Starting phenix.real_space_refine on Sun Aug 9 07:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yjp_73030/08_2026/9yjp_73030.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yjp_73030/08_2026/9yjp_73030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yjp_73030/08_2026/9yjp_73030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yjp_73030/08_2026/9yjp_73030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yjp_73030/08_2026/9yjp_73030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yjp_73030/08_2026/9yjp_73030.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.196 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 8 5.49 5 Mg 4 5.21 5 S 189 5.16 5 C 20923 2.51 5 N 5658 2.21 5 O 6426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33211 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1495 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 1, 'TRANS': 184} Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1495 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 1, 'TRANS': 184} Chain: "G" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1274 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "I" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 643 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "J" Number of atoms: 6475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6475 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "K" Number of atoms: 6475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6475 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "L" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "M" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.64, per 1000 atoms: 0.20 Number of scatterers: 33211 At special positions: 0 Unit cell: (173.568, 127.464, 283.404, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 189 16.00 P 8 15.00 Mg 4 11.99 O 6426 8.00 N 5658 7.00 C 20923 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7792 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 38 sheets defined 57.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.018A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.761A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.536A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.893A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 4.483A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.713A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.720A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.996A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.614A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 4.198A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.804A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.789A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.591A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.520A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.839A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.767A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 128 removed outlier: 4.155A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.653A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.852A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.903A pdb=" N ARG C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.657A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.701A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.618A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.791A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.603A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.516A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.510A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.018A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.608A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.641A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.672A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.516A pdb=" N LEU D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.560A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.651A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.804A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.573A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.827A pdb=" N GLY D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 356 removed outlier: 3.804A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 370 removed outlier: 4.299A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing helix chain 'E' and resid 51 through 235 Proline residue: E 64 - end of helix removed outlier: 3.625A pdb=" N GLU E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 235 Proline residue: F 64 - end of helix removed outlier: 4.158A pdb=" N LYS F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.841A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 29 Processing helix chain 'G' and resid 37 through 47 removed outlier: 3.688A pdb=" N MET G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 63 Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 113 through 122 Processing helix chain 'G' and resid 129 through 141 Processing helix chain 'G' and resid 149 through 157 Processing helix chain 'H' and resid 43 through 77 Processing helix chain 'H' and resid 90 through 137 removed outlier: 3.828A pdb=" N LEU H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 159 removed outlier: 4.157A pdb=" N MET H 155 " --> pdb=" O SER H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 removed outlier: 3.643A pdb=" N ARG H 163 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA H 164 " --> pdb=" O GLY H 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 164' Processing helix chain 'I' and resid 199 through 213 removed outlier: 3.565A pdb=" N ARG I 213 " --> pdb=" O LEU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 269 Processing helix chain 'J' and resid 5 through 10 Processing helix chain 'J' and resid 11 through 17 Proline residue: J 14 - end of helix removed outlier: 4.036A pdb=" N ARG J 17 " --> pdb=" O PRO J 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 11 through 17' Processing helix chain 'J' and resid 19 through 27 Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'J' and resid 97 through 110 Processing helix chain 'J' and resid 135 through 143 removed outlier: 3.564A pdb=" N ARG J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 169 removed outlier: 3.802A pdb=" N ILE J 157 " --> pdb=" O HIS J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 183 Processing helix chain 'J' and resid 184 through 199 removed outlier: 3.628A pdb=" N ILE J 192 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 209 removed outlier: 3.610A pdb=" N GLU J 208 " --> pdb=" O SER J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 231 removed outlier: 3.634A pdb=" N GLN J 219 " --> pdb=" O THR J 215 " (cutoff:3.500A) Proline residue: J 225 - end of helix Processing helix chain 'J' and resid 270 through 274 removed outlier: 3.574A pdb=" N VAL J 273 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 291 removed outlier: 4.457A pdb=" N TYR J 287 " --> pdb=" O TYR J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 302 removed outlier: 3.914A pdb=" N LEU J 298 " --> pdb=" O LYS J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 315 removed outlier: 3.985A pdb=" N GLN J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 340 removed outlier: 4.184A pdb=" N LEU J 329 " --> pdb=" O ASP J 325 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET J 330 " --> pdb=" O ALA J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 355 Processing helix chain 'J' and resid 355 through 360 removed outlier: 4.119A pdb=" N PHE J 359 " --> pdb=" O ALA J 355 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 360 " --> pdb=" O ILE J 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 355 through 360' Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 391 through 401 Processing helix chain 'J' and resid 416 through 447 removed outlier: 3.730A pdb=" N THR J 445 " --> pdb=" O THR J 441 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR J 446 " --> pdb=" O ARG J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 504 removed outlier: 3.577A pdb=" N THR J 481 " --> pdb=" O CYS J 477 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN J 498 " --> pdb=" O PHE J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 526 removed outlier: 4.061A pdb=" N ALA J 519 " --> pdb=" O MET J 515 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS J 520 " --> pdb=" O ASP J 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU J 523 " --> pdb=" O ALA J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 removed outlier: 3.570A pdb=" N GLU J 537 " --> pdb=" O ILE J 533 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS J 538 " --> pdb=" O LEU J 534 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 544 through 557 Processing helix chain 'J' and resid 592 through 596 Processing helix chain 'J' and resid 602 through 612 removed outlier: 3.926A pdb=" N VAL J 606 " --> pdb=" O ASN J 602 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU J 608 " --> pdb=" O THR J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 623 removed outlier: 4.704A pdb=" N ASN J 623 " --> pdb=" O ASN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 663 removed outlier: 4.033A pdb=" N LEU J 650 " --> pdb=" O THR J 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 685 through 696 removed outlier: 3.794A pdb=" N VAL J 689 " --> pdb=" O ASP J 685 " (cutoff:3.500A) Processing helix chain 'J' and resid 697 through 708 removed outlier: 3.722A pdb=" N GLY J 701 " --> pdb=" O GLY J 697 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY J 708 " --> pdb=" O ILE J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 715 through 723 removed outlier: 3.910A pdb=" N ARG J 719 " --> pdb=" O TYR J 715 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN J 720 " --> pdb=" O GLY J 716 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 747 Processing helix chain 'J' and resid 752 through 754 No H-bonds generated for 'chain 'J' and resid 752 through 754' Processing helix chain 'J' and resid 768 through 808 removed outlier: 3.548A pdb=" N LEU J 772 " --> pdb=" O GLY J 768 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 17 Processing helix chain 'K' and resid 19 through 28 removed outlier: 3.512A pdb=" N ARG K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 removed outlier: 4.062A pdb=" N MET K 92 " --> pdb=" O ASP K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 111 removed outlier: 4.055A pdb=" N VAL K 101 " --> pdb=" O HIS K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 134 removed outlier: 3.876A pdb=" N TYR K 134 " --> pdb=" O LEU K 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 131 through 134' Processing helix chain 'K' and resid 135 through 142 Processing helix chain 'K' and resid 153 through 169 removed outlier: 3.688A pdb=" N ILE K 157 " --> pdb=" O HIS K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 200 removed outlier: 4.015A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE K 192 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN K 193 " --> pdb=" O LYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 222 removed outlier: 3.696A pdb=" N GLN K 219 " --> pdb=" O THR K 215 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE K 221 " --> pdb=" O GLU K 217 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN K 222 " --> pdb=" O ASP K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 229 Processing helix chain 'K' and resid 270 through 274 removed outlier: 3.509A pdb=" N VAL K 273 " --> pdb=" O LYS K 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE K 274 " --> pdb=" O SER K 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 270 through 274' Processing helix chain 'K' and resid 283 through 291 removed outlier: 4.287A pdb=" N TYR K 287 " --> pdb=" O TYR K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 302 removed outlier: 4.142A pdb=" N LEU K 298 " --> pdb=" O LYS K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 310 removed outlier: 3.900A pdb=" N ASP K 309 " --> pdb=" O ASN K 306 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR K 310 " --> pdb=" O PRO K 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 306 through 310' Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.563A pdb=" N GLU K 328 " --> pdb=" O ASP K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 360 removed outlier: 4.001A pdb=" N GLY K 360 " --> pdb=" O ILE K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 389 Processing helix chain 'K' and resid 391 through 401 Processing helix chain 'K' and resid 416 through 447 Processing helix chain 'K' and resid 472 through 505 removed outlier: 3.596A pdb=" N LEU K 476 " --> pdb=" O SER K 472 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR K 481 " --> pdb=" O CYS K 477 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN K 482 " --> pdb=" O ILE K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 526 