Starting phenix.real_space_refine on Thu Jul 31 17:16:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ja7_36125/07_2025/8ja7_36125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ja7_36125/07_2025/8ja7_36125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ja7_36125/07_2025/8ja7_36125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ja7_36125/07_2025/8ja7_36125.map" model { file = "/net/cci-nas-00/data/ceres_data/8ja7_36125/07_2025/8ja7_36125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ja7_36125/07_2025/8ja7_36125.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 8728 2.51 5 N 2326 2.21 5 O 2504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13601 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2164 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2043 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 16, 'TRANS': 254} Chain: "E" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3335 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 410} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3018 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 372} Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3018 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 372} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.09, per 1000 atoms: 0.67 Number of scatterers: 13601 At special positions: 0 Unit cell: (84.864, 92.352, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2504 8.00 N 2326 7.00 C 8728 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 Links applied ALPHA1-1 " GLC F 1 " - " GLC F 2 " Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 2.0 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 14 sheets defined 51.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.652A pdb=" N MET A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 4.354A pdb=" N TYR A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 79 through 113 removed outlier: 3.682A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.895A pdb=" N VAL A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 163 through 192 Proline residue: A 181 - end of helix removed outlier: 3.646A pdb=" N GLY A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.817A pdb=" N LEU A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 5.497A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.702A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 294 removed outlier: 4.137A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.901A pdb=" N THR B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Proline residue: B 23 - end of helix removed outlier: 4.044A pdb=" N ILE B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.122A pdb=" N LYS B 39 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 94 removed outlier: 4.245A pdb=" N ASN B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 110 through 113 Proline residue: B 113 - end of helix No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.697A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Proline residue: B 120 - end of helix removed outlier: 4.192A pdb=" N ALA B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Proline residue: B 140 - end of helix removed outlier: 4.436A pdb=" N THR B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Proline residue: B 147 - end of helix removed outlier: 3.576A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 4.222A pdb=" N LYS B 166 " --> pdb=" O TRP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.