Starting phenix.real_space_refine on Thu Aug 6 14:04:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uke_64236/08_2026/9uke_64236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uke_64236/08_2026/9uke_64236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uke_64236/08_2026/9uke_64236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uke_64236/08_2026/9uke_64236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uke_64236/08_2026/9uke_64236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uke_64236/08_2026/9uke_64236.map" } resolution = 3.04 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= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 60 5.16 5 C 9577 2.51 5 N 2659 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 15199 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2350 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2362 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2481 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "D" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2520 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "G" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.57, per 1000 atoms: 0.23 Number of scatterers: 15199 At special positions: 0 Unit cell: (91.438, 127.036, 128.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 18 15.00 Mg 5 11.99 O 2880 8.00 N 2659 7.00 C 9577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 699.6 milliseconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 24 sheets defined 47.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.767A pdb=" N ILE A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.531A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.885A pdb=" N GLN A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.177A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.754A pdb=" N ALA A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.702A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 143 through 146 removed outlier: 3.760A pdb=" N GLY B 146 " --> pdb=" O TYR B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 143 through 146' Processing helix chain 'B' and resid 147 through 160 removed outlier: 4.029A pdb=" N VAL B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 241 through 261 Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.530A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.884A pdb=" N TRP C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.880A pdb=" N ILE C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.719A pdb=" N TRP C 211 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 234 through 237 removed outlier: 3.904A pdb=" N GLN C 237 " --> pdb=" O LYS C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 237' Processing helix chain 'C' and resid 238 through 261 removed outlier: 3.762A pdb=" N ARG C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.673A pdb=" N ALA C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.678A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 149 through 156 removed outlier: 3.793A pdb=" N PHE D 152 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 154 " --> pdb=" O MET D 151 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG D 156 " --> pdb=" O VAL D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 removed outlier: 3.932A pdb=" N ARG D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.950A pdb=" N GLN D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 238 through 261 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.568A pdb=" N ALA D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.726A pdb=" N ALA D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 153 through 156 removed outlier: 4.257A pdb=" N ARG E 156 " --> pdb=" O VAL E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 221 through 232 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.783A pdb=" N GLN E 237 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 262 removed outlier: 3.819A pdb=" N ARG E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.524A pdb=" N VAL E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.542A pdb=" N THR F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU F 55 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 89 Processing helix chain 'F' and resid 102 through 107 removed outlier: 3.606A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.920A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.658A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 238 through 262 removed outlier: 3.613A pdb=" N ARG F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.508A pdb=" N ALA F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 Processing helix chain 'F' and resid 302 through 315 removed outlier: 3.581A pdb=" N VAL F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA F 307 " --> pdb=" O ARG F 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 391 through 397 removed outlier: 4.146A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.706A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 185 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET A 68 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.563A pdb=" N LYS A 109 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.588A pdb=" N VAL B 93 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASP B 141 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 95 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN B 186 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 67 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 185 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 217 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER B 70 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 115 Processing sheet with id=AA8, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.907A pdb=" N VAL C 93 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP C 141 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 95 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 165 removed outlier: 3.605A pdb=" N LEU C 164 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.447A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 removed outlier: 3.503A pdb=" N ARG D 171 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.713A pdb=" N VAL E 93 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP E 141 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL E 95 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 185 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AC1, first strand: chain 'E' and resid 164 through 166 removed outlier: 3.530A pdb=" N LEU E 164 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.738A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 114 removed outlier: 3.722A pdb=" N LYS F 109 " --> pdb=" O LYS F 124 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 164 through 165 Processing sheet with id=AC6, first strand: chain 'G' and resid 378 through 381 removed outlier: 3.536A pdb=" N GLN G 406 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP G 380 " --> pdb=" O TYR G 404 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR G 404 " --> pdb=" O ASP G 380 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1800 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: 2.36 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5104 1.34 - 1.46: 3492 1.46 - 1.58: 6804 1.58 - 1.70: 15 1.70 - 1.82: 108 Bond restraints: 15523 Sorted by residual: bond pdb=" N ASP D 209 " pdb=" CA ASP D 209 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.23e+00 bond pdb=" N ASP B 98 " pdb=" CA ASP B 98 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.40e+00 bond pdb=" N GLU A 243 " pdb=" CA GLU A 243 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.30e+00 bond pdb=" N LEU B 97 " pdb=" CA LEU B 97 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.31e-02 5.83e+03 5.00e+00 bond pdb=" N ARG A 242 " pdb=" CA ARG A 242 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.16e-02 7.43e+03 4.94e+00 ... (remaining 15518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 20965 2.10 - 4.20: 183 4.20 - 6.30: 18 6.30 - 8.40: 1 8.40 - 10.50: 3 Bond angle restraints: 21170 Sorted by residual: angle pdb=" CA THR A 79 " pdb=" CB THR A 79 " pdb=" OG1 THR A 79 " ideal model delta sigma weight residual 109.60 103.47 6.13 1.50e+00 4.44e-01 1.67e+01 angle pdb=" N ASP B 98 " pdb=" CA ASP B 98 " pdb=" C ASP B 98 " ideal model delta sigma weight residual 113.01 108.51 4.50 1.20e+00 6.94e-01 1.40e+01 angle pdb=" CB MET C 29 " pdb=" CG MET C 29 " pdb=" SD MET C 29 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" C LEU B 97 " ideal model delta sigma weight residual 113.18 109.38 3.80 1.21e+00 6.83e-01 9.86e+00 angle pdb=" CA LEU F 167 " pdb=" CB LEU F 167 " pdb=" CG LEU F 167 " ideal model delta sigma weight residual 116.30 126.51 -10.21 3.50e+00 8.16e-02 8.51e+00 ... (remaining 21165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7680 17.75 - 35.49: 1111 35.49 - 53.24: 394 53.24 - 70.98: 93 70.98 - 88.73: 34 Dihedral angle restraints: 9312 sinusoidal: 3777 harmonic: 5535 Sorted by residual: dihedral pdb=" CA ASP C 46 " pdb=" CB ASP C 46 " pdb=" CG ASP C 46 " pdb=" OD1 ASP C 46 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB GLU D 320 " pdb=" CG GLU D 320 " pdb=" CD GLU D 320 " pdb=" OE1 GLU D 320 " ideal model delta sinusoidal sigma weight residual 0.00 88.73 -88.73 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " pdb=" CG ASP A 25 " pdb=" OD1 ASP A 25 " ideal model delta sinusoidal sigma weight residual -30.00 -85.32 55.32 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 9309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1306 0.027 - 0.054: 657 0.054 - 0.081: 261 0.081 - 0.107: 135 0.107 - 0.134: 40 Chirality restraints: 2399 Sorted by residual: chirality pdb=" CA MET C 29 " pdb=" N MET C 29 " pdb=" C MET C 29 " pdb=" CB MET C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CG LEU B 230 " pdb=" CB LEU B 230 " pdb=" CD1 LEU B 230 " pdb=" CD2 LEU B 230 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL E 172 " pdb=" N VAL E 172 " pdb=" C VAL E 172 " pdb=" CB VAL E 172 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 