removed outlier: 3.928A pdb=" N ALA K 519 " --> pdb=" O MET K 515 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N CYS K 520 " --> pdb=" O ASP K 516 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE K 521 " --> pdb=" O LEU K 517 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU K 523 " --> pdb=" O ALA K 519 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE K 524 " --> pdb=" O CYS K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 538 Processing helix chain 'K' and resid 544 through 555 Processing helix chain 'K' and resid 592 through 598 removed outlier: 3.932A pdb=" N LYS K 596 " --> pdb=" O GLY K 592 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN K 597 " --> pdb=" O TRP K 593 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS K 598 " --> pdb=" O LEU K 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 592 through 598' Processing helix chain 'K' and resid 602 through 611 removed outlier: 3.520A pdb=" N VAL K 606 " --> pdb=" O ASN K 602 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU K 608 " --> pdb=" O THR K 604 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR K 609 " --> pdb=" O VAL K 605 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS K 610 " --> pdb=" O VAL K 606 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 621 removed outlier: 4.109A pdb=" N PHE K 621 " --> pdb=" O LEU K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 646 through 663 removed outlier: 3.572A pdb=" N LEU K 650 " --> pdb=" O THR K 646 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU K 653 " --> pdb=" O ALA K 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 685 through 697 Processing helix chain 'K' and resid 697 through 708 removed outlier: 3.738A pdb=" N GLY K 701 " --> pdb=" O GLY K 697 " (cutoff:3.500A) Processing helix chain 'K' and resid 715 through 722 removed outlier: 3.604A pdb=" N ARG K 719 " --> pdb=" O TYR K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 747 Processing helix chain 'K' and resid 770 through 806 Processing helix chain 'L' and resid 48 through 61 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 91 through 96 Processing helix chain 'L' and resid 101 through 108 removed outlier: 3.644A pdb=" N LYS L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 124 Proline residue: L 117 - end of helix Processing helix chain 'L' and resid 130 through 140 removed outlier: 3.699A pdb=" N VAL L 140 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 160 removed outlier: 3.764A pdb=" N ARG L 155 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS L 156 " --> pdb=" O ALA L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 175 removed outlier: 3.639A pdb=" N VAL L 170 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 195 removed outlier: 3.945A pdb=" N PHE L 189 " --> pdb=" O ASN L 185 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 55 removed outlier: 3.774A pdb=" N ILE M 52 " --> pdb=" O THR M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.595A pdb=" N MET M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 82 Processing helix chain 'M' and resid 91 through 95 removed outlier: 3.531A pdb=" N ARG M 95 " --> pdb=" O GLU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 120 Proline residue: M 117 - end of helix removed outlier: 3.533A pdb=" N GLN M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'M' and resid 151 through 161 Processing helix chain 'M' and resid 167 through 172 removed outlier: 4.103A pdb=" N LYS M 172 " --> pdb=" O ASP M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 194 removed outlier: 3.693A pdb=" N LYS M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.522A pdb=" N ILE A 357 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.660A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.882A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.521A pdb=" N ASP B 11 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.757A pdb=" N GLY B 36 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.738A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.758A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.447A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.432A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.563A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.700A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.740A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.562A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.564A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 66 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.629A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 242 removed outlier: 7.072A pdb=" N LYS D 238 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR D 249 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR D 240 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL D 247 " --> pdb=" O TYR D 240 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 242 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 67 through 72 removed outlier: 3.534A pdb=" N LYS J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG J 54 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR J 60 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 115 through 118 removed outlier: 3.640A pdb=" N SER J 118 " --> pdb=" O PHE J 121 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS J 122 " --> pdb=" O ARG J 671 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE J 673 " --> pdb=" O CYS J 122 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR J 124 " --> pdb=" O ILE J 673 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS J 672 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN J 172 " --> pdb=" O GLY J 458 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU J 460 " --> pdb=" O GLN J 172 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE J 174 " --> pdb=" O LEU J 460 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER J 260 " --> pdb=" O HIS J 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 232 through 233 Processing sheet with id=AC8, first strand: chain 'J' and resid 364 through 366 Processing sheet with id=AC9, first strand: chain 'J' and resid 403 through 406 Processing sheet with id=AD1, first strand: chain 'J' and resid 563 through 564 removed outlier: 3.995A pdb=" N PHE J 577 " --> pdb=" O TYR J 588 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 711 through 714 removed outlier: 3.513A pdb=" N ILE J 713 " --> pdb=" O VAL J 763 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 67 through 71 removed outlier: 4.051A pdb=" N VAL K 59 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 115 through 118 removed outlier: 5.892A pdb=" N CYS K 122 " --> pdb=" O ARG K 671 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE K 673 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR K 124 " --> pdb=" O ILE K 673 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AD6, first strand: chain 'K' and resid 364 through 366 Processing sheet with id=AD7, first strand: chain 'K' and resid 403 through 406 Processing sheet with id=AD8, first strand: chain 'K' and resid 563 through 564 removed outlier: 3.716A pdb=" N PHE K 577 " --> pdb=" O TYR K 588 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 711 through 714 Processing sheet with id=AE1, first strand: chain 'L' and resid 72 through 73 removed outlier: 4.094A pdb=" N ILE L 72 " --> pdb=" O MET L 110 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 149 through 150 1755 hydrogen bonds defined for protein. 4950 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: 6.74 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 5800 1.30 - 1.43: 8261 1.43 - 1.57: 19385 1.57 - 1.70: 31 1.70 - 1.83: 330 Bond restraints: 33807 Sorted by residual: bond pdb=" C THR C 6 " pdb=" O THR C 6 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.26e-02 6.30e+03 3.17e+01 bond pdb=" CE1 HIS C 101 " pdb=" NE2 HIS C 101 " ideal model delta sigma weight residual 1.321 1.364 -0.043 1.00e-02 1.00e+04 1.82e+01 bond pdb=" CE1 HIS C 73 " pdb=" NE2 HIS C 73 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" CE1 HIS C 87 " pdb=" NE2 HIS C 87 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.70e+01 bond pdb=" CE1 HIS C 275 " pdb=" NE2 HIS C 275 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+01 ... (remaining 33802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 44399 2.81 - 5.63: 1071 5.63 - 8.44: 81 8.44 - 11.26: 5 11.26 - 14.07: 4 Bond angle restraints: 45560 Sorted by residual: angle pdb=" C ALA H 152 " pdb=" N ASP H 153 " pdb=" CA ASP H 153 " ideal model delta sigma weight residual 120.28 133.92 -13.64 1.44e+00 4.82e-01 8.97e+01 angle pdb=" CA PRO C 332 " pdb=" C PRO C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 118.06 125.49 -7.43 8.30e-01 1.45e+00 8.02e+01 angle pdb=" C ASP A 1 " pdb=" N ASP A 2 " pdb=" CA ASP A 2 " ideal model delta sigma weight residual 121.70 135.77 -14.07 1.80e+00 3.09e-01 6.11e+01 angle pdb=" CA ASN C 12 " pdb=" CB ASN C 12 " pdb=" CG ASN C 12 " ideal model delta sigma weight residual 112.60 105.04 7.56 1.00e+00 1.00e+00 5.72e+01 angle pdb=" C GLY L 182 " pdb=" N CYS L 183 " pdb=" CA CYS L 183 " ideal model delta sigma weight residual 121.70 134.36 -12.66 1.80e+00 3.09e-01 4.94e+01 ... (remaining 45555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 18858 17.69 - 35.38: 1413 35.38 - 53.08: 330 53.08 - 70.77: 97 70.77 - 88.46: 33 Dihedral angle restraints: 20731 sinusoidal: 8648 harmonic: 12083 Sorted by residual: dihedral pdb=" N THR C 6 " pdb=" C THR C 6 " pdb=" CA THR C 6 " pdb=" CB THR C 6 " ideal model delta harmonic sigma weight residual 123.40 137.65 -14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" C THR C 6 " pdb=" N THR C 6 " pdb=" CA THR C 6 " pdb=" CB THR C 6 " ideal model delta harmonic sigma weight residual -122.00 -136.17 14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CA LYS H 141 " pdb=" C LYS H 141 " pdb=" N ARG H 142 " pdb=" CA ARG H 142 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 20728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4642 0.098 - 0.196: 304 0.196 - 0.295: 28 0.295 - 0.393: 8 0.393 - 0.491: 2 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CA THR C 6 " pdb=" N THR C 6 " pdb=" C THR C 6 " pdb=" CB THR C 6 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA GLN C 246 " pdb=" N GLN C 246 " pdb=" C GLN C 246 " pdb=" CB GLN C 246 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA ARG H 112 " pdb=" N ARG H 112 " pdb=" C ARG H 112 " pdb=" CB ARG H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 4981 not shown) Planarity restraints: 5928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 69 " -0.150 2.00e-02 2.50e+03 9.44e-02 1.78e+02 pdb=" CG TYR C 69 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 69 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR C 69 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR C 69 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR C 69 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR C 69 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR C 69 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 240 " 0.105 2.00e-02 2.50e+03 6.32e-02 8.00e+01 pdb=" CG TYR C 240 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 240 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR C 240 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR C 240 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR C 240 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR C 240 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 240 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 166 " 0.057 2.00e-02 2.50e+03 5.05e-02 5.09e+01 pdb=" CG TYR C 166 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 166 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 166 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 166 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR C 166 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR C 166 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 166 " 0.092 2.00e-02 2.50e+03 ... (remaining 5925 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 15 2.00 - 2.73: 1823 2.73 - 3.45: 48125 3.45 - 4.18: 73920 4.18 - 4.90: 133840 Nonbonded interactions: 257723 Sorted by model distance: nonbonded pdb=" OD1 ASN G 143 " pdb="CA CA G 202 " model vdw 1.280 2.510 nonbonded pdb=" C LYS H 165 " pdb=" NZ LYS H 165 " model vdw 1.317 3.350 nonbonded pdb=" NH2 ARG K 567 " pdb=" OG1 THR K 585 " model vdw 1.553 3.120 nonbonded pdb=" O THR G 71 " pdb="CA CA G 201 " model vdw 1.659 2.510 nonbonded pdb=" OE1 GLN K 564 " pdb=" NH1 ARG K 567 " model vdw 1.827 3.120 ... (remaining 257718 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.050 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.007 0.071 33808 Z= 0.392 Angle : 0.941 14.075 45560 Z= 0.597 Chirality : 0.055 0.491 4984 Planarity : 0.007 0.122 5928 Dihedral : 14.198 88.460 12939 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.33 % Favored : 95.52 % Rotamer: Outliers : 4.31 % Allowed : 7.90 % Favored : 87.79 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4130 helix: 1.04 (0.11), residues: 2033 sheet: -0.22 (0.25), residues: 393 loop : -0.87 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG C 183 TYR 0.169 0.004 TYR C 69 PHE 0.052 0.003 PHE H 140 TRP 0.048 0.003 TRP C 340 HIS 0.007 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.39 (33807) covalent geometry : angle 0.94075 / 0.60 (45560) hydrogen bonds : bond 0.15542 / 10.54 ( 1747) hydrogen bonds : angle 5.96936 / 4.27 ( 4950) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1340 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.9305 (mt) cc_final: 0.8959 (mt) REVERT: A 115 ASN cc_start: 0.8190 (t0) cc_final: 0.7323 (t0) REVERT: A 151 ILE cc_start: 0.9492 (tt) cc_final: 0.9282 (tt) REVERT: A 154 ASP cc_start: 0.6795 (t70) cc_final: 0.6434 (t70) REVERT: A 161 HIS cc_start: 0.7729 (p-80) cc_final: 0.6892 (p-80) REVERT: A 184 ASP cc_start: 0.8191 (m-30) cc_final: 0.7561 (m-30) REVERT: A 186 THR cc_start: 0.8423 (m) cc_final: 0.7703 (p) REVERT: A 190 MET cc_start: 0.8199 (ttt) cc_final: 0.7972 (ttt) REVERT: A 208 ILE cc_start: 0.9342 (mt) cc_final: 0.9127 (mp) REVERT: A 248 ILE cc_start: 0.9153 (pt) cc_final: 0.8903 (pt) REVERT: A 260 THR cc_start: 0.9144 (m) cc_final: 0.8811 (t) REVERT: A 288 ASP cc_start: 0.8496 (m-30) cc_final: 0.7999 (m-30) REVERT: A 304 THR cc_start: 0.9118 (p) cc_final: 0.8762 (t) REVERT: A 340 TRP cc_start: 0.8879 (t60) cc_final: 0.8231 (t60) REVERT: A 356 TRP cc_start: 0.8407 (m100) cc_final: 0.7240 (m100) REVERT: A 369 ILE cc_start: 0.8818 (tp) cc_final: 0.8528 (tp) REVERT: A 375 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: B 16 LEU cc_start: 0.8625 (mp) cc_final: 0.8397 (mt) REVERT: B 61 LYS cc_start: 0.9321 (mttt) cc_final: 0.9035 (mmtt) REVERT: B 78 ASN cc_start: 0.7743 (t0) cc_final: 0.7247 (m110) REVERT: B 119 MET cc_start: 0.8614 (ttm) cc_final: 0.8401 (ttm) REVERT: B 140 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8534 (mt) REVERT: B 210 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7777 (ttp80) REVERT: B 296 ASN cc_start: 0.7920 (m-40) cc_final: 0.7634 (m110) REVERT: B 300 SER cc_start: 0.9091 (t) cc_final: 0.8858 (p) REVERT: B 355 MET cc_start: 0.7334 (mmm) cc_final: 0.6985 (mmt) REVERT: C 12 ASN cc_start: 0.9041 (m-40) cc_final: 0.8656 (t0) REVERT: C 61 LYS cc_start: 0.8590 (mttt) cc_final: 0.8287 (mttp) REVERT: C 64 ILE cc_start: 0.9022 (pt) cc_final: 0.8699 (mm) REVERT: C 82 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7928 (tpp) REVERT: C 111 ASN cc_start: 0.8283 (m-40) cc_final: 0.7990 (m110) REVERT: C 122 ILE cc_start: 0.9179 (mm) cc_final: 0.8960 (tp) REVERT: C 129 VAL cc_start: 0.9195 (m) cc_final: 0.8824 (t) REVERT: C 140 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8382 (mt) REVERT: C 176 MET cc_start: 0.8162 (mmm) cc_final: 0.7602 (mmm) REVERT: C 186 THR cc_start: 0.9018 (m) cc_final: 0.8712 (p) REVERT: C 189 LEU cc_start: 0.9123 (tp) cc_final: 0.8735 (mt) REVERT: C 212 ILE cc_start: 0.9185 (mt) cc_final: 0.8761 (mt) REVERT: C 213 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8156 (tmtt) REVERT: C 262 PHE cc_start: 0.8414 (m-80) cc_final: 0.8062 (m-10) REVERT: C 274 ILE cc_start: 0.8782 (pt) cc_final: 0.7805 (pt) REVERT: C 292 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.6453 (m-30) REVERT: C 296 ASN cc_start: 0.8786 (m-40) cc_final: 0.8069 (t0) REVERT: C 297 ASN cc_start: 0.8706 (t0) cc_final: 0.8107 (t0) REVERT: C 299 LEU cc_start: 0.8961 (mt) cc_final: 0.8205 (mt) REVERT: C 334 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: D 86 TRP cc_start: 0.8307 (m-10) cc_final: 0.7459 (m-10) REVERT: D 132 MET cc_start: 0.8351 (ppp) cc_final: 0.8075 (ppp) REVERT: D 133 TYR cc_start: 0.7394 (t80) cc_final: 0.7155 (t80) REVERT: D 260 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8081 (p) REVERT: D 278 THR cc_start: 0.8638 (m) cc_final: 0.8359 (m) REVERT: D 305 MET cc_start: 0.8844 (mmm) cc_final: 0.6786 (mmt) REVERT: D 375 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: E 99 LEU cc_start: 0.8666 (tp) cc_final: 0.7277 (tp) REVERT: E 121 ASP cc_start: 0.7903 (m-30) cc_final: 0.7425 (m-30) REVERT: E 172 ILE cc_start: 0.7753 (mm) cc_final: 0.7473 (mm) REVERT: E 196 GLU cc_start: 0.7895 (tt0) cc_final: 0.7668 (tt0) REVERT: E 225 ILE cc_start: 0.5939 (mt) cc_final: 0.5420 (mt) REVERT: F 99 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7919 (tp) REVERT: G 45 MET cc_start: 0.8917 (mmt) cc_final: 0.8711 (mmp) REVERT: G 112 ILE cc_start: 0.8424 (mt) cc_final: 0.8193 (mm) REVERT: G 136 LEU cc_start: 0.6438 (mt) cc_final: 0.6225 (pp) REVERT: H 54 MET cc_start: 0.4930 (mmm) cc_final: 0.3873 (mmm) REVERT: H 96 ASP cc_start: 0.6539 (m-30) cc_final: 0.6191 (m-30) REVERT: H 140 PHE cc_start: 0.8039 (m-80) cc_final: 0.7694 (m-80) REVERT: J 6 MET cc_start: 0.8409 (mmp) cc_final: 0.8147 (mpp) REVERT: J 28 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.7137 (m) REVERT: J 87 ILE cc_start: 0.8761 (tt) cc_final: 0.8411 (tp) REVERT: J 216 LEU cc_start: 0.7112 (mt) cc_final: 0.6825 (mp) REVERT: J 241 SER cc_start: 0.7428 (t) cc_final: 0.7033 (t) REVERT: J 287 TYR cc_start: 0.6574 (m-80) cc_final: 0.5976 (m-10) REVERT: J 435 MET cc_start: 0.7329 (tmm) cc_final: 0.6381 (tmm) REVERT: J 476 LEU cc_start: 0.8552 (tp) cc_final: 0.8251 (tt) REVERT: J 483 GLU cc_start: 0.6851 (tt0) cc_final: 0.5945 (tt0) REVERT: J 531 MET cc_start: 0.8328 (mmt) cc_final: 0.8117 (mmm) REVERT: J 532 SER cc_start: 0.9205 (m) cc_final: 0.8970 (m) REVERT: J 655 LEU cc_start: 0.9388 (tp) cc_final: 0.9126 (tp) REVERT: J 690 MET cc_start: 0.8707 (mmm) cc_final: 0.8284 (tpp) REVERT: K 87 ILE cc_start: 0.8313 (tt) cc_final: 0.7960 (mm) REVERT: K 105 LEU cc_start: 0.8468 (pp) cc_final: 0.7737 (tp) REVERT: K 108 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6753 (mtp85) REVERT: K 274 ILE cc_start: 0.8156 (mm) cc_final: 0.7454 (mm) REVERT: K 295 PRO cc_start: 0.7407 (Cg_exo) cc_final: 0.6815 (Cg_endo) REVERT: K 298 LEU cc_start: 0.8343 (mt) cc_final: 0.7995 (mt) REVERT: K 313 ILE cc_start: 0.8985 (pt) cc_final: 0.8784 (mm) REVERT: K 349 MET cc_start: 0.7741 (tpp) cc_final: 0.7084 (mmm) REVERT: K 359 PHE cc_start: 0.7447 (t80) cc_final: 0.7211 (t80) REVERT: K 375 PRO cc_start: 0.9023 (Cg_exo) cc_final: 0.8664 (Cg_endo) REVERT: K 417 VAL cc_start: 0.8160 (m) cc_final: 0.7682 (m) REVERT: K 421 MET cc_start: 0.8483 (mmm) cc_final: 0.8184 (mmt) REVERT: K 435 MET cc_start: 0.8053 (ttp) cc_final: 0.6903 (ttp) REVERT: K 483 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8153 (mm-30) REVERT: K 521 ILE cc_start: 0.9406 (mt) cc_final: 0.9138 (mm) REVERT: K 531 MET cc_start: 0.7719 (mmt) cc_final: 0.7356 (mmt) REVERT: K 533 ILE cc_start: 0.9450 (mm) cc_final: 0.8923 (tp) REVERT: K 538 CYS cc_start: 0.8122 (m) cc_final: 0.7917 (m) REVERT: K 587 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7323 (p0) REVERT: K 589 ASN cc_start: 0.8787 (m110) cc_final: 0.8416 (t0) REVERT: K 704 ILE cc_start: 0.8809 (mt) cc_final: 0.8536 (mt) REVERT: K 717 ASP cc_start: 0.5350 (t70) cc_final: 0.4766 (t70) REVERT: K 749 LEU cc_start: 0.6783 (mt) cc_final: 0.6573 (mt) REVERT: L 80 VAL cc_start: 0.5951 (m) cc_final: 0.5715 (p) REVERT: L 122 ILE cc_start: 0.8766 (mt) cc_final: 0.8543 (mt) REVERT: L 135 VAL cc_start: 0.5987 (t) cc_final: 0.5664 (t) REVERT: L 143 LYS cc_start: 0.7305 (ptmt) cc_final: 0.6845 (pttm) REVERT: L 186 TYR cc_start: 0.6183 (p90) cc_final: 0.5823 (p90) REVERT: M 110 MET cc_start: 0.8197 (ttp) cc_final: 0.7862 (ttp) REVERT: M 185 ASN cc_start: 0.8834 (m110) cc_final: 0.8554 (m-40) outliers start: 154 outliers final: 49 residues processed: 1435 average time/residue: 0.2195 time to fit residues: 494.0765 Evaluate side-chains 839 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 779 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.0980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS B 12 ASN C 78 ASN C 225 ASN D 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 275 HIS D 314 GLN E 93 GLN F 216 GLN H 82 GLN I 254 GLN I 266 ASN I 268 ASN J 27 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 ASN J 193 GLN J 251 HIS J 284 HIS J 358 HIS ** J 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN J 401 HIS J 408 ASN J 471 ASN J 562 ASN ** J 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN K 172 GLN K 492 HIS K 576 HIS L 87 ASN L 146 ASN M 76 GLN M 192 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093515 restraints weight = 105869.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094197 restraints weight = 71820.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094571 restraints weight = 53947.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094935 restraints weight = 46992.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095153 restraints weight = 41505.391| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33808 Z= 0.180 Angle : 0.671 7.947 45560 Z= 0.354 Chirality : 0.044 0.315 4984 Planarity : 0.005 0.083 5928 Dihedral : 5.388 48.098 4550 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 4130 helix: 1.07 (0.12), residues: 2072 sheet: 0.09 (0.26), residues: 384 loop : -0.77 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 69 TYR 0.024 0.002 TYR F 214 PHE 0.037 0.002 PHE G 156 TRP 0.026 0.002 TRP I 234 HIS 0.010 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (33807) covalent geometry : angle 0.67069 / 0.35 (45560) hydrogen bonds : bond 0.05087 / 3.43 ( 1747) hydrogen bonds : angle 4.84129 / 3.42 ( 4950) Misc. bond : bond 0.00200 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 996 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7741 (ttt) cc_final: 0.7431 (mtp) REVERT: A 47 MET cc_start: 0.5129 (mtt) cc_final: 0.4451 (mtt) REVERT: A 86 TRP cc_start: 0.8956 (m-10) cc_final: 0.8741 (m100) REVERT: A 99 GLU cc_start: 0.8653 (pm20) cc_final: 0.8073 (pm20) REVERT: A 100 GLU cc_start: 0.7908 (mp0) cc_final: 0.7434 (mp0) REVERT: A 105 LEU cc_start: 0.9204 (mm) cc_final: 0.8763 (mm) REVERT: A 107 GLU cc_start: 0.9342 (tp30) cc_final: 0.8744 (tp30) REVERT: A 186 THR cc_start: 0.8025 (m) cc_final: 0.7800 (p) REVERT: A 190 MET cc_start: 0.8270 (ttt) cc_final: 0.7888 (ttt) REVERT: A 221 LEU cc_start: 0.8580 (tp) cc_final: 0.8233 (tp) REVERT: A 288 ASP cc_start: 0.8631 (m-30) cc_final: 0.8144 (m-30) REVERT: A 304 THR cc_start: 0.9372 (p) cc_final: 0.9028 (t) REVERT: A 356 TRP cc_start: 0.8931 (m100) cc_final: 0.8008 (m100) REVERT: B 16 LEU cc_start: 0.8939 (mp) cc_final: 0.8598 (mt) REVERT: B 61 LYS cc_start: 0.9341 (mttt) cc_final: 0.8963 (mptt) REVERT: B 78 ASN cc_start: 0.8209 (t0) cc_final: 0.7857 (m-40) REVERT: B 119 MET cc_start: 0.8698 (ttm) cc_final: 0.8120 (ttm) REVERT: B 305 MET cc_start: 0.8673 (tpp) cc_final: 0.8054 (tpt) REVERT: B 345 ILE cc_start: 0.9698 (mm) cc_final: 0.9488 (tp) REVERT: C 107 GLU cc_start: 0.8712 (tp30) cc_final: 0.8368 (tp30) REVERT: C 111 ASN cc_start: 0.8527 (m-40) cc_final: 0.8162 (m110) REVERT: C 186 THR cc_start: 0.9110 (m) cc_final: 0.8887 (p) REVERT: C 189 LEU cc_start: 0.9055 (tp) cc_final: 0.8575 (tp) REVERT: C 192 ILE cc_start: 0.9303 (pt) cc_final: 0.8921 (mm) REVERT: C 213 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8454 (tmtt) REVERT: C 260 THR cc_start: 0.9597 (m) cc_final: 0.9243 (t) REVERT: C 276 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 296 ASN cc_start: 0.9234 (m-40) cc_final: 0.8526 (t0) REVERT: C 297 ASN cc_start: 0.9156 (t0) cc_final: 0.8522 (t0) REVERT: C 335 ARG cc_start: 0.8973 (mtm180) cc_final: 0.8445 (mtt180) REVERT: D 82 MET cc_start: 0.8734 (tpp) cc_final: 0.8524 (tpp) REVERT: D 132 MET cc_start: 0.8901 (ppp) cc_final: 0.8288 (ppp) REVERT: D 153 LEU cc_start: 0.8619 (tp) cc_final: 0.8382 (tt) REVERT: D 161 HIS cc_start: 0.8644 (p-80) cc_final: 0.8424 (p-80) REVERT: D 189 LEU cc_start: 0.9429 (tt) cc_final: 0.9058 (tt) REVERT: D 213 LYS cc_start: 0.8451 (tppt) cc_final: 0.8110 (tppt) REVERT: D 289 ILE cc_start: 0.8833 (pt) cc_final: 0.8572 (pt) REVERT: D 305 MET cc_start: 0.9219 (mmm) cc_final: 0.8996 (tpt) REVERT: E 99 LEU cc_start: 0.8073 (tp) cc_final: 0.7054 (tp) REVERT: F 85 VAL cc_start: 0.8095 (t) cc_final: 0.7807 (t) REVERT: F 127 MET cc_start: 0.7398 (ttt) cc_final: 0.7074 (ttm) REVERT: F 227 VAL cc_start: 0.8445 (p) cc_final: 0.8161 (m) REVERT: G 45 MET cc_start: 0.7527 (mmt) cc_final: 0.6870 (mmp) REVERT: G 103 MET cc_start: 0.5382 (tpp) cc_final: 0.5142 (tpp) REVERT: G 112 ILE cc_start: 0.8604 (mt) cc_final: 0.8296 (mm) REVERT: G 117 LEU cc_start: 0.8768 (tt) cc_final: 0.8466 (pp) REVERT: G 136 LEU cc_start: 0.6458 (mt) cc_final: 0.6247 (pp) REVERT: H 96 ASP cc_start: 0.6244 (m-30) cc_final: 0.5891 (m-30) REVERT: H 140 PHE cc_start: 0.8358 (m-80) cc_final: 0.7932 (m-80) REVERT: J 67 LYS cc_start: 0.8490 (tptp) cc_final: 0.8264 (tptp) REVERT: J 116 THR cc_start: 0.8104 (t) cc_final: 0.7870 (t) REVERT: J 166 LEU cc_start: 0.8998 (mt) cc_final: 0.8729 (mt) REVERT: J 356 ILE cc_start: 0.9371 (tt) cc_final: 0.8911 (mm) REVERT: J 357 MET cc_start: 0.8855 (mtm) cc_final: 0.8154 (mtm) REVERT: J 387 LEU cc_start: 0.8722 (tp) cc_final: 0.8407 (tp) REVERT: J 388 MET cc_start: 0.8872 (mmm) cc_final: 0.8411 (mmm) REVERT: J 435 MET cc_start: 0.8101 (tmm) cc_final: 0.7513 (tmm) REVERT: J 531 MET cc_start: 0.8459 (mmt) cc_final: 0.7042 (mmm) REVERT: J 533 ILE cc_start: 0.9506 (tt) cc_final: 0.8879 (tt) REVERT: J 535 GLU cc_start: 0.7815 (mp0) cc_final: 0.7172 (mp0) REVERT: J 537 GLU cc_start: 0.8794 (mp0) cc_final: 0.8214 (mp0) REVERT: J 538 CYS cc_start: 0.9073 (p) cc_final: 0.8665 (p) REVERT: J 588 TYR cc_start: 0.7773 (m-10) cc_final: 0.7520 (m-10) REVERT: J 711 ASN cc_start: 0.9020 (m110) cc_final: 0.8550 (m110) REVERT: K 64 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7387 (tp30) REVERT: K 87 ILE cc_start: 0.8856 (tt) cc_final: 0.8202 (mm) REVERT: K 105 LEU cc_start: 0.9057 (pp) cc_final: 0.8397 (tp) REVERT: K 108 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6907 (mmm-85) REVERT: K 224 ASN cc_start: 0.8090 (m110) cc_final: 0.7276 (t0) REVERT: K 274 ILE cc_start: 0.8288 (mm) cc_final: 0.7497 (mm) REVERT: K 275 PHE cc_start: 0.8574 (m-10) cc_final: 0.8095 (m-10) REVERT: K 295 PRO cc_start: 0.7561 (Cg_exo) cc_final: 0.7028 (Cg_endo) REVERT: K 351 LYS cc_start: 0.9304 (ttpt) cc_final: 0.8804 (tttm) REVERT: K 372 GLN cc_start: 0.8502 (pm20) cc_final: 0.8263 (pm20) REVERT: K 435 MET cc_start: 0.8710 (ttp) cc_final: 0.8350 (ttp) REVERT: K 479 ASN cc_start: 0.9527 (m-40) cc_final: 0.8147 (m-40) REVERT: K 483 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8296 (mm-30) REVERT: K 521 ILE cc_start: 0.9098 (mt) cc_final: 0.8706 (mp) REVERT: K 531 MET cc_start: 0.7876 (mmt) cc_final: 0.7065 (mmt) REVERT: K 535 GLU cc_start: 0.8240 (pt0) cc_final: 0.7985 (pt0) REVERT: K 567 ARG cc_start: 0.7587 (ptp90) cc_final: 0.7095 (ptp90) REVERT: K 581 HIS cc_start: 0.8707 (m-70) cc_final: 0.8100 (m170) REVERT: K 620 LEU cc_start: 0.9069 (mt) cc_final: 0.8847 (mt) REVERT: K 659 MET cc_start: 0.7414 (mtm) cc_final: 0.6339 (mtm) REVERT: K 669 PHE cc_start: 0.7598 (m-80) cc_final: 0.7351 (m-80) REVERT: K 749 LEU cc_start: 0.7338 (mt) cc_final: 0.7005 (mt) REVERT: L 96 VAL cc_start: 0.5112 (m) cc_final: 0.4488 (m) REVERT: L 109 MET cc_start: 0.4379 (mtt) cc_final: 0.4038 (mtt) REVERT: L 118 MET cc_start: 0.4253 (mmt) cc_final: 0.3693 (tpt) REVERT: L 122 ILE cc_start: 0.8823 (mt) cc_final: 0.8385 (mt) REVERT: L 186 TYR cc_start: 0.5939 (p90) cc_final: 0.5629 (p90) REVERT: L 193 ILE cc_start: 0.7221 (mm) cc_final: 0.6838 (mm) outliers start: 3 outliers final: 0 residues processed: 999 average time/residue: 0.2128 time to fit residues: 337.8021 Evaluate side-chains 695 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 13 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 337 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN A 252 ASN B 296 ASN C 78 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 GLN J 437 ASN ** J 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 GLN K 401 HIS ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087647 restraints weight = 107305.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088794 restraints weight = 68192.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090181 restraints weight = 46445.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.090346 restraints weight = 34130.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090300 restraints weight = 30714.784| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33808 Z= 0.193 Angle : 0.682 8.657 45560 Z= 0.358 Chirality : 0.044 0.295 4984 Planarity : 0.005 0.068 5928 Dihedral : 5.429 43.801 4550 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 0.14 % Allowed : 4.17 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.13), residues: 4130 helix: 1.00 (0.12), residues: 2050 sheet: -0.11 (0.26), residues: 364 loop : -0.80 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 75 TYR 0.025 0.002 TYR C 166 PHE 0.033 0.002 PHE G 104 TRP 0.039 0.002 TRP D 86 HIS 0.011 0.002 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (33807) covalent geometry : angle 0.68232 / 0.36 (45560) hydrogen bonds : bond 0.05027 / 3.37 ( 1747) hydrogen bonds : angle 4.71976 / 3.35 ( 4950) Misc. bond : bond 0.01062 / 0.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 897 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8705 (pm20) cc_final: 0.8167 (pm20) REVERT: A 100 GLU cc_start: 0.8191 (mp0) cc_final: 0.7724 (mp0) REVERT: A 103 THR cc_start: 0.8891 (t) cc_final: 0.8665 (p) REVERT: A 107 GLU cc_start: 0.9321 (tp30) cc_final: 0.8773 (tp30) REVERT: A 208 ILE cc_start: 0.9538 (mp) cc_final: 0.9327 (mp) REVERT: A 221 LEU cc_start: 0.8594 (tp) cc_final: 0.8356 (tp) REVERT: A 288 ASP cc_start: 0.8140 (m-30) cc_final: 0.7839 (m-30) REVERT: A 325 MET cc_start: 0.8522 (mmm) cc_final: 0.8316 (mmm) REVERT: A 356 TRP cc_start: 0.8910 (m100) cc_final: 0.8396 (m100) REVERT: B 16 LEU cc_start: 0.8817 (mp) cc_final: 0.8607 (mt) REVERT: B 119 MET cc_start: 0.8614 (ttm) cc_final: 0.8268 (ttm) REVERT: B 345 ILE cc_start: 0.9690 (mm) cc_final: 0.9428 (tp) REVERT: B 352 PHE cc_start: 0.8865 (t80) cc_final: 0.8445 (t80) REVERT: C 21 PHE cc_start: 0.8238 (m-80) cc_final: 0.7840 (m-80) REVERT: C 103 THR cc_start: 0.9507 (p) cc_final: 0.9112 (p) REVERT: C 104 LEU cc_start: 0.9023 (tp) cc_final: 0.8454 (tp) REVERT: C 105 LEU cc_start: 0.8791 (mt) cc_final: 0.8477 (mt) REVERT: C 107 GLU cc_start: 0.8649 (tp30) cc_final: 0.8357 (tp30) REVERT: C 111 ASN cc_start: 0.8529 (m-40) cc_final: 0.7806 (m110) REVERT: C 209 VAL cc_start: 0.9377 (t) cc_final: 0.8764 (p) REVERT: C 213 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8628 (tmtt) REVERT: C 237 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8153 (tt0) REVERT: C 260 THR cc_start: 0.9687 (m) cc_final: 0.9396 (t) REVERT: C 276 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6880 (tm-30) REVERT: D 34 ILE cc_start: 0.9279 (mp) cc_final: 0.8647 (mp) REVERT: D 86 TRP cc_start: 0.8870 (m-10) cc_final: 0.8595 (m-90) REVERT: D 132 MET cc_start: 0.8832 (ppp) cc_final: 0.8378 (ppp) REVERT: D 183 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7900 (tpp-160) REVERT: D 213 LYS cc_start: 0.8596 (tppt) cc_final: 0.8108 (tppt) REVERT: D 257 CYS cc_start: 0.8349 (t) cc_final: 0.8058 (t) REVERT: D 283 MET cc_start: 0.8696 (mmp) cc_final: 0.8369 (mmp) REVERT: D 305 MET cc_start: 0.9271 (mmm) cc_final: 0.9011 (tpt) REVERT: D 318 THR cc_start: 0.8863 (p) cc_final: 0.8603 (t) REVERT: E 96 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6431 (tp30) REVERT: E 99 LEU cc_start: 0.8290 (tp) cc_final: 0.7189 (tp) REVERT: E 144 GLN cc_start: 0.7066 (mt0) cc_final: 0.6295 (mt0) REVERT: F 85 VAL cc_start: 0.8446 (t) cc_final: 0.8122 (t) REVERT: F 138 GLU cc_start: 0.6620 (tt0) cc_final: 0.6323 (tt0) REVERT: F 227 VAL cc_start: 0.8585 (p) cc_final: 0.8280 (m) REVERT: G 45 MET cc_start: 0.7592 (mmt) cc_final: 0.6964 (mmp) REVERT: G 103 MET cc_start: 0.5820 (tpp) cc_final: 0.5475 (tpp) REVERT: G 112 ILE cc_start: 0.8548 (mt) cc_final: 0.8271 (mm) REVERT: H 96 ASP cc_start: 0.6353 (m-30) cc_final: 0.5917 (m-30) REVERT: J 270 LYS cc_start: 0.7899 (ptmm) cc_final: 0.7540 (ptmm) REVERT: J 369 ARG cc_start: 0.7492 (mmt-90) cc_final: 0.7072 (mpt180) REVERT: J 387 LEU cc_start: 0.8604 (tp) cc_final: 0.8226 (tp) REVERT: J 388 MET cc_start: 0.9012 (mmm) cc_final: 0.8673 (mmm) REVERT: J 433 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7521 (tm-30) REVERT: J 437 ASN cc_start: 0.8970 (m110) cc_final: 0.8070 (m-40) REVERT: J 439 MET cc_start: 0.8491 (ptp) cc_final: 0.7693 (ptm) REVERT: J 531 MET cc_start: 0.8835 (mmt) cc_final: 0.7547 (mmm) REVERT: J 533 ILE cc_start: 0.9146 (tt) cc_final: 0.7838 (tt) REVERT: J 537 GLU cc_start: 0.9059 (mp0) cc_final: 0.6724 (mp0) REVERT: J 538 CYS cc_start: 0.8935 (p) cc_final: 0.8690 (p) REVERT: J 563 PHE cc_start: 0.8698 (t80) cc_final: 0.8488 (t80) REVERT: J 588 TYR cc_start: 0.7941 (m-10) cc_final: 0.7515 (m-10) REVERT: J 711 ASN cc_start: 0.9028 (m110) cc_final: 0.8461 (m110) REVERT: K 64 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7469 (tp30) REVERT: K 87 ILE cc_start: 0.8839 (tt) cc_final: 0.8188 (mm) REVERT: K 105 LEU cc_start: 0.9188 (pp) cc_final: 0.8398 (tp) REVERT: K 113 MET cc_start: 0.8344 (mtp) cc_final: 0.7872 (mmt) REVERT: K 224 ASN cc_start: 0.7787 (m110) cc_final: 0.7188 (t0) REVERT: K 274 ILE cc_start: 0.8320 (mm) cc_final: 0.7629 (mm) REVERT: K 275 PHE cc_start: 0.8356 (m-10) cc_final: 0.8001 (m-10) REVERT: K 285 ILE cc_start: 0.8954 (tp) cc_final: 0.8742 (tp) REVERT: K 295 PRO cc_start: 0.7641 (Cg_exo) cc_final: 0.7012 (Cg_endo) REVERT: K 349 MET cc_start: 0.7841 (mmt) cc_final: 0.7379 (mmm) REVERT: K 372 GLN cc_start: 0.8294 (pm20) cc_final: 0.7976 (pm20) REVERT: K 435 MET cc_start: 0.8847 (ttp) cc_final: 0.7647 (ttp) REVERT: K 439 MET cc_start: 0.8928 (mtt) cc_final: 0.8564 (mmm) REVERT: K 479 ASN cc_start: 0.9581 (m-40) cc_final: 0.8415 (m-40) REVERT: K 483 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8318 (mm-30) REVERT: K 521 ILE cc_start: 0.9226 (mt) cc_final: 0.8624 (mm) REVERT: K 565 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8602 (ptpp) REVERT: K 581 HIS cc_start: 0.8729 (m-70) cc_final: 0.8184 (m170) REVERT: K 585 THR cc_start: 0.8846 (t) cc_final: 0.8460 (p) REVERT: K 620 LEU cc_start: 0.9262 (mt) cc_final: 0.8943 (mt) REVERT: K 623 ASN cc_start: 0.8591 (m-40) cc_final: 0.8317 (m-40) REVERT: K 659 MET cc_start: 0.7561 (mtm) cc_final: 0.7303 (mtm) REVERT: K 669 PHE cc_start: 0.7653 (m-80) cc_final: 0.7386 (m-80) REVERT: K 672 CYS cc_start: 0.8406 (p) cc_final: 0.8121 (t) REVERT: K 720 GLN cc_start: 0.7545 (mp10) cc_final: 0.7224 (mp10) REVERT: K 736 ILE cc_start: 0.7192 (mp) cc_final: 0.6913 (mm) REVERT: K 749 LEU cc_start: 0.7503 (mt) cc_final: 0.7039 (mt) REVERT: K 799 MET cc_start: 0.6539 (mtp) cc_final: 0.5992 (mtp) REVERT: L 96 VAL cc_start: 0.5250 (m) cc_final: 0.4918 (m) REVERT: L 110 MET cc_start: 0.3987 (mmt) cc_final: 0.3732 (tpt) REVERT: L 122 ILE cc_start: 0.8788 (mt) cc_final: 0.8508 (mt) REVERT: L 193 ILE cc_start: 0.7471 (mm) cc_final: 0.7129 (mm) REVERT: M 111 ASP cc_start: 0.7260 (t0) cc_final: 0.6942 (t0) outliers start: 5 outliers final: 0 residues processed: 901 average time/residue: 0.2161 time to fit residues: 311.4320 Evaluate side-chains 673 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 400 optimal weight: 0.0980 chunk 162 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 371 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 144 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 254 GLN J 372 GLN J 486 GLN J 568 ASN K 97 HIS K 172 GLN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089454 restraints weight = 106798.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090329 restraints weight = 73288.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090604 restraints weight = 54733.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090987 restraints weight = 49643.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091171 restraints weight = 42649.676| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33808 Z= 0.140 Angle : 0.622 8.928 45560 Z= 0.325 Chirality : 0.043 0.314 4984 Planarity : 0.004 0.061 5928 Dihedral : 5.278 43.712 4550 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4130 helix: 1.02 (0.12), residues: 2054 sheet: -0.08 (0.26), residues: 392 loop : -0.81 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.023 0.001 TYR F 214 PHE 0.029 0.002 PHE G 104 TRP 0.060 0.002 TRP D 86 HIS 0.008 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (33807) covalent geometry : angle 0.62228 / 0.33 (45560) hydrogen bonds : bond 0.04680 / 3.16 ( 1747) hydrogen bonds : angle 4.56456 / 3.23 ( 4950) Misc. bond : bond 0.00387 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 910 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PRO cc_start: 0.9004 (Cg_exo) cc_final: 0.8696 (Cg_endo) REVERT: A 107 GLU cc_start: 0.9286 (tp30) cc_final: 0.8644 (tp30) REVERT: A 167 GLU cc_start: 0.7763 (mm-30) cc_final: 0.6912 (tp30) REVERT: A 193 LEU cc_start: 0.9185 (mt) cc_final: 0.8890 (tp) REVERT: A 208 ILE cc_start: 0.9484 (mp) cc_final: 0.9211 (mp) REVERT: A 209 VAL cc_start: 0.9702 (t) cc_final: 0.9451 (t) REVERT: A 274 ILE cc_start: 0.8815 (pt) cc_final: 0.8565 (pt) REVERT: A 288 ASP cc_start: 0.8012 (m-30) cc_final: 0.7748 (m-30) REVERT: A 356 TRP cc_start: 0.9022 (m100) cc_final: 0.8417 (m100) REVERT: B 61 LYS cc_start: 0.9142 (mptt) cc_final: 0.8625 (mptt) REVERT: B 96 VAL cc_start: 0.9142 (m) cc_final: 0.8709 (m) REVERT: B 119 MET cc_start: 0.8741 (ttm) cc_final: 0.8323 (ttm) REVERT: B 209 VAL cc_start: 0.9430 (m) cc_final: 0.9214 (p) REVERT: B 345 ILE cc_start: 0.9635 (mm) cc_final: 0.9378 (tp) REVERT: B 352 PHE cc_start: 0.8977 (t80) cc_final: 0.8695 (t80) REVERT: C 103 THR cc_start: 0.9461 (p) cc_final: 0.9209 (p) REVERT: C 104 LEU cc_start: 0.9068 (tp) cc_final: 0.8644 (tp) REVERT: C 107 GLU cc_start: 0.8422 (tp30) cc_final: 