluded: chain a residue 235 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 8.9990 chunk 522 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 452 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 491 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 504 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS D 23 GLN D 164 HIS E 113 ASN E 255 GLN E 328 HIS F 190 ASN F 225 GLN F 311 GLN H 266 GLN J 31 GLN K 72 GLN L 192 HIS L 291 GLN M 154 ASN M 280 ASN M 303 ASN M 330 GLN Q 186 HIS R 23 GLN R 164 HIS S 113 ASN S 255 GLN S 328 HIS T 190 ASN T 225 GLN V 266 GLN Y 72 GLN Z 192 HIS Z 291 GLN a 280 ASN a 330 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099378 restraints weight = 55260.632| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.28 r_work: 0.2924 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 49860 Z= 0.333 Angle : 0.602 8.470 67458 Z= 0.321 Chirality : 0.045 0.163 7516 Planarity : 0.005 0.059 8744 Dihedral : 5.696 59.791 7006 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.16 % Rotamer: Outliers : 2.11 % Allowed : 18.27 % Favored : 79.62 % 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: 0.97 (0.10), residues: 6256 helix: 1.77 (0.10), residues: 2342 sheet: 0.10 (0.12), residues: 1584 loop : 0.02 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 185 HIS 0.005 0.001 HIS U 68 PHE 0.026 0.002 PHE T 389 TYR 0.024 0.002 TYR Y 128 ARG 0.010 0.001 ARG a 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27693.13 seconds wall clock time: 482 minutes 33.63 seconds (28953.63 seconds total)