2396 not shown) Planarity restraints: 2731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 269 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 270 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 291 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C ARG C 291 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG C 291 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 292 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 291 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ARG F 291 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG F 291 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU F 292 " 0.010 2.00e-02 2.50e+03 ... (remaining 2728 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 124 2.55 - 3.14: 11528 3.14 - 3.73: 23880 3.73 - 4.31: 33046 4.31 - 4.90: 56252 Nonbonded interactions: 124830 Sorted by model distance: nonbonded pdb=" O2G ATP F 401 " pdb="MG MG F 402 " model vdw 1.968 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 2.015 2.170 nonbonded pdb=" O3G ATP A 401 " pdb="MG MG A 402 " model vdw 2.019 2.170 nonbonded pdb=" OG SER F 78 " pdb="MG MG F 402 " model vdw 2.050 2.170 nonbonded pdb=" OG SER E 78 " pdb="MG MG E 402 " model vdw 2.058 2.170 ... (remaining 124825 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' and resid 9 through 318) selection = (chain 'B' and (resid 9 through 187 or resid 203 through 318)) selection = (chain 'C' and (resid 9 through 187 or resid 203 through 318)) selection = (chain 'D' and (resid 9 through 187 or resid 203 through 318)) selection = (chain 'E' and (resid 9 through 187 or resid 203 through 318)) selection = (chain 'F' and (resid 9 through 187 or resid 203 through 318)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.004 0.050 15523 Z= 0.164 Angle : 0.494 10.496 21170 Z= 0.264 Chirality : 0.041 0.134 2399 Planarity : 0.004 0.050 2731 Dihedral : 19.707 88.726 5732 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.25 % Allowed : 34.57 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.43 (0.20), residues: 1880 helix: 0.63 (0.19), residues: 765 sheet: -0.96 (0.33), residues: 280 loop : -0.82 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 65 TYR 0.015 0.001 TYR F 47 PHE 0.011 0.001 PHE B 288 TRP 0.009 0.001 TRP C 90 HIS 0.006 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15523) covalent geometry : angle 0.49391 / 0.26 (21170) hydrogen bonds : bond 0.16410 / 11.08 ( 627) hydrogen bonds : angle 7.49287 / 5.36 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 432 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 291 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7668 (mtt-85) outliers start: 4 outliers final: 4 residues processed: 433 average time/residue: 0.1285 time to fit residues: 78.7000 Evaluate side-chains 431 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 427 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 HIS E 96 ASN E 119 GLN ** E 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 83 GLN F 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115800 restraints weight = 21227.213| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.35 r_work: 0.3329 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15523 Z= 0.135 Angle : 0.473 9.878 21170 Z= 0.250 Chirality : 0.041 0.121 2399 Planarity : 0.004 0.048 2731 Dihedral : 9.955 86.418 2297 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.72 % Allowed : 30.86 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.42 (0.20), residues: 1880 helix: 0.61 (0.19), residues: 802 sheet: -0.97 (0.33), residues: 262 loop : -0.84 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 210 TYR 0.008 0.001 TYR C 143 PHE 0.006 0.001 PHE D 290 TRP 0.007 0.001 TRP A 90 HIS 0.005 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (15523) covalent geometry : angle 0.47349 / 0.25 (21170) hydrogen bonds : bond 0.04211 / 2.87 ( 627) hydrogen bonds : angle 5.75487 / 4.15 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 421 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.5244 (OUTLIER) cc_final: 0.4794 (t0) REVERT: A 261 ASN cc_start: 0.7722 (t0) cc_final: 0.7479 (t0) REVERT: A 317 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5805 (pp20) REVERT: B 29 MET cc_start: 0.6406 (mmt) cc_final: 0.6191 (mmt) REVERT: B 98 ASP cc_start: 0.7716 (t0) cc_final: 0.7185 (t0) REVERT: B 142 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: C 29 MET cc_start: 0.7745 (mmm) cc_final: 0.7152 (mmm) REVERT: D 94 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7233 (mmm-85) REVERT: D 151 MET cc_start: 0.7816 (mmm) cc_final: 0.7560 (mmm) REVERT: E 308 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6918 (tm-30) REVERT: F 46 ASP cc_start: 0.7051 (p0) cc_final: 0.6810 (p0) REVERT: F 123 PHE cc_start: 0.8420 (t80) cc_final: 0.8155 (t80) REVERT: F 135 ASN cc_start: 0.8469 (p0) cc_final: 0.8268 (p0) REVERT: F 174 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7252 (mmt180) REVERT: F 202 GLN cc_start: 0.8085 (mt0) cc_final: 0.7720 (mt0) REVERT: F 217 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7759 (tp) REVERT: F 278 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7083 (mt-10) REVERT: F 303 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8221 (mtt90) REVERT: G 405 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8171 (ptpt) outliers start: 60 outliers final: 29 residues processed: 453 average time/residue: 0.1331 time to fit residues: 84.0742 Evaluate side-chains 462 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 428 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 405 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 4 optimal weight: 0.5980 chunk 74 optimal weight: 0.0170 chunk 172 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 64 ASN B 96 ASN B 186 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 207 GLN E 119 GLN ** E 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 222 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116391 restraints weight = 21416.564| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.36 r_work: 0.3346 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15523 Z= 0.113 Angle : 0.450 9.605 21170 Z= 0.237 Chirality : 0.040 0.124 2399 Planarity : 0.004 0.048 2731 Dihedral : 9.544 85.418 2290 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.52 % Allowed : 30.48 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 1880 helix: 0.71 (0.19), residues: 801 sheet: -0.79 (0.35), residues: 242 loop : -0.89 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 65 TYR 0.008 0.001 TYR F 33 PHE 0.006 0.001 PHE F 290 TRP 0.007 0.001 TRP A 90 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (15523) covalent geometry : angle 0.44973 / 0.24 (21170) hydrogen bonds : bond 0.03523 / 2.40 ( 627) hydrogen bonds : angle 5.40707 / 3.91 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 421 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6272 (p0) cc_final: 0.6000 (p0) REVERT: A 19 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7701 (mtm-85) REVERT: A 317 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5815 (pp20) REVERT: B 98 ASP cc_start: 0.7751 (t0) cc_final: 0.7312 (t0) REVERT: B 142 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: B 226 VAL cc_start: 0.8423 (m) cc_final: 0.8167 (t) REVERT: B 292 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8152 (mt) REVERT: C 15 THR cc_start: 0.8564 (p) cc_final: 0.8265 (m) REVERT: C 29 MET cc_start: 0.7762 (mmm) cc_final: 0.7076 (mmm) REVERT: D 116 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: D 156 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7934 (ttt90) REVERT: D 190 LEU cc_start: 0.8512 (mt) cc_final: 0.8299 (mp) REVERT: E 218 ASN cc_start: 0.8354 (m-40) cc_final: 0.8104 (m-40) REVERT: E 291 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.7930 (mtm-85) REVERT: E 308 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6967 (tm-30) REVERT: F 46 ASP cc_start: 0.7006 (p0) cc_final: 0.6770 (p0) REVERT: F 94 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7489 (mtm-85) REVERT: F 123 PHE cc_start: 0.8481 (t80) cc_final: 0.8239 (t80) REVERT: F 202 GLN cc_start: 0.8079 (mt0) cc_final: 0.7747 (mt0) REVERT: F 207 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7199 (mp-120) REVERT: F 217 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7799 (tp) REVERT: F 227 ASN cc_start: 0.7696 (m110) cc_final: 0.7413 (m-40) REVERT: F 303 ARG cc_start: 0.8403 (mtt90) cc_final: 0.8185 (mtt90) REVERT: G 405 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8164 (ptpt) outliers start: 73 outliers final: 40 residues processed: 466 average time/residue: 0.1257 time to fit residues: 82.4663 Evaluate side-chains 468 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 419 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 405 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 296 ASN B 96 ASN B 186 ASN C 73 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 96 ASN D 207 GLN E 96 ASN E 119 GLN E 224 ASN ** E 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114083 restraints weight = 21316.153| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.33 r_work: 0.3311 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15523 Z= 0.210 Angle : 0.492 9.011 21170 Z= 0.260 Chirality : 0.043 0.130 2399 Planarity : 0.004 0.048 2731 Dihedral : 9.641 83.191 2290 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.27 % Allowed : 29.12 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.48 (0.19), residues: 1880 helix: 0.52 (0.18), residues: 800 sheet: -0.80 (0.35), residues: 242 loop : -0.91 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 94 TYR 0.014 0.001 TYR F 310 PHE 0.010 0.001 PHE D 290 TRP 0.009 0.001 TRP B 90 HIS 0.006 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (15523) covalent geometry : angle 0.49192 / 0.26 (21170) hydrogen bonds : bond 0.04328 / 2.97 ( 627) hydrogen bonds : angle 5.44743 / 3.94 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 434 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7605 (mtm-85) REVERT: A 110 ASP cc_start: 0.5293 (OUTLIER) cc_final: 0.4861 (t0) REVERT: A 266 THR cc_start: 0.8345 (p) cc_final: 0.8100 (p) REVERT: A 317 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5819 (pp20) REVERT: B 98 ASP cc_start: 0.7800 (t0) cc_final: 0.7329 (t0) REVERT: B 142 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: C 15 THR cc_start: 0.8596 (p) cc_final: 0.8360 (m) REVERT: C 29 MET cc_start: 0.7791 (mmm) cc_final: 0.7163 (mmm) REVERT: C 186 ASN cc_start: 0.8325 (m-40) cc_final: 0.8005 (m110) REVERT: D 116 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: D 156 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7948 (ttt90) REVERT: D 301 LEU cc_start: 0.8548 (mt) cc_final: 0.8338 (mm) REVERT: E 291 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7944 (mtm-85) REVERT: E 308 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7124 (tm-30) REVERT: F 123 PHE cc_start: 0.8505 (t80) cc_final: 0.8216 (t80) REVERT: F 202 GLN cc_start: 0.8091 (mt0) cc_final: 0.7764 (mt0) REVERT: F 207 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7193 (mp-120) REVERT: F 208 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6962 (tmm) REVERT: F 217 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7822 (tp) REVERT: F 278 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7044 (mt-10) REVERT: G 405 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8183 (ptpt) outliers start: 85 outliers final: 51 residues processed: 490 average time/residue: 0.1295 time to fit residues: 88.9254 Evaluate side-chains 490 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 430 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 169 GLN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 405 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 261 ASN B 96 ASN B 133 GLN B 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 96 ASN D 207 GLN E 80 HIS E 96 ASN E 119 GLN ** E 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 205 GLN F 224 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114191 restraints weight = 21230.847| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.35 r_work: 0.3315 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15523 Z= 0.194 Angle : 0.489 8.778 21170 Z= 0.257 Chirality : 0.043 0.124 2399 Planarity : 0.004 0.049 2731 Dihedral : 9.494 84.686 2290 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.45 % Allowed : 28.31 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.47 (0.19), residues: 1880 helix: 0.52 (0.18), residues: 800 sheet: -0.75 (0.34), residues: 257 loop : -0.90 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 291 TYR 0.014 0.001 TYR F 310 PHE 0.013 0.001 PHE D 123 TRP 0.010 0.001 TRP B 90 HIS 0.007 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (15523) covalent geometry : angle 0.48926 / 0.26 (21170) hydrogen bonds : bond 0.04224 / 2.89 ( 627) hydrogen bonds : angle 5.41144 / 3.91 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 414 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6241 (p0) cc_final: 0.5990 (p0) REVERT: A 110 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4841 (t0) REVERT: A 317 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5799 (pp20) REVERT: B 98 ASP cc_start: 0.7822 (t0) cc_final: 0.7317 (t0) REVERT: B 142 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: C 163 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5757 (mtp180) REVERT: C 186 ASN cc_start: 0.8311 (m-40) cc_final: 0.8056 (m110) REVERT: D 116 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: D 156 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7932 (ttt90) REVERT: D 165 THR cc_start: 0.8249 (t) cc_final: 0.7996 (p) REVERT: D 301 LEU cc_start: 0.8530 (mt) cc_final: 0.8323 (mm) REVERT: F 94 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7545 (mtm-85) REVERT: F 202 GLN cc_start: 0.8102 (mt0) cc_final: 0.7773 (mt0) REVERT: F 207 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7163 (mp-120) REVERT: F 208 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.6930 (tmm) REVERT: F 217 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7793 (tp) REVERT: G 405 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8189 (ptpt) outliers start: 88 outliers final: 53 residues processed: 469 average time/residue: 0.1310 time to fit residues: 86.0217 Evaluate side-chains 478 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 414 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 169 GLN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 405 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 96 ASN B 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 207 GLN E 80 HIS E 96 ASN F 155 GLN F 205 GLN F 224 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112610 restraints weight = 21282.912| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.38 r_work: 0.3286 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15523 Z= 0.306 Angle : 0.542 8.641 21170 Z= 0.286 Chirality : 0.046 0.135 2399 Planarity : 0.005 0.051 2731 Dihedral : 9.730 89.385 2290 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.51 % Allowed : 28.50 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.19), residues: 