0.8044 (tp30) REVERT: C 111 ASN cc_start: 0.8537 (m-40) cc_final: 0.7883 (m110) REVERT: C 123 MET cc_start: 0.8960 (mmm) cc_final: 0.8388 (mmm) REVERT: C 166 TYR cc_start: 0.8681 (t80) cc_final: 0.8477 (t80) REVERT: C 209 VAL cc_start: 0.9321 (t) cc_final: 0.8763 (p) REVERT: C 213 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8602 (tmtt) REVERT: C 260 THR cc_start: 0.9722 (m) cc_final: 0.9443 (t) REVERT: C 276 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6911 (tm-30) REVERT: C 296 ASN cc_start: 0.9226 (m-40) cc_final: 0.8870 (m-40) REVERT: C 297 ASN cc_start: 0.9238 (t0) cc_final: 0.8659 (t0) REVERT: C 341 ILE cc_start: 0.9632 (mt) cc_final: 0.9429 (tp) REVERT: D 86 TRP cc_start: 0.8551 (m-90) cc_final: 0.7894 (m-90) REVERT: D 132 MET cc_start: 0.8656 (ppp) cc_final: 0.8221 (ppp) REVERT: D 189 LEU cc_start: 0.9358 (tt) cc_final: 0.8921 (tt) REVERT: D 213 LYS cc_start: 0.8681 (tppt) cc_final: 0.8221 (tppt) REVERT: D 283 MET cc_start: 0.9042 (mmp) cc_final: 0.8554 (mmp) REVERT: D 318 THR cc_start: 0.8838 (p) cc_final: 0.8571 (t) REVERT: E 99 LEU cc_start: 0.8282 (tp) cc_final: 0.7262 (tp) REVERT: E 106 LEU cc_start: 0.8287 (tp) cc_final: 0.7842 (tp) REVERT: E 144 GLN cc_start: 0.7254 (mt0) cc_final: 0.6135 (mt0) REVERT: F 56 GLU cc_start: 0.7734 (tp30) cc_final: 0.7201 (tp30) REVERT: F 85 VAL cc_start: 0.8424 (t) cc_final: 0.8182 (t) REVERT: F 127 MET cc_start: 0.7371 (ttm) cc_final: 0.7123 (tpp) REVERT: F 227 VAL cc_start: 0.8621 (p) cc_final: 0.8400 (m) REVERT: G 45 MET cc_start: 0.7735 (mmt) cc_final: 0.7325 (mmp) REVERT: G 57 LEU cc_start: 0.7641 (mm) cc_final: 0.7374 (mm) REVERT: G 103 MET cc_start: 0.5769 (tpp) cc_final: 0.5353 (tpp) REVERT: G 112 ILE cc_start: 0.8580 (mt) cc_final: 0.8268 (mm) REVERT: H 60 GLN cc_start: 0.8689 (mt0) cc_final: 0.8470 (mt0) REVERT: H 150 ILE cc_start: 0.8545 (pt) cc_final: 0.8342 (pt) REVERT: J 38 TYR cc_start: 0.8293 (m-80) cc_final: 0.7706 (m-80) REVERT: J 78 GLN cc_start: 0.7799 (mp10) cc_final: 0.7470 (mp10) REVERT: J 142 TYR cc_start: 0.8097 (m-10) cc_final: 0.7646 (m-10) REVERT: J 356 ILE cc_start: 0.9398 (tt) cc_final: 0.9004 (mm) REVERT: J 369 ARG cc_start: 0.7605 (mmt-90) cc_final: 0.7291 (mpt180) REVERT: J 387 LEU cc_start: 0.8555 (tp) cc_final: 0.8227 (tp) REVERT: J 388 MET cc_start: 0.8908 (mmm) cc_final: 0.8516 (mmm) REVERT: J 433 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7324 (tm-30) REVERT: J 435 MET cc_start: 0.8435 (tmm) cc_final: 0.7952 (tmm) REVERT: J 437 ASN cc_start: 0.8764 (m110) cc_final: 0.8228 (m110) REVERT: J 439 MET cc_start: 0.8476 (ptp) cc_final: 0.7820 (ptm) REVERT: J 447 LEU cc_start: 0.8972 (mp) cc_final: 0.8769 (mp) REVERT: J 531 MET cc_start: 0.8675 (mmt) cc_final: 0.7875 (mmm) REVERT: J 533 ILE cc_start: 0.9445 (tt) cc_final: 0.7668 (tt) REVERT: J 537 GLU cc_start: 0.8637 (mp0) cc_final: 0.7524 (mp0) REVERT: J 563 PHE cc_start: 0.8834 (t80) cc_final: 0.8504 (t80) REVERT: J 588 TYR cc_start: 0.7761 (m-10) cc_final: 0.7522 (m-10) REVERT: J 711 ASN cc_start: 0.8982 (m110) cc_final: 0.8383 (m110) REVERT: K 33 LEU cc_start: 0.8105 (tp) cc_final: 0.7832 (tp) REVERT: K 35 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7984 (ptmt) REVERT: K 64 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7699 (tp30) REVERT: K 87 ILE cc_start: 0.8871 (tt) cc_final: 0.8152 (mm) REVERT: K 105 LEU cc_start: 0.9060 (pp) cc_final: 0.8385 (tp) REVERT: K 173 SER cc_start: 0.8137 (t) cc_final: 0.7925 (p) REVERT: K 192 ILE cc_start: 0.7701 (pt) cc_final: 0.6718 (pt) REVERT: K 217 GLU cc_start: 0.7886 (mp0) cc_final: 0.6862 (mp0) REVERT: K 224 ASN cc_start: 0.7827 (m110) cc_final: 0.7373 (t0) REVERT: K 274 ILE cc_start: 0.8304 (mm) cc_final: 0.7716 (mm) REVERT: K 275 PHE cc_start: 0.8337 (m-10) cc_final: 0.7886 (m-10) REVERT: K 295 PRO cc_start: 0.7542 (Cg_exo) cc_final: 0.6999 (Cg_endo) REVERT: K 359 PHE cc_start: 0.8487 (t80) cc_final: 0.8144 (t80) REVERT: K 362 MET cc_start: 0.8423 (mmt) cc_final: 0.7901 (mmt) REVERT: K 435 MET cc_start: 0.8773 (ttp) cc_final: 0.8491 (mmp) REVERT: K 476 LEU cc_start: 0.8983 (tp) cc_final: 0.8750 (tt) REVERT: K 479 ASN cc_start: 0.9493 (m-40) cc_final: 0.9287 (m-40) REVERT: K 483 GLU cc_start: 0.8585 (mm-30) cc_final: 0.6527 (mm-30) REVERT: K 520 CYS cc_start: 0.9059 (p) cc_final: 0.8684 (p) REVERT: K 521 ILE cc_start: 0.9226 (mt) cc_final: 0.8752 (mm) REVERT: K 526 LYS cc_start: 0.8386 (mppt) cc_final: 0.8168 (mmtm) REVERT: K 531 MET cc_start: 0.7896 (mmt) cc_final: 0.7316 (mmt) REVERT: K 535 GLU cc_start: 0.8100 (pt0) cc_final: 0.7749 (pt0) REVERT: K 539 MET cc_start: 0.8888 (mtm) cc_final: 0.8559 (mtm) REVERT: K 581 HIS cc_start: 0.9040 (m-70) cc_final: 0.8005 (m-70) REVERT: K 620 LEU cc_start: 0.9281 (mt) cc_final: 0.8854 (mt) REVERT: K 623 ASN cc_start: 0.8627 (m-40) cc_final: 0.8377 (m-40) REVERT: K 669 PHE cc_start: 0.7620 (m-80) cc_final: 0.7328 (m-80) REVERT: K 672 CYS cc_start: 0.8449 (p) cc_final: 0.8074 (t) REVERT: K 736 ILE cc_start: 0.7128 (mp) cc_final: 0.6816 (mm) REVERT: K 749 LEU cc_start: 0.7471 (mt) cc_final: 0.7120 (mt) REVERT: K 799 MET cc_start: 0.6230 (mtp) cc_final: 0.5594 (mtp) REVERT: L 110 MET cc_start: 0.3685 (mmt) cc_final: 0.3473 (tpt) REVERT: L 122 ILE cc_start: 0.8696 (mt) cc_final: 0.8329 (mt) REVERT: L 136 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6077 (mm-30) REVERT: M 111 ASP cc_start: 0.6978 (t0) cc_final: 0.6775 (t0) outliers start: 3 outliers final: 0 residues processed: 912 average time/residue: 0.2036 time to fit residues: 298.2136 Evaluate side-chains 679 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 257 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 409 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 352 optimal weight: 0.7980 chunk 263 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 101 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 HIS J 79 GLN J 482 ASN J 568 ASN J 668 HIS J 734 GLN K 172 GLN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 ASN K 490 ASN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086656 restraints weight = 106915.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087910 restraints weight = 69974.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088792 restraints weight = 49639.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089396 restraints weight = 38199.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.089799 restraints weight = 31365.675| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33808 Z= 0.174 Angle : 0.656 11.555 45560 Z= 0.344 Chirality : 0.043 0.209 4984 Planarity : 0.004 0.056 5928 Dihedral : 5.320 44.713 4550 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4130 helix: 1.10 (0.12), residues: 2045 sheet: -0.14 (0.26), residues: 392 loop : -0.82 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.027 0.002 TYR F 214 PHE 0.028 0.002 PHE G 104 TRP 0.037 0.002 TRP C 356 HIS 0.010 0.001 HIS L 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (33807) covalent geometry : angle 0.65608 / 0.34 (45560) hydrogen bonds : bond 0.04760 / 3.18 ( 1747) hydrogen bonds : angle 4.57320 / 3.23 ( 4950) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 855 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8608 (m-30) cc_final: 0.7462 (m-30) REVERT: A 47 MET cc_start: 0.5784 (mtt) cc_final: 0.5388 (tpp) REVERT: A 99 GLU cc_start: 0.8730 (pm20) cc_final: 0.8247 (pm20) REVERT: A 100 GLU cc_start: 0.8086 (mp0) cc_final: 0.7814 (mp0) REVERT: A 102 PRO cc_start: 0.9071 (Cg_exo) cc_final: 0.8619 (Cg_endo) REVERT: A 107 GLU cc_start: 0.9237 (tp30) cc_final: 0.8751 (tp30) REVERT: A 288 ASP cc_start: 0.8273 (m-30) cc_final: 0.8020 (m-30) REVERT: A 356 TRP cc_start: 0.9036 (m100) cc_final: 0.8499 (m100) REVERT: B 61 LYS cc_start: 0.9173 (mptt) cc_final: 0.8907 (mptt) REVERT: B 95 ARG cc_start: 0.8542 (ttm110) cc_final: 0.8046 (ttm110) REVERT: B 119 MET cc_start: 0.8842 (ttm) cc_final: 0.8429 (ttm) REVERT: B 192 ILE cc_start: 0.9434 (pt) cc_final: 0.9119 (tp) REVERT: B 209 VAL cc_start: 0.9487 (m) cc_final: 0.9177 (p) REVERT: B 211 ASP cc_start: 0.8669 (t0) cc_final: 0.8461 (t0) REVERT: B 345 ILE cc_start: 0.9613 (mm) cc_final: 0.9388 (tp) REVERT: B 352 PHE cc_start: 0.9064 (t80) cc_final: 0.8755 (t80) REVERT: C 82 MET cc_start: 0.8457 (ttm) cc_final: 0.8236 (ttm) REVERT: C 104 LEU cc_start: 0.9038 (tp) cc_final: 0.8702 (tp) REVERT: C 107 GLU cc_start: 0.8408 (tp30) cc_final: 0.8070 (tp30) REVERT: C 111 ASN cc_start: 0.8478 (m-40) cc_final: 0.7733 (m110) REVERT: C 123 MET cc_start: 0.8729 (mmm) cc_final: 0.8429 (mmm) REVERT: C 209 VAL cc_start: 0.9335 (t) cc_final: 0.8788 (p) REVERT: C 244 ASP cc_start: 0.9047 (p0) cc_final: 0.8725 (p0) REVERT: C 260 THR cc_start: 0.9704 (m) cc_final: 0.9484 (t) REVERT: C 296 ASN cc_start: 0.9276 (m-40) cc_final: 0.8996 (m-40) REVERT: C 297 ASN cc_start: 0.9289 (t0) cc_final: 0.8760 (t0) REVERT: C 335 ARG cc_start: 0.9128 (mtm180) cc_final: 0.8772 (mtt180) REVERT: C 341 ILE cc_start: 0.9631 (mt) cc_final: 0.9357 (tt) REVERT: D 132 MET cc_start: 0.8722 (ppp) cc_final: 0.8361 (ppp) REVERT: D 189 LEU cc_start: 0.9446 (tt) cc_final: 0.9116 (tt) REVERT: D 190 MET cc_start: 0.8624 (tpp) cc_final: 0.8030 (tpp) REVERT: D 213 LYS cc_start: 0.8845 (tppt) cc_final: 0.8450 (tppt) REVERT: D 283 MET cc_start: 0.9125 (mmp) cc_final: 0.8646 (mmp) REVERT: D 305 MET cc_start: 0.9199 (mmt) cc_final: 0.8821 (mmt) REVERT: D 318 THR cc_start: 0.8823 (p) cc_final: 0.8593 (t) REVERT: E 99 LEU cc_start: 0.8475 (tp) cc_final: 0.7568 (tp) REVERT: E 141 MET cc_start: 0.2791 (mtp) cc_final: 0.2514 (mtp) REVERT: F 60 TYR cc_start: 0.7565 (m-80) cc_final: 0.7176 (m-80) REVERT: F 171 ILE cc_start: 0.5742 (pt) cc_final: 0.5503 (pt) REVERT: F 227 VAL cc_start: 0.8635 (p) cc_final: 0.8395 (m) REVERT: G 45 MET cc_start: 0.7785 (mmt) cc_final: 0.7456 (mmp) REVERT: G 90 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6692 (mttm) REVERT: G 103 MET cc_start: 0.5860 (tpp) cc_final: 0.5244 (tpp) REVERT: G 112 ILE cc_start: 0.8535 (mt) cc_final: 0.8327 (mm) REVERT: H 49 GLN cc_start: 0.5408 (tm-30) cc_final: 0.5028 (tm-30) REVERT: H 56 GLN cc_start: 0.8486 (tp40) cc_final: 0.8069 (tp-100) REVERT: H 60 GLN cc_start: 0.8754 (mt0) cc_final: 0.8390 (mt0) REVERT: H 96 ASP cc_start: 0.6143 (m-30) cc_final: 0.5778 (m-30) REVERT: I 234 TRP cc_start: 0.5562 (t60) cc_final: 0.5207 (t60) REVERT: J 78 GLN cc_start: 0.7841 (mp10) cc_final: 0.7609 (mp10) REVERT: J 142 TYR cc_start: 0.8120 (m-10) cc_final: 0.7659 (m-10) REVERT: J 166 LEU cc_start: 0.9041 (mt) cc_final: 0.8831 (mt) REVERT: J 248 ILE cc_start: 0.9124 (mt) cc_final: 0.8561 (mt) REVERT: J 300 MET cc_start: 0.6787 (tmm) cc_final: 0.6546 (tmm) REVERT: J 357 MET cc_start: 0.9036 (mtm) cc_final: 0.8233 (mtm) REVERT: J 387 LEU cc_start: 0.8569 (tp) cc_final: 0.8256 (tp) REVERT: J 388 MET cc_start: 0.8918 (mmm) cc_final: 0.8499 (mmm) REVERT: J 433 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7320 (tm-30) REVERT: J 435 MET cc_start: 0.8425 (tmm) cc_final: 0.7916 (tmm) REVERT: J 437 ASN cc_start: 0.8776 (m110) cc_final: 0.7936 (m110) REVERT: J 439 MET cc_start: 0.8847 (ptp) cc_final: 0.8069 (ptm) REVERT: J 531 MET cc_start: 0.8692 (mmt) cc_final: 0.8086 (mmm) REVERT: J 533 ILE cc_start: 0.9288 (tt) cc_final: 0.8658 (tt) REVERT: J 588 TYR cc_start: 0.7874 (m-10) cc_final: 0.7580 (m-10) REVERT: J 711 ASN cc_start: 0.8972 (m110) cc_final: 0.8397 (m110) REVERT: J 762 LYS cc_start: 0.8750 (mmmm) cc_final: 0.8488 (mmmm) REVERT: K 33 LEU cc_start: 0.8257 (tp) cc_final: 0.7969 (tp) REVERT: K 35 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7989 (ptmt) REVERT: K 87 ILE cc_start: 0.9039 (tt) cc_final: 0.8436 (mm) REVERT: K 143 ARG cc_start: 0.7238 (tpt170) cc_final: 0.7032 (tpt170) REVERT: K 274 ILE cc_start: 0.8452 (mm) cc_final: 0.7905 (mm) REVERT: K 275 PHE cc_start: 0.8345 (m-10) cc_final: 0.8021 (m-10) REVERT: K 285 ILE cc_start: 0.8879 (tp) cc_final: 0.8660 (tp) REVERT: K 295 PRO cc_start: 0.7645 (Cg_exo) cc_final: 0.7042 (Cg_endo) REVERT: K 349 MET cc_start: 0.8005 (mmt) cc_final: 0.7396 (mmt) REVERT: K 362 MET cc_start: 0.8581 (mmt) cc_final: 0.7854 (mmm) REVERT: K 435 MET cc_start: 0.8808 (ttp) cc_final: 0.7472 (ttp) REVERT: K 454 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8292 (tp40) REVERT: K 476 LEU cc_start: 0.9205 (tp) cc_final: 0.8889 (tt) REVERT: K 479 ASN cc_start: 0.9554 (m-40) cc_final: 0.8595 (m-40) REVERT: K 483 GLU cc_start: 0.8740 (mm-30) cc_final: 0.7870 (mm-30) REVERT: K 521 ILE cc_start: 0.9326 (mt) cc_final: 0.8620 (mm) REVERT: K 531 MET cc_start: 0.7894 (mmt) cc_final: 0.7332 (mmt) REVERT: K 535 GLU cc_start: 0.8160 (pt0) cc_final: 0.7802 (pt0) REVERT: K 539 MET cc_start: 0.8862 (mtm) cc_final: 0.8634 (mtm) REVERT: K 581 HIS cc_start: 0.9027 (m-70) cc_final: 0.8361 (m170) REVERT: K 620 LEU cc_start: 0.9338 (mt) cc_final: 0.8945 (mt) REVERT: K 672 CYS cc_start: 0.8506 (p) cc_final: 0.8208 (t) REVERT: K 736 ILE cc_start: 0.6901 (mp) cc_final: 0.6576 (mm) REVERT: K 749 LEU cc_start: 0.7303 (mt) cc_final: 0.6952 (mt) REVERT: L 136 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6224 (mm-30) REVERT: L 139 ARG cc_start: 0.7836 (mpt-90) cc_final: 0.7620 (tpp80) outliers start: 3 outliers final: 1 residues processed: 857 average time/residue: 0.2174 time to fit residues: 299.9513 Evaluate side-chains 649 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 648 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 139 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 173 HIS C 87 HIS C 137 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN H 56 GLN J 65 HIS J 568 ASN J 668 HIS K 172 GLN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 ASN K 498 GLN M 76 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086009 restraints weight = 107425.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086999 restraints weight = 74061.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087440 restraints weight = 52585.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087802 restraints weight = 47145.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087917 restraints weight = 39135.750| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33808 Z= 0.172 Angle : 0.660 10.789 45560 Z= 0.344 Chirality : 0.043 0.210 4984 Planarity : 0.004 0.061 5928 Dihedral : 5.338 44.137 4550 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4130 helix: 1.00 (0.12), residues: 2077 sheet: -0.19 (0.26), residues: 382 loop : -0.85 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 183 TYR 0.020 0.002 TYR K 287 PHE 0.027 0.002 PHE K 247 TRP 0.044 0.002 TRP C 356 HIS 0.007 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (33807) covalent geometry : angle 0.65957 / 0.34 (45560) hydrogen bonds : bond 0.04759 / 3.19 ( 1747) hydrogen bonds : angle 4.60874 / 3.24 ( 4950) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 849 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8752 (pm20) cc_final: 0.8312 (pm20) REVERT: A 100 GLU cc_start: 0.8041 (mp0) cc_final: 0.7744 (mp0) REVERT: A 102 PRO cc_start: 0.9221 (Cg_exo) cc_final: 0.8645 (Cg_endo) REVERT: A 107 GLU cc_start: 0.9248 (tp30) cc_final: 0.8696 (tp30) REVERT: A 129 VAL cc_start: 0.8254 (m) cc_final: 0.7878 (t) REVERT: A 288 ASP cc_start: 0.8387 (m-30) cc_final: 0.8166 (m-30) REVERT: A 356 TRP cc_start: 0.9050 (m100) cc_final: 0.8506 (m100) REVERT: B 61 LYS cc_start: 0.9187 (mptt) cc_final: 0.8897 (mptt) REVERT: B 95 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8104 (ttm110) REVERT: B 119 MET cc_start: 0.8747 (ttm) cc_final: 0.8382 (ttm) REVERT: B 142 LEU cc_start: 0.9380 (tp) cc_final: 0.9074 (tp) REVERT: B 167 GLU cc_start: 0.6376 (tt0) cc_final: 0.6074 (tt0) REVERT: B 192 ILE cc_start: 0.9483 (pt) cc_final: 0.9241 (mm) REVERT: B 209 VAL cc_start: 0.9427 (m) cc_final: 0.9213 (p) REVERT: B 269 MET cc_start: 0.8179 (mmm) cc_final: 0.7075 (mmm) REVERT: B 345 ILE cc_start: 0.9595 (mm) cc_final: 0.9329 (tp) REVERT: B 352 PHE cc_start: 0.9129 (t80) cc_final: 0.8816 (t80) REVERT: C 47 MET cc_start: 0.5313 (tpt) cc_final: 0.4904 (tpp) REVERT: C 103 THR cc_start: 0.9294 (p) cc_final: 0.9045 (t) REVERT: C 104 LEU cc_start: 0.9067 (tp) cc_final: 0.8680 (tp) REVERT: C 111 ASN cc_start: 0.8467 (m-40) cc_final: 0.7752 (m110) REVERT: C 260 THR cc_start: 0.9723 (m) cc_final: 0.9470 (t) REVERT: C 276 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 283 MET cc_start: 0.8535 (mtp) cc_final: 0.6962 (mmm) REVERT: C 296 ASN cc_start: 0.9248 (m-40) cc_final: 0.8977 (m-40) REVERT: C 297 ASN cc_start: 0.9243 (t0) cc_final: 0.8798 (t0) REVERT: C 341 ILE cc_start: 0.9641 (mt) cc_final: 0.9357 (tt) REVERT: D 132 MET cc_start: 0.8589 (ppp) cc_final: 0.8342 (ppp) REVERT: D 153 LEU cc_start: 0.8813 (tt) cc_final: 0.8510 (tt) REVERT: D 189 LEU cc_start: 0.9396 (tt) cc_final: 0.9096 (tt) REVERT: D 190 MET cc_start: 0.8724 (tpp) cc_final: 0.8056 (tpp) REVERT: D 213 LYS cc_start: 0.8757 (tppt) cc_final: 0.8411 (tppt) REVERT: D 283 MET cc_start: 0.9047 (mmp) cc_final: 0.8607 (mmp) REVERT: D 305 MET cc_start: 0.9123 (mmt) cc_final: 0.8834 (mmt) REVERT: D 318 THR cc_start: 0.8889 (p) cc_final: 0.8612 (t) REVERT: F 227 VAL cc_start: 0.8616 (p) cc_final: 0.8387 (m) REVERT: G 45 MET cc_start: 0.7817 (mmt) cc_final: 0.7441 (mmp) REVERT: G 77 PHE cc_start: 0.7317 (t80) cc_final: 0.6849 (t80) REVERT: G 80 MET cc_start: 0.7516 (ptt) cc_final: 0.7141 (mtt) REVERT: H 49 GLN cc_start: 0.5720 (tm130) cc_final: 0.5152 (tm-30) REVERT: H 56 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8133 (tp-100) REVERT: H 60 GLN cc_start: 0.8801 (mt0) cc_final: 0.8462 (mt0) REVERT: H 150 ILE cc_start: 0.8396 (pt) cc_final: 0.8192 (pt) REVERT: H 156 MET cc_start: 0.2777 (mtm) cc_final: 0.2468 (mtm) REVERT: J 67 LYS cc_start: 0.8639 (tptp) cc_final: 0.8317 (tptp) REVERT: J 78 GLN cc_start: 0.7962 (mp10) cc_final: 0.7756 (mp10) REVERT: J 142 TYR cc_start: 0.8289 (m-10) cc_final: 0.7919 (m-10) REVERT: J 166 LEU cc_start: 0.9065 (mt) cc_final: 0.8807 (mt) REVERT: J 248 ILE cc_start: 0.9100 (mt) cc_final: 0.8711 (mt) REVERT: J 349 MET cc_start: 0.7400 (ptt) cc_final: 0.7195 (ptt) REVERT: J 357 MET cc_start: 0.9063 (mtm) cc_final: 0.8242 (mtm) REVERT: J 369 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7073 (mmt-90) REVERT: J 371 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7186 (tm-30) REVERT: J 387 LEU cc_start: 0.8613 (tp) cc_final: 0.8320 (tp) REVERT: J 388 MET cc_start: 0.8904 (mmm) cc_final: 0.8542 (mmm) REVERT: J 433 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7278 (tm-30) REVERT: J 435 MET cc_start: 0.8461 (tmm) cc_final: 0.7897 (tmm) REVERT: J 437 ASN cc_start: 0.8750 (m110) cc_final: 0.7960 (m110) REVERT: J 439 MET cc_start: 0.8875 (ptp) cc_final: 0.8386 (ptm) REVERT: J 447 LEU cc_start: 0.9069 (mp) cc_final: 0.8732 (mp) REVERT: J 448 GLU cc_start: 0.8041 (pp20) cc_final: 0.7825 (pp20) REVERT: J 531 MET cc_start: 0.8634 (mmt) cc_final: 0.7639 (mmm) REVERT: J 588 TYR cc_start: 0.7761 (m-10) cc_final: 0.7510 (m-10) REVERT: J 640 LYS cc_start: 0.7896 (tmtt) cc_final: 0.7575 (tmtt) REVERT: J 704 ILE cc_start: 0.9524 (mm) cc_final: 0.8668 (mm) REVERT: J 711 ASN cc_start: 0.8970 (m110) cc_final: 0.8379 (m110) REVERT: K 87 ILE cc_start: 0.8965 (tt) cc_final: 0.8572 (mm) REVERT: K 92 MET cc_start: 0.7417 (tpt) cc_final: 0.7209 (tpp) REVERT: K 105 LEU cc_start: 0.9035 (pp) cc_final: 0.8229 (tp) REVERT: K 173 SER cc_start: 0.8518 (p) cc_final: 0.8283 (p) REVERT: K 271 SER cc_start: 0.8836 (t) cc_final: 0.8571 (t) REVERT: K 274 ILE cc_start: 0.8517 (mm) cc_final: 0.7986 (mm) REVERT: K 275 PHE cc_start: 0.8466 (m-10) cc_final: 0.8112 (m-10) REVERT: K 295 PRO cc_start: 0.7477 (Cg_exo) cc_final: 0.6880 (Cg_endo) REVERT: K 362 MET cc_start: 0.8603 (mmt) cc_final: 0.7825 (mmm) REVERT: K 435 MET cc_start: 0.8673 (ttp) cc_final: 0.8059 (ttp) REVERT: K 454 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8288 (tp40) REVERT: K 476 LEU cc_start: 0.9162 (tp) cc_final: 0.8767 (tt) REVERT: K 479 ASN cc_start: 0.9567 (m-40) cc_final: 0.8549 (m-40) REVERT: K 483 GLU cc_start: 0.8739 (mm-30) cc_final: 0.7737 (mm-30) REVERT: K 521 ILE cc_start: 0.9282 (mt) cc_final: 0.8736 (mm) REVERT: K 526 LYS cc_start: 0.8434 (mppt) cc_final: 0.8228 (mmtt) REVERT: K 531 MET cc_start: 0.7819 (mmt) cc_final: 0.7353 (mmt) REVERT: K 535 GLU cc_start: 0.8109 (pt0) cc_final: 0.7755 (pt0) REVERT: K 539 MET cc_start: 0.8860 (mtm) cc_final: 0.8574 (mtm) REVERT: K 581 HIS cc_start: 0.8984 (m-70) cc_final: 0.8114 (m170) REVERT: K 620 LEU cc_start: 0.9300 (mt) cc_final: 0.8914 (mt) REVERT: K 672 CYS cc_start: 0.8597 (p) cc_final: 0.8268 (t) REVERT: K 736 ILE cc_start: 0.6982 (mp) cc_final: 0.6691 (mm) REVERT: K 749 LEU cc_start: 0.7399 (mt) cc_final: 0.7015 (mt) outliers start: 2 outliers final: 1 residues processed: 850 average time/residue: 0.2254 time to fit residues: 307.1557 Evaluate side-chains 639 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 228 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 162 ASN C 78 ASN C 173 HIS ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 HIS J 482 ASN J 568 ASN ** J 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 711 ASN K 27 GLN K 172 GLN K 482 ASN K 668 HIS ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080429 restraints weight = 111102.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081146 restraints weight = 73609.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081442 restraints weight = 55775.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.081768 restraints weight = 48139.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081862 restraints weight = 45571.059| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 33808 Z= 0.318 Angle : 0.860 11.097 45560 Z= 0.450 Chirality : 0.050 0.352 4984 Planarity : 0.006 0.177 5928 Dihedral : 6.054 49.157 4550 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4130 helix: 0.36 (0.11), residues: 2062 sheet: -0.59 (0.25), residues: 393 loop : -1.23 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 75 TYR 0.034 0.003 TYR B 306 PHE 0.027 0.003 PHE C 352 TRP 0.038 0.003 TRP C 356 HIS 0.022 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.32 (33807) covalent geometry : angle 0.86038 / 0.45 (45560) hydrogen bonds : bond 0.05667 / 3.79 ( 1747) hydrogen bonds : angle 5.21348 / 3.68 ( 4950) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 778 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8838 (m-30) cc_final: 0.8108 (m-30) REVERT: A 99 GLU cc_start: 0.8509 (pm20) cc_final: 0.8004 (pm20) REVERT: A 100 GLU cc_start: 0.8259 (mp0) cc_final: 0.8001 (mp0) REVERT: A 102 PRO cc_start: 0.9357 (Cg_exo) cc_final: 0.9022 (Cg_endo) REVERT: A 107 GLU cc_start: 0.9255 (tp30) cc_final: 0.8776 (tp30) REVERT: A 129 VAL cc_start: 0.8385 (m) cc_final: 0.8126 (t) REVERT: A 160 THR cc_start: 0.9019 (m) cc_final: 0.8814 (m) REVERT: A 171 LEU cc_start: 0.9095 (mp) cc_final: 0.8691 (mp) REVERT: A 193 LEU cc_start: 0.9189 (tp) cc_final: 0.8982 (tp) REVERT: A 200 PHE cc_start: 0.8114 (m-80) cc_final: 0.7906 (m-10) REVERT: A 247 VAL cc_start: 0.9632 (m) cc_final: 0.9408 (p) REVERT: A 274 ILE cc_start: 0.8850 (pt) cc_final: 0.8005 (mm) REVERT: A 288 ASP cc_start: 0.8364 (m-30) cc_final: 0.8161 (m-30) REVERT: A 356 TRP cc_start: 0.9072 (m100) cc_final: 0.8827 (m100) REVERT: B 61 LYS cc_start: 0.9186 (mptt) cc_final: 0.8908 (mmtm) REVERT: B 119 MET cc_start: 0.8775 (ttm) cc_final: 0.8425 (ttm) REVERT: B 192 ILE cc_start: 0.9614 (pt) cc_final: 0.9364 (mm) REVERT: C 104 LEU cc_start: 0.9164 (tp) cc_final: 0.8455 (tp) REVERT: C 111 ASN cc_start: 0.8398 (m-40) cc_final: 0.7929 (m110) REVERT: C 202 THR cc_start: 0.9319 (m) cc_final: 0.9026 (t) REVERT: C 237 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8469 (tt0) REVERT: C 244 ASP cc_start: 0.9328 (p0) cc_final: 0.9043 (p0) REVERT: C 276 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6980 (tm-30) REVERT: C 296 ASN cc_start: 0.9260 (m-40) cc_final: 0.8965 (m-40) REVERT: C 297 ASN cc_start: 0.9359 (t0) cc_final: 0.8924 (t0) REVERT: C 341 ILE cc_start: 0.9633 (mt) cc_final: 0.9354 (tt) REVERT: D 34 ILE cc_start: 0.9428 (mp) cc_final: 0.8927 (mp) REVERT: D 132 MET cc_start: 0.9036 (ppp) cc_final: 0.8212 (ppp) REVERT: D 153 LEU cc_start: 0.9047 (tt) cc_final: 0.8726 (tt) REVERT: D 213 LYS cc_start: 0.8803 (tppt) cc_final: 0.8372 (tppt) REVERT: D 227 MET cc_start: 0.8407 (mmt) cc_final: 0.8041 (mmt) REVERT: D 283 MET cc_start: 0.8973 (mmp) cc_final: 0.8692 (mmp) REVERT: D 318 THR cc_start: 0.8989 (p) cc_final: 0.8709 (t) REVERT: E 106 LEU cc_start: 0.8103 (tp) cc_final: 0.7392 (tt) REVERT: F 85 VAL cc_start: 0.8675 (t) cc_final: 0.8437 (t) REVERT: G 45 MET cc_start: 0.7541 (mmt) cc_final: 0.7162 (mmp) REVERT: G 57 LEU cc_start: 0.7337 (mm) cc_final: 0.6996 (mm) REVERT: G 90 LYS cc_start: 0.7118 (mttm) cc_final: 0.6524 (mttp) REVERT: G 161 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7680 (mm-30) REVERT: H 49 GLN cc_start: 0.6007 (tm130) cc_final: 0.5392 (tm-30) REVERT: H 56 GLN cc_start: 0.8268 (tp-100) cc_final: 0.7818 (tp-100) REVERT: H 60 GLN cc_start: 0.8888 (mt0) cc_final: 0.8536 (mt0) REVERT: H 96 ASP cc_start: 0.6408 (m-30) cc_final: 0.6135 (m-30) REVERT: J 166 LEU cc_start: 0.9110 (mt) cc_final: 0.8901 (mt) REVERT: J 248 ILE cc_start: 0.8985 (mt) cc_final: 0.8694 (mt) REVERT: J 328 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6607 (mm-30) REVERT: J 357 MET cc_start: 0.9277 (mtm) cc_final: 0.8580 (mtm) REVERT: J 369 ARG cc_start: 0.7461 (mpt180) cc_final: 0.7225 (mmt-90) REVERT: J 371 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7217 (tm-30) REVERT: J 382 ASP cc_start: 0.8099 (m-30) cc_final: 0.7894 (m-30) REVERT: J 387 LEU cc_start: 0.8716 (tp) cc_final: 0.8397 (tp) REVERT: J 388 MET cc_start: 0.9061 (mmm) cc_final: 0.8809 (mmm) REVERT: J 433 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7077 (tm-30) REVERT: J 435 MET cc_start: 0.8380 (tmm) cc_final: 0.7860 (tmm) REVERT: J 437 ASN cc_start: 0.8883 (m110) cc_final: 0.7927 (m110) REVERT: J 439 MET cc_start: 0.8981 (ptp) cc_final: 0.8616 (ptm) REVERT: J 490 ASN cc_start: 