1880 helix: 0.29 (0.18), residues: 794 sheet: -0.97 (0.33), residues: 268 loop : -0.98 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 94 TYR 0.017 0.001 TYR F 310 PHE 0.017 0.002 PHE D 123 TRP 0.012 0.002 TRP B 90 HIS 0.007 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.31 (15523) covalent geometry : angle 0.54201 / 0.29 (21170) hydrogen bonds : bond 0.05058 / 3.47 ( 627) hydrogen bonds : angle 5.56847 / 4.02 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 450 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.6143 (p90) REVERT: A 110 ASP cc_start: 0.5270 (OUTLIER) cc_final: 0.4842 (t0) REVERT: A 266 THR cc_start: 0.8464 (p) cc_final: 0.8184 (p) REVERT: A 317 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: B 98 ASP cc_start: 0.7826 (t0) cc_final: 0.7338 (t0) REVERT: B 142 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: B 156 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8133 (mtp-110) REVERT: C 29 MET cc_start: 0.7774 (mmm) cc_final: 0.7493 (mmm) REVERT: C 151 MET cc_start: 0.7651 (mmp) cc_final: 0.6816 (mmp) REVERT: C 186 ASN cc_start: 0.8329 (m-40) cc_final: 0.8078 (m110) REVERT: D 116 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: D 156 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7913 (ttt90) REVERT: D 165 THR cc_start: 0.8304 (t) cc_final: 0.8065 (p) REVERT: E 94 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7605 (mtp180) REVERT: E 163 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.7679 (mpt180) REVERT: F 202 GLN cc_start: 0.8127 (mt0) cc_final: 0.7786 (mt0) REVERT: F 207 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7132 (mp-120) REVERT: F 208 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6965 (tmm) outliers start: 89 outliers final: 63 residues processed: 509 average time/residue: 0.1189 time to fit residues: 85.4682 Evaluate side-chains 514 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 443 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 169 GLN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 283 PHE Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 405 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 134 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 chunk 183 optimal weight: 1.9990 chunk 153 optimal weight: 0.1980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 186 ASN B 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN E 80 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 80 HIS F 205 GLN F 222 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120342 restraints weight = 20994.028| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.41 r_work: 0.3348 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15523 Z= 0.106 Angle : 0.466 8.812 21170 Z= 0.245 Chirality : 0.041 0.140 2399 Planarity : 0.004 0.050 2731 Dihedral : 9.212 88.438 2290 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.09 % Allowed : 30.42 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.19), residues: 1880 helix: 0.70 (0.19), residues: 797 sheet: -0.84 (0.35), residues: 250 loop : -0.84 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.012 0.001 TYR F 310 PHE 0.012 0.001 PHE D 123 TRP 0.009 0.001 TRP B 90 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15523) covalent geometry : angle 0.46569 / 0.25 (21170) hydrogen bonds : bond 0.03314 / 2.25 ( 627) hydrogen bonds : angle 5.25030 / 3.79 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 422 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6200 (p0) cc_final: 0.5944 (p0) REVERT: A 79 THR cc_start: 0.7868 (m) cc_final: 0.7508 (p) REVERT: A 100 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.6186 (p90) REVERT: A 110 ASP cc_start: 0.5092 (OUTLIER) cc_final: 0.4712 (t0) REVERT: A 138 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 266 THR cc_start: 0.8331 (p) cc_final: 0.8038 (p) REVERT: A 317 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5802 (pp20) REVERT: B 98 ASP cc_start: 0.7841 (t0) cc_final: 0.7342 (t0) REVERT: B 142 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: B 156 ARG cc_start: 0.8392 (mtp180) cc_final: 0.8156 (mtp-110) REVERT: C 29 MET cc_start: 0.7737 (mmm) cc_final: 0.7492 (mmm) REVERT: C 163 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5696 (mtp180) REVERT: D 116 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: D 156 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7877 (ttt90) REVERT: D 165 THR cc_start: 0.8303 (t) cc_final: 0.8096 (p) REVERT: D 190 LEU cc_start: 0.8502 (mt) cc_final: 0.8281 (mp) REVERT: E 163 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7490 (mpt180) REVERT: E 218 ASN cc_start: 0.8294 (m-40) cc_final: 0.8070 (m-40) REVERT: E 291 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.7793 (mtm-85) REVERT: F 46 ASP cc_start: 0.7090 (p0) cc_final: 0.6833 (p0) REVERT: F 94 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7488 (mtm-85) REVERT: F 174 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7063 (mmt180) REVERT: F 202 GLN cc_start: 0.8093 (mt0) cc_final: 0.7762 (mt0) REVERT: F 253 ASP cc_start: 