0.8428 (m110) cc_final: 0.8181 (m110) REVERT: J 531 MET cc_start: 0.8833 (mmt) cc_final: 0.8363 (mmp) REVERT: J 588 TYR cc_start: 0.7507 (m-10) cc_final: 0.7170 (m-10) REVERT: J 640 LYS cc_start: 0.7893 (tmtt) cc_final: 0.7416 (tmtt) REVERT: J 704 ILE cc_start: 0.9533 (mm) cc_final: 0.8967 (mm) REVERT: J 762 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8199 (mmmm) REVERT: K 87 ILE cc_start: 0.8969 (tt) cc_final: 0.8538 (mm) REVERT: K 92 MET cc_start: 0.7402 (tpt) cc_final: 0.7189 (tpp) REVERT: K 143 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6930 (tpt170) REVERT: K 232 ASN cc_start: 0.6336 (t0) cc_final: 0.6092 (t0) REVERT: K 271 SER cc_start: 0.8952 (t) cc_final: 0.8706 (t) REVERT: K 274 ILE cc_start: 0.8720 (mm) cc_final: 0.8388 (mm) REVERT: K 275 PHE cc_start: 0.8490 (m-10) cc_final: 0.8197 (m-10) REVERT: K 295 PRO cc_start: 0.7697 (Cg_exo) cc_final: 0.7036 (Cg_endo) REVERT: K 362 MET cc_start: 0.8356 (mmt) cc_final: 0.8139 (mmt) REVERT: K 435 MET cc_start: 0.9078 (ttp) cc_final: 0.8535 (tpp) REVERT: K 476 LEU cc_start: 0.9265 (tp) cc_final: 0.8945 (tt) REVERT: K 479 ASN cc_start: 0.9518 (m-40) cc_final: 0.8817 (m-40) REVERT: K 581 HIS cc_start: 0.8868 (m-70) cc_final: 0.8401 (m170) REVERT: K 620 LEU cc_start: 0.9376 (mt) cc_final: 0.8771 (mt) REVERT: K 672 CYS cc_start: 0.8622 (p) cc_final: 0.8352 (t) REVERT: K 736 ILE cc_start: 0.7136 (mp) cc_final: 0.6888 (mm) REVERT: K 749 LEU cc_start: 0.7676 (mt) cc_final: 0.7053 (mt) REVERT: L 122 ILE cc_start: 0.8688 (mt) cc_final: 0.8248 (mt) REVERT: L 136 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7173 (mm-30) REVERT: M 111 ASP cc_start: 0.6635 (t0) cc_final: 0.6408 (t0) outliers start: 1 outliers final: 0 residues processed: 778 average time/residue: 0.2161 time to fit residues: 272.5113 Evaluate side-chains 592 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 303 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN D 162 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN J 65 HIS ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN J 568 ASN ** J 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084045 restraints weight = 108035.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085208 restraints weight = 71669.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086028 restraints weight = 51799.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086596 restraints weight = 40214.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086942 restraints weight = 33459.563| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33808 Z= 0.169 Angle : 0.710 10.892 45560 Z= 0.373 Chirality : 0.045 0.296 4984 Planarity : 0.005 0.055 5928 Dihedral : 5.640 50.548 4550 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4130 helix: 0.60 (0.11), residues: 2079 sheet: -0.56 (0.26), residues: 380 loop : -1.12 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 95 TYR 0.032 0.002 TYR I 238 PHE 0.039 0.002 PHE G 77 TRP 0.027 0.002 TRP C 356 HIS 0.007 0.001 HIS K 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (33807) covalent geometry : angle 0.71035 / 0.37 (45560) hydrogen bonds : bond 0.05072 / 3.39 ( 1747) hydrogen bonds : angle 4.86606 / 3.45 ( 4950) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 809 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8834 (m-30) cc_final: 0.8070 (m-30) REVERT: A 99 GLU cc_start: 0.8636 (pm20) cc_final: 0.8195 (pm20) REVERT: A 100 GLU cc_start: 0.8325 (mp0) cc_final: 0.8053 (mp0) REVERT: A 107 GLU cc_start: 0.9145 (tp30) cc_final: 0.8754 (tp30) REVERT: A 208 ILE cc_start: 0.9316 (mp) cc_final: 0.8758 (tp) REVERT: A 211 ASP cc_start: 0.8072 (m-30) cc_final: 0.7823 (m-30) REVERT: A 214 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 274 ILE cc_start: 0.8809 (pt) cc_final: 0.7877 (mm) REVERT: A 279 TYR cc_start: 0.8146 (t80) cc_final: 0.7885 (t80) REVERT: A 288 ASP cc_start: 0.8466 (m-30) cc_final: 0.8209 (m-30) REVERT: A 305 MET cc_start: 0.7810 (tpp) cc_final: 0.7566 (tpp) REVERT: B 61 LYS cc_start: 0.9146 (mptt) cc_final: 0.8850 (mmtm) REVERT: B 176 MET cc_start: 0.7550 (mtp) cc_final: 0.7081 (ttm) REVERT: B 269 MET cc_start: 0.8349 (mmm) cc_final: 0.7261 (mmm) REVERT: B 352 PHE cc_start: 0.9200 (t80) cc_final: 0.8998 (t80) REVERT: C 104 LEU cc_start: 0.8833 (tp) cc_final: 0.8489 (tp) REVERT: C 107 GLU cc_start: 0.8615 (tp30) cc_final: 0.8407 (tp30) REVERT: C 111 ASN cc_start: 0.8407 (m-40) cc_final: 0.7725 (m110) REVERT: C 123 MET cc_start: 0.8579 (mmm) cc_final: 0.8186 (tpp) REVERT: C 209 VAL cc_start: 0.9490 (t) cc_final: 0.9274 (t) REVERT: C 276 GLU cc_start: 0.7269 (tm-30) cc_final: 0.7003 (tm-30) REVERT: C 283 MET cc_start: 0.8539 (mtp) cc_final: 0.7324 (mmm) REVERT: C 296 ASN cc_start: 0.9282 (m-40) cc_final: 0.8740 (m-40) REVERT: C 297 ASN cc_start: 0.9372 (t0) cc_final: 0.8975 (t0) REVERT: C 335 ARG cc_start: 0.9043 (mtm180) cc_final: 0.8508 (mtt180) REVERT: C 341 ILE cc_start: 0.9619 (mt) cc_final: 0.9308 (tt) REVERT: C 356 TRP cc_start: 0.8464 (m-10) cc_final: 0.8119 (m-10) REVERT: D 34 ILE cc_start: 0.9355 (mp) cc_final: 0.8791 (mp) REVERT: D 132 MET cc_start: 0.9013 (ppp) cc_final: 0.8268 (ppp) REVERT: D 153 LEU cc_start: 0.8931 (tt) cc_final: 0.8705 (tt) REVERT: D 189 LEU cc_start: 0.9334 (tt) cc_final: 0.9030 (tt) REVERT: D 213 LYS cc_start: 0.8792 (tppt) cc_final: 0.8413 (tppt) REVERT: D 227 MET cc_start: 0.8251 (mmt) cc_final: 0.7919 (mmt) REVERT: D 318 THR cc_start: 0.8938 (p) cc_final: 0.8644 (t) REVERT: E 90 ARG cc_start: 0.7142 (mtm110) cc_final: 0.6877 (mtm-85) REVERT: E 111 GLN cc_start: 0.8381 (mt0) cc_final: 0.8165 (mt0) REVERT: F 89 ASN cc_start: 0.7806 (m-40) cc_final: 0.7265 (m110) REVERT: F 167 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7745 (mtp85) REVERT: G 45 MET cc_start: 0.7828 (mmt) cc_final: 0.7477 (mmp) REVERT: G 112 ILE cc_start: 0.8730 (mm) cc_final: 0.8527 (mm) REVERT: G 161 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7460 (mm-30) REVERT: H 60 GLN cc_start: 0.8828 (mt0) cc_final: 0.8508 (mt0) REVERT: H 96 ASP cc_start: 0.6263 (m-30) cc_final: 0.5934 (m-30) REVERT: H 150 ILE cc_start: 0.8387 (pt) cc_final: 0.8147 (pt) REVERT: H 156 MET cc_start: 0.2786 (mtm) cc_final: 0.2320 (mtm) REVERT: I 234 TRP cc_start: 0.6254 (t60) cc_final: 0.5985 (t60) REVERT: J 67 LYS cc_start: 0.8524 (tptp) cc_final: 0.8282 (tptm) REVERT: J 142 TYR cc_start: 0.8322 (m-10) cc_final: 0.8122 (m-10) REVERT: J 357 MET cc_start: 0.9158 (mtm) cc_final: 0.8393 (mtm) REVERT: J 369 ARG cc_start: 0.7611 (mpt180) cc_final: 0.7320 (mmt-90) REVERT: J 371 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7259 (tm-30) REVERT: J 382 ASP cc_start: 0.7963 (m-30) cc_final: 0.7734 (m-30) REVERT: J 387 LEU cc_start: 0.8491 (tp) cc_final: 0.8240 (tp) REVERT: J 433 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7037 (tm-30) REVERT: J 435 MET cc_start: 0.8419 (tmm) cc_final: 0.7647 (tmm) REVERT: J 437 ASN cc_start: 0.8836 (m110) cc_final: 0.7954 (m110) REVERT: J 439 MET cc_start: 0.8747 (ptp) cc_final: 0.8235 (ptm) REVERT: J 531 MET cc_start: 0.8848 (mmt) cc_final: 0.8182 (mmm) REVERT: J 588 TYR cc_start: 0.7566 (m-10) cc_final: 0.7328 (m-10) REVERT: J 640 LYS cc_start: 0.7694 (tmtt) cc_final: 0.7301 (tmtt) REVERT: J 704 ILE cc_start: 0.9489 (mm) cc_final: 0.8844 (mm) REVERT: J 711 ASN cc_start: 0.8930 (m-40) cc_final: 0.8347 (m110) REVERT: J 762 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8177 (mmmm) REVERT: K 87 ILE cc_start: 0.8941 (tt) cc_final: 0.8313 (mm) REVERT: K 92 MET cc_start: 0.7400 (tpt) cc_final: 0.7131 (tpp) REVERT: K 105 LEU cc_start: 0.9115 (pp) cc_final: 0.8369 (tp) REVERT: K 232 ASN cc_start: 0.6230 (t0) cc_final: 0.5943 (t0) REVERT: K 271 SER cc_start: 0.8866 (t) cc_final: 0.8628 (t) REVERT: K 274 ILE cc_start: 0.8673 (mm) cc_final: 0.8309 (mm) REVERT: K 275 PHE cc_start: 0.8636 (m-10) cc_final: 0.8379 (m-10) REVERT: K 295 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7076 (Cg_endo) REVERT: K 362 MET cc_start: 0.8445 (mmt) cc_final: 0.7881 (mmt) REVERT: K 454 GLN cc_start: 0.9414 (tp-100) cc_final: 0.8221 (tp40) REVERT: K 476 LEU cc_start: 0.9145 (tp) cc_final: 0.8876 (tt) REVERT: K 521 ILE cc_start: 0.9361 (mt) cc_final: 0.9136 (mm) REVERT: K 524 ILE cc_start: 0.8894 (tt) cc_final: 0.8122 (tt) REVERT: K 531 MET cc_start: 0.7752 (mmt) cc_final: 0.7291 (mmt) REVERT: K 539 MET cc_start: 0.8810 (mtm) cc_final: 0.8585 (mtt) REVERT: K 582 TYR cc_start: 0.7781 (p90) cc_final: 0.7428 (p90) REVERT: K 620 LEU cc_start: 0.9328 (mt) cc_final: 0.8802 (mt) REVERT: K 672 CYS cc_start: 0.8611 (p) cc_final: 0.8348 (t) REVERT: K 736 ILE cc_start: 0.6854 (mp) cc_final: 0.6543 (mm) REVERT: K 749 LEU cc_start: 0.7684 (mt) cc_final: 0.7231 (mt) REVERT: K 799 MET cc_start: 0.5430 (mtp) cc_final: 0.5174 (mtp) REVERT: L 122 ILE cc_start: 0.8645 (mt) cc_final: 0.8383 (mt) REVERT: L 136 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7233 (mm-30) REVERT: L 193 ILE cc_start: 0.7475 (mm) cc_final: 0.7171 (mm) outliers start: 2 outliers final: 1 residues processed: 809 average time/residue: 0.2128 time to fit residues: 277.8210 Evaluate side-chains 608 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 607 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 167 optimal weight: 0.0970 chunk 223 optimal weight: 0.7980 chunk 376 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 327 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN J 568 ASN K 172 GLN K 479 ASN L 121 HIS M 120 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.086478 restraints weight = 107086.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.087309 restraints weight = 72610.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087873 restraints weight = 54940.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.088435 restraints weight = 43473.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.088414 restraints weight = 39097.782| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33808 Z= 0.147 Angle : 0.705 12.429 45560 Z= 0.364 Chirality : 0.045 0.282 4984 Planarity : 0.004 0.052 5928 Dihedral : 5.421 45.757 4550 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.06 % Allowed : 0.78 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4130 helix: 0.78 (0.11), residues: 2078 sheet: -0.38 (0.26), residues: 372 loop : -1.02 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 169 TYR 0.044 0.002 TYR D 133 PHE 0.028 0.002 PHE G 77 TRP 0.024 0.002 TRP C 356 HIS 0.005 0.001 HIS J 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (33807) covalent geometry : angle 0.70471 / 0.36 (45560) hydrogen bonds : bond 0.04885 / 3.26 ( 1747) hydrogen bonds : angle 4.71539 / 3.33 ( 4950) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 812 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8836 (m-30) cc_final: 0.7911 (m-30) REVERT: A 99 GLU cc_start: 0.8671 (pm20) cc_final: 0.8333 (pm20) REVERT: A 100 GLU cc_start: 0.8452 (mp0) cc_final: 0.8177 (mp0) REVERT: A 107 GLU cc_start: 0.9074 (tp30) cc_final: 0.8661 (tp30) REVERT: A 160 THR cc_start: 0.9052 (m) cc_final: 0.8851 (m) REVERT: A 208 ILE cc_start: 0.9258 (mp) cc_final: 0.8724 (tp) REVERT: A 211 ASP cc_start: 0.8037 (m-30) cc_final: 0.7793 (m-30) REVERT: A 214 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 274 ILE cc_start: 0.8890 (pt) cc_final: 0.7989 (mm) REVERT: A 279 TYR cc_start: 0.8417 (t80) cc_final: 0.7798 (t80) REVERT: A 285 CYS cc_start: 0.8941 (m) cc_final: 0.8702 (p) REVERT: A 288 ASP cc_start: 0.8424 (m-30) cc_final: 0.8192 (m-30) REVERT: A 305 MET cc_start: 0.7894 (tpp) cc_final: 0.7646 (tpp) REVERT: B 140 LEU cc_start: 0.9111 (mp) cc_final: 0.8506 (mt) REVERT: B 145 SER cc_start: 0.9697 (m) cc_final: 0.9060 (t) REVERT: B 176 MET cc_start: 0.7555 (mtp) cc_final: 0.7102 (ttm) REVERT: B 269 MET cc_start: 0.8349 (mmm) cc_final: 0.7258 (mmm) REVERT: B 352 PHE cc_start: 0.9111 (t80) cc_final: 0.8636 (t80) REVERT: C 104 LEU cc_start: 0.8777 (tp) cc_final: 0.8543 (tp) REVERT: C 111 ASN cc_start: 0.8465 (m-40) cc_final: 0.7856 (m110) REVERT: C 123 MET cc_start: 0.8694 (mmm) cc_final: 0.8289 (tpp) REVERT: C 244 ASP cc_start: 0.9179 (p0) cc_final: 0.8820 (p0) REVERT: C 276 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6935 (tm-30) REVERT: C 283 MET cc_start: 0.8629 (mtp) cc_final: 0.7222 (mmm) REVERT: C 296 ASN cc_start: 0.9196 (m-40) cc_final: 0.8651 (m-40) REVERT: C 297 ASN cc_start: 0.9283 (t0) cc_final: 0.8909 (t0) REVERT: C 335 ARG cc_start: 0.9067 (mtm180) cc_final: 0.8689 (mtt180) REVERT: C 341 ILE cc_start: 0.9615 (mt) cc_final: 0.9313 (tt) REVERT: C 356 TRP cc_start: 0.8129 (m-10) cc_final: 0.7917 (m-10) REVERT: D 82 MET cc_start: 0.8809 (tpt) cc_final: 0.8458 (tpp) REVERT: D 86 TRP cc_start: 0.8890 (m-10) cc_final: 0.8564 (m-90) REVERT: D 132 MET cc_start: 0.8852 (ppp) cc_final: 0.8117 (ppp) REVERT: D 213 LYS cc_start: 0.8758 (tppt) cc_final: 0.8254 (tppt) REVERT: D 227 MET cc_start: 0.8243 (mmt) cc_final: 0.7925 (mmt) REVERT: D 283 MET cc_start: 0.9064 (mmm) cc_final: 0.8813 (mmt) REVERT: D 318 THR cc_start: 0.8883 (p) cc_final: 0.8586 (t) REVERT: D 335 ARG cc_start: 0.8001 (mpp80) cc_final: 0.7245 (mtt90) REVERT: E 111 GLN cc_start: 0.8242 (mt0) cc_final: 0.7937 (mt0) REVERT: E 125 ARG cc_start: 0.8552 (tmm160) cc_final: 0.8309 (ttt180) REVERT: E 196 GLU cc_start: 0.8724 (tt0) cc_final: 0.8414 (tt0) REVERT: F 89 ASN cc_start: 0.7689 (m-40) cc_final: 0.7218 (m-40) REVERT: F 167 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7689 (mtp85) REVERT: G 45 MET cc_start: 0.7848 (mmt) cc_final: 0.7612 (mmp) REVERT: G 80 MET cc_start: 0.8167 (ppp) cc_final: 0.7853 (ppp) REVERT: G 112 ILE cc_start: 0.8794 (mm) cc_final: 0.8570 (mm) REVERT: G 157 MET cc_start: 0.5918 (tpp) cc_final: 0.5413 (tpp) REVERT: H 56 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8086 (tp-100) REVERT: H 60 GLN cc_start: 0.8732 (mt0) cc_final: 0.8416 (mt0) REVERT: H 96 ASP cc_start: 0.6078 (m-30) cc_final: 0.5675 (m-30) REVERT: H 150 ILE cc_start: 0.8064 (pt) cc_final: 0.7849 (pt) REVERT: J 67 LYS cc_start: 0.8540 (tptp) cc_final: 0.8334 (tptm) REVERT: J 248 ILE cc_start: 0.9073 (mt) cc_final: 0.8610 (mt) REVERT: J 357 MET cc_start: 0.9067 (mtm) cc_final: 0.8344 (mtm) REVERT: J 369 ARG cc_start: 0.7543 (mpt180) cc_final: 0.7325 (mmt-90) REVERT: J 371 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7249 (tm-30) REVERT: J 433 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6904 (tm-30) REVERT: J 435 MET cc_start: 0.8448 (tmm) cc_final: 0.7774 (tmm) REVERT: J 437 ASN cc_start: 0.8833 (m110) cc_final: 0.7945 (m110) REVERT: J 439 MET cc_start: 0.8789 (ptp) cc_final: 0.8182 (ptm) REVERT: J 531 MET cc_start: 0.9172 (mmt) cc_final: 0.8665 (mmm) REVERT: J 537 GLU cc_start: 0.7923 (pm20) cc_final: 0.7088 (pm20) REVERT: J 594 LEU cc_start: 0.9241 (mm) cc_final: 0.8589 (mm) REVERT: J 640 LYS cc_start: 0.7845 (tmtt) cc_final: 0.7497 (tmtt) REVERT: J 704 ILE cc_start: 0.9493 (mm) cc_final: 0.8787 (mm) REVERT: J 711 ASN cc_start: 0.9028 (m-40) cc_final: 0.8464 (m110) REVERT: J 754 ASN cc_start: 0.9147 (p0) cc_final: 0.8513 (t0) REVERT: J 762 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8290 (mmmm) REVERT: K 87 ILE cc_start: 0.8874 (tt) cc_final: 0.8317 (mt) REVERT: K 92 MET cc_start: 0.7302 (tpt) cc_final: 0.6923 (tpp) REVERT: K 105 LEU cc_start: 0.9039 (pp) cc_final: 0.8325 (tp) REVERT: K 172 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8539 (mm110) REVERT: K 232 ASN cc_start: 0.6266 (t0) cc_final: 0.5995 (t0) REVERT: K 271 SER cc_start: 0.8792 (t) cc_final: 0.8393 (t) REVERT: K 274 ILE cc_start: 0.8690 (mm) cc_final: 0.8331 (mm) REVERT: K 275 PHE cc_start: 0.8619 (m-10) cc_final: 0.8391 (m-10) REVERT: K 295 PRO cc_start: 0.8072 (Cg_exo) cc_final: 0.7446 (Cg_endo) REVERT: K 362 MET cc_start: 0.8423 (mmt) cc_final: 0.7863 (mmt) REVERT: K 435 MET cc_start: 0.8445 (tpp) cc_final: 0.8075 (mmp) REVERT: K 454 GLN cc_start: 0.9363 (tp-100) cc_final: 0.8340 (tp40) REVERT: K 474 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8708 (pt0) REVERT: K 476 LEU cc_start: 0.9087 (tp) cc_final: 0.8781 (tt) REVERT: K 479 ASN cc_start: 0.9166 (m-40) cc_final: 0.8902 (m-40) REVERT: K 524 ILE cc_start: 0.8735 (tt) cc_final: 0.8209 (tt) REVERT: K 531 MET cc_start: 0.7771 (mmt) cc_final: 0.7352 (mmt) REVERT: K 539 MET cc_start: 0.8883 (mtm) cc_final: 0.8632 (mtt) REVERT: K 581 HIS cc_start: 0.8278 (m-70) cc_final: 0.8046 (m170) REVERT: K 620 LEU cc_start: 0.9316 (mt) cc_final: 0.8705 (mt) REVERT: K 672 CYS cc_start: 0.8553 (p) cc_final: 0.8199 (t) REVERT: K 736 ILE cc_start: 0.6785 (mp) cc_final: 0.6502 (mm) REVERT: K 749 LEU cc_start: 0.7431 (mt) cc_final: 0.7218 (mt) REVERT: K 799 MET cc_start: 0.5535 (mtp) cc_final: 0.5334 (mtp) REVERT: L 60 MET cc_start: 0.5469 (ptm) cc_final: 0.5227 (ptm) REVERT: L 122 ILE cc_start: 0.8526 (mt) cc_final: 0.8118 (mt) REVERT: L 136 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7592 (mm-30) outliers start: 2 outliers final: 0 residues processed: 813 average time/residue: 0.2138 time to fit residues: 281.3529 Evaluate side-chains 627 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 61 optimal weight: 0.8980 chunk 292 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 287 optimal weight: 0.6980 chunk 368 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 337 optimal weight: 0.5980 chunk 317 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 HIS J 193 GLN J 482 ASN J 555 ASN J 568 ASN ** J 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085813 restraints weight = 108113.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086862 restraints weight = 68749.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087227 restraints weight = 48233.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087479 restraints weight = 42584.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087585 restraints weight = 39466.275| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33808 Z= 0.157 Angle : 0.712 14.335 45560 Z= 0.369 Chirality : 0.045 0.273 4984 Planarity : 0.004 0.054 5928 Dihedral : 5.374 46.792 4550 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.08 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4130 helix: 0.74 (0.11), residues: 2087 sheet: -0.38 (0.26), residues: 372 loop : -1.03 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.039 0.002 TYR F 214 PHE 0.028 0.002 PHE G 104 TRP 0.020 0.002 TRP C 356 HIS 0.005 0.001 HIS J 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (33807) covalent geometry : angle 0.71182 / 0.37 (45560) hydrogen bonds : bond 0.04898 / 3.28 ( 1747) hydrogen bonds : angle 4.71375 / 3.32 ( 4950) Misc. bond : bond 0.00009 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 791 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8868 (m-30) cc_final: 0.8058 (m-30) REVERT: A 99 GLU cc_start: 0.8611 (pm20) cc_final: 0.8255 (pm20) REVERT: A 100 GLU cc_start: 0.8469 (mp0) cc_final: 0.8164 (mp0) REVERT: A 107 GLU cc_start: 0.9081 (tp30) cc_final: 0.8758 (tp30) REVERT: A 132 MET cc_start: 0.8391 (tmm) cc_final: 0.8142 (tmm) REVERT: A 160 THR cc_start: 0.9096 (m) cc_final: 0.8841 (m) REVERT: A 211 ASP cc_start: 0.8134 (m-30) cc_final: 0.7827 (m-30) REVERT: A 214 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7482 (mt-10) REVERT: A 274 ILE cc_start: 0.8835 (pt) cc_final: 0.7949 (mm) REVERT: A 279 TYR cc_start: 0.8185 (t80) cc_final: 0.7614 (t80) REVERT: A 305 MET cc_start: 0.7945 (tpp) cc_final: 0.7717 (tpp) REVERT: B 140 LEU cc_start: 0.8977 (mp) cc_final: 0.8542 (tp) REVERT: B 145 SER cc_start: 0.9714 (m) cc_final: 0.9075 (t) REVERT: B 176 MET cc_start: 0.7524 (mtp) cc_final: 0.7059 (ttm) REVERT: B 269 MET cc_start: 0.8375 (mmm) cc_final: 0.7274 (mmm) REVERT: B 352 PHE cc_start: 0.9104 (t80) cc_final: 0.8449 (t80) REVERT: B 372 ARG cc_start: 0.5843 (mtt90) cc_final: 0.5589 (ptp90) REVERT: B 374 CYS cc_start: 0.6847 (p) cc_final: 0.6642 (p) REVERT: C 44 MET cc_start: 0.8645 (ptp) cc_final: 0.8145 (ptt) REVERT: C 104 LEU cc_start: 0.8678 (tp) cc_final: 0.8437 (tp) REVERT: C 111 ASN cc_start: 0.8534 (m-40) cc_final: 0.7924 (m110) REVERT: C 123 MET cc_start: 0.8546 (mmm) cc_final: 0.8333 (tpp) REVERT: C 276 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6948 (tm-30) REVERT: C 283 MET cc_start: 0.8634 (mtp) cc_final: 0.7177 (mmm) REVERT: C 296 ASN cc_start: 0.9214 (m-40) cc_final: 0.8659 (m-40) REVERT: C 297 ASN cc_start: 0.9341 (t0) cc_final: 0.8943 (t0) REVERT: C 335 ARG cc_start: 0.9022 (mtm180) cc_final: 0.8655 (mtt180) REVERT: C 341 ILE cc_start: 0.9599 (mt) cc_final: 0.9360 (tt) REVERT: C 356 TRP cc_start: 0.8087 (m-10) cc_final: 0.7849 (m-10) REVERT: D 82 MET cc_start: 0.8958 (tpt) cc_final: 0.8500 (tpp) REVERT: D 86 TRP cc_start: 0.8940 (m-10) cc_final: 0.8521 (m-90) REVERT: D 132 MET cc_start: 0.8799 (ppp) cc_final: 0.8142 (ppp) REVERT: D 133 TYR cc_start: 0.7604 (t80) cc_final: 0.7377 (t80) REVERT: D 213 LYS cc_start: 0.8757 (tppt) cc_final: 0.8242 (tppt) REVERT: D 227 MET cc_start: 0.8258 (mmt) cc_final: 0.7972 (mmt) REVERT: D 318 THR cc_start: 0.8862 (p) cc_final: 0.8597 (t) REVERT: D 335 ARG cc_start: 0.8124 (mpp80) cc_final: 0.7311 (mtt90) REVERT: E 90 ARG cc_start: 0.6991 (mtm110) cc_final: 0.6741 (ptt90) REVERT: E 125 ARG cc_start: 0.8524 (tmm160) cc_final: 0.8301 (ttt180) REVERT: F 89 ASN cc_start: 0.7986 (m-40) cc_final: 0.7383 (m-40) REVERT: G 45 MET cc_start: 0.7782 (mmt) cc_final: 0.7322 (mmp) REVERT: G 112 ILE cc_start: 0.8700 (mm) cc_final: 0.8452 (mm) REVERT: G 157 MET cc_start: 0.5857 (tpp) cc_final: 0.5436 (tpp) REVERT: H 96 ASP cc_start: 0.5972 (m-30) cc_final: 0.5517 (m-30) REVERT: H 150 ILE cc_start: 0.8163 (pt) cc_final: 0.7823 (pt) REVERT: J 248 ILE cc_start: 0.9046 (mt) cc_final: 0.8583 (mt) REVERT: J 349 MET cc_start: 0.7830 (ptp) cc_final: 0.7561 (ptt) REVERT: J 357 MET cc_start: 0.9111 (mtm) cc_final: 0.8356 (mtm) REVERT: J 371 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7295 (tm-30) REVERT: J 433 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6973 (tm-30) REVERT: J 435 MET cc_start: 0.8453 (tmm) cc_final: 0.7786 (tmm) REVERT: J 437 ASN cc_start: 0.8842 (m110) cc_final: 0.7937 (m110) REVERT: J 439 MET cc_start: 0.8844 (ptp) cc_final: 0.8219 (ptm) REVERT: J 490 ASN cc_start: 0.8493 (m110) cc_final: 0.8000 (m-40) REVERT: J 531 MET cc_start: 0.9207 (mmt) cc_final: 0.8622 (mmm) REVERT: J 555 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8203 (t0) REVERT: J 594 LEU cc_start: 0.9193 (mm) cc_final: 0.8533 (mm) REVERT: J 640 LYS cc_start: 0.7863 (tmtt) cc_final: 0.7477 (tmtt) REVERT: J 711 ASN cc_start: 0.9039 (m-40) cc_final: 0.8500 (m110) REVERT: J 754 ASN cc_start: 0.9142 (p0) cc_final: 0.8587 (t0) REVERT: J 762 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8415 (mmmm) REVERT: K 5 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6750 (tt0) REVERT: K 87 ILE cc_start: 0.8884 (tt) cc_final: 0.8351 (mt) REVERT: K 232 ASN cc_start: 0.6402 (t0) cc_final: 0.6110 (t0) REVERT: K 271 SER cc_start: 0.8801 (t) cc_final: 0.8420 (t) REVERT: K 274 ILE cc_start: 0.8721 (mm) cc_final: 0.8288 (mm) REVERT: K 275 PHE cc_start: 0.8651 (m-10) cc_final: 0.8394 (m-10) REVERT: K 295 PRO cc_start: 0.7889 (Cg_exo) cc_final: 0.7118 (Cg_endo) REVERT: K 351 LYS cc_start: 0.9305 (tptm) cc_final: 0.8725 (tptm) REVERT: K 362 MET cc_start: 0.8433 (mmt) cc_final: 0.7749 (mmt) REVERT: K 435 MET cc_start: 0.8707 (tpp) cc_final: 0.8287 (tpp) REVERT: K 453 ARG cc_start: 0.7696 (ptp90) cc_final: 0.7359 (ptp90) REVERT: K 454 GLN cc_start: 0.9369 (tp-100) cc_final: 0.8365 (tp40) REVERT: K 460 LEU cc_start: 0.8969 (tt) cc_final: 0.8496 (tp) REVERT: K 474 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8689 (pt0) REVERT: K 476 LEU cc_start: 0.9084 (tp) cc_final: 0.8798 (tt) REVERT: K 531 MET cc_start: 0.7766 (mmt) cc_final: 0.7547 (mmt) REVERT: K 620 LEU cc_start: 0.9358 (mt) cc_final: 0.8839 (mt) REVERT: K 672 CYS cc_start: 0.8495 (p) cc_final: 0.8255 (t) REVERT: K 736 ILE cc_start: 0.6824 (mp) cc_final: 0.6490 (mm) REVERT: K 749 LEU cc_start: 0.7482 (mt) cc_final: 0.7228 (mt) REVERT: L 122 ILE cc_start: 0.8436 (mt) cc_final: 0.8153 (mt) REVERT: L 136 GLU cc_start: 0.7954 (mm-30) cc_final: 0.6941 (mm-30) REVERT: M 149 VAL cc_start: 0.8521 (p) cc_final: 0.8294 (t) outliers start: 3 outliers final: 1 residues processed: 792 average time/residue: 0.2095 time to fit residues: 269.9973 Evaluate side-chains 621 residues out of total 3571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 619 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 187 optimal weight: 0.3980 chunk 364 optimal weight: 0.7980 chunk 391 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 406 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 363 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 HIS J 482 ASN J 568 ASN ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 GLN ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085345 restraints weight = 109892.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086321 restraints weight = 72854.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086976 restraints weight = 50847.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087311 restraints weight = 42964.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087440 restraints weight = 37448.610| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33808 Z= 0.154 Angle : 0.704 16.249 45560 Z= 0.363 Chirality : 0.045 0.275 4984 Planarity : 0.004 0.063 5928 Dihedral : 5.344 46.402 4550 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4130 helix: 0.79 (0.12), residues: 2086 sheet: -0.33 (0.27), residues: 351 loop : -1.03 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.035 0.002 TYR E 221 PHE 0.038 0.002 PHE A 124 TRP 0.025 0.002 TRP I 234 HIS 0.005 0.001 HIS J 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (33807) covalent geometry : angle 0.70417 / 0.36 (45560) hydrogen bonds : bond 0.04841 / 3.23 ( 1747) hydrogen bonds : angle 4.68774 / 3.30 ( 4950) Misc. bond : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6324.55 seconds wall clock time: 110 minutes 10.32 seconds (6610.32 seconds total)