0.7555 (t0) cc_final: 0.7294 (t0) outliers start: 66 outliers final: 43 residues processed: 469 average time/residue: 0.1182 time to fit residues: 78.2255 Evaluate side-chains 471 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 174 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 279 ASN A 296 ASN B 96 ASN B 186 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 96 ASN E 80 HIS E 96 ASN F 155 GLN F 205 GLN F 222 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114953 restraints weight = 21163.552| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.33 r_work: 0.3327 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15523 Z= 0.185 Angle : 0.497 8.220 21170 Z= 0.261 Chirality : 0.043 0.134 2399 Planarity : 0.005 0.058 2731 Dihedral : 9.347 86.431 2290 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.52 % Allowed : 29.99 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.35 (0.19), residues: 1880 helix: 0.63 (0.18), residues: 794 sheet: -0.78 (0.33), residues: 279 loop : -0.80 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 291 TYR 0.014 0.001 TYR F 310 PHE 0.018 0.001 PHE D 123 TRP 0.010 0.001 TRP A 90 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (15523) covalent geometry : angle 0.49687 / 0.26 (21170) hydrogen bonds : bond 0.04069 / 2.78 ( 627) hydrogen bonds : angle 5.31652 / 3.84 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 428 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6344 (p0) cc_final: 0.6081 (p0) REVERT: A 100 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6393 (p90) REVERT: A 110 ASP cc_start: 0.5098 (OUTLIER) cc_final: 0.4719 (t0) REVERT: A 227 ASN cc_start: 0.8373 (m-40) cc_final: 0.8150 (m110) REVERT: A 266 THR cc_start: 0.8465 (p) cc_final: 0.8186 (p) REVERT: A 317 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6070 (pp20) REVERT: B 98 ASP cc_start: 0.8128 (t0) cc_final: 0.7646 (t0) REVERT: B 142 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: C 29 MET cc_start: 0.8001 (mmm) cc_final: 0.7720 (mmm) REVERT: D 116 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: D 156 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7997 (ttt90) REVERT: D 190 LEU cc_start: 0.8589 (mt) cc_final: 0.8367 (mp) REVERT: E 163 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7655 (mpt180) REVERT: F 201 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: F 202 GLN cc_start: 0.8259 (mt0) cc_final: 0.7942 (mt0) REVERT: F 207 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7238 (mp-120) REVERT: F 217 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7825 (tp) outliers start: 73 outliers final: 45 residues processed: 476 average time/residue: 0.1321 time to fit residues: 87.8249 Evaluate side-chains 481 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 427 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 174 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 201 GLN Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 145 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 chunk 178 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 96 ASN B 133 GLN B 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN E 80 HIS E 96 ASN F 155 GLN F 205 GLN F 222 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119657 restraints weight = 21104.688| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.38 r_work: 0.3335 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15523 Z= 0.145 Angle : 0.489 9.038 21170 Z= 0.256 Chirality : 0.042 0.147 2399 Planarity : 0.004 0.062 2731 Dihedral : 9.263 88.322 2290 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.72 % Allowed : 30.67 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.31 (0.20), residues: 1880 helix: 0.66 (0.18), residues: 801 sheet: -0.80 (0.34), residues: 264 loop : -0.77 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 291 TYR 0.021 0.001 TYR C 132 PHE 0.016 0.001 PHE D 123 TRP 0.009 0.001 TRP B 90 HIS 0.008 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15523) covalent geometry : angle 0.48928 / 0.26 (21170) hydrogen bonds : bond 0.03753 / 2.56 ( 627) hydrogen bonds : angle 5.27152 / 3.80 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 425 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.6175 (p0) cc_final: 0.5923 (p0) REVERT: A 19 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7327 (ttm110) REVERT: A 29 MET cc_start: 0.6978 (mpt) cc_final: 0.6739 (mpt) REVERT: A 100 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.6153 (p90) REVERT: A 110 ASP cc_start: 0.5078 (OUTLIER) cc_final: 0.4709 (t0) REVERT: A 266 THR cc_start: 0.8317 (p) cc_final: 0.8027 (p) REVERT: A 317 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5785 (pp20) REVERT: B 98 ASP cc_start: 0.7855 (t0) cc_final: 0.7393 (t0) REVERT: B 292 LEU cc_start: 0.8292 (mt) cc_final: 0.7788 (mp) REVERT: C 29 MET cc_start: 0.7786 (mmm) cc_final: 0.7524 (mmm) REVERT: C 163 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5645 (mtp-110) REVERT: D 116 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: D 156 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7897 (ttt90) REVERT: D 190 LEU cc_start: 0.8514 (mt) cc_final: 0.8302 (mp) REVERT: E 94 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7489 (mtp180) REVERT: E 163 ARG cc_start: 0.7937 (mmt-90) cc_final: 0.7519 (mpt180) REVERT: E 218 ASN cc_start: 0.8327 (m-40) cc_final: 0.8105 (m-40) REVERT: F 202 GLN cc_start: 0.8092 (mt0) cc_final: 0.7756 (mt0) REVERT: F 207 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7034 (mp-120) REVERT: F 217 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7779 (tp) REVERT: F 253 ASP cc_start: 0.7553 (t0) cc_final: 0.7305 (t0) REVERT: G 383 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6715 (pp20) outliers start: 60 outliers final: 47 residues processed: 464 average time/residue: 0.1480 time to fit residues: 96.5429 Evaluate side-chains 481 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 425 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 174 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 383 GLU Chi-restraints excluded: chain G residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 134 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 96 ASN B 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN E 80 HIS E 96 ASN F 155 GLN F 205 GLN F 222 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119186 restraints weight = 21256.413| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.40 r_work: 0.3318 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15523 Z= 0.169 Angle : 0.497 8.285 21170 Z= 0.262 Chirality : 0.043 0.140 2399 Planarity : 0.005 0.066 2731 Dihedral : 9.277 87.974 2290 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.72 % Allowed : 30.79 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.29 (0.20), residues: 1880 helix: 0.61 (0.18), residues: 800 sheet: -0.73 (0.35), residues: 256 loop : -0.72 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 291 TYR 0.018 0.001 TYR C 132 PHE 0.017 0.001 PHE D 123 TRP 0.009 0.001 TRP B 90 HIS 0.009 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (15523) covalent geometry : angle 0.49738 / 0.26 (21170) hydrogen bonds : bond 0.03918 / 2.68 ( 627) hydrogen bonds : angle 5.28606 / 3.81 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 431 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7298 (ttm110) REVERT: A 100 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.6143 (p90) REVERT: A 110 ASP cc_start: 0.5068 (OUTLIER) cc_final: 0.4711 (t0) REVERT: A 254 MET cc_start: 0.8323 (mtm) cc_final: 0.8006 (mtt) REVERT: A 266 THR cc_start: 0.8317 (p) cc_final: 0.8026 (p) REVERT: A 317 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5789 (pp20) REVERT: B 98 ASP cc_start: 0.7860 (t0) cc_final: 0.7410 (t0) REVERT: B 292 LEU cc_start: 0.8307 (mt) cc_final: 0.8044 (mt) REVERT: C 29 MET cc_start: 0.7819 (mmm) cc_final: 0.7547 (mmm) REVERT: D 116 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: D 156 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7882 (ttt90) REVERT: D 190 LEU cc_start: 0.8506 (mt) cc_final: 0.8297 (mp) REVERT: E 163 ARG cc_start: 0.7943 (mmt-90) cc_final: 0.7532 (mpt180) REVERT: F 201 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: F 202 GLN cc_start: 0.8102 (mt0) cc_final: 0.7767 (mt0) REVERT: F 207 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7014 (mp-120) REVERT: F 217 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7795 (tp) REVERT: F 253 ASP cc_start: 0.7567 (t0) cc_final: 0.7309 (t0) REVERT: G 383 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6706 (pp20) outliers start: 60 outliers final: 48 residues processed: 466 average time/residue: 0.1553 time to fit residues: 100.9892 Evaluate side-chains 487 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 430 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 201 GLN Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 383 GLU Chi-restraints excluded: chain G residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN B 96 ASN B 296 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 96 ASN E 80 HIS E 96 ASN F 222 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119526 restraints weight = 21079.862| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.39 r_work: 0.3332 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15523 Z= 0.157 Angle : 0.497 9.328 21170 Z= 0.260 Chirality : 0.042 0.124 2399 Planarity : 0.005 0.066 2731 Dihedral : 9.235 88.671 2290 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.78 % Allowed : 30.92 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.20), residues: 1880 helix: 0.64 (0.18), residues: 801 sheet: -0.64 (0.35), residues: 257 loop : -0.68 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 291 TYR 0.016 0.001 TYR C 132 PHE 0.017 0.001 PHE D 123 TRP 0.009 0.001 TRP B 90 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15523) covalent geometry : angle 0.49673 / 0.26 (21170) hydrogen bonds : bond 0.03826 / 2.62 ( 627) hydrogen bonds : angle 5.27202 / 3.80 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.41 seconds wall clock time: 56 minutes 23.17 seconds (3383.17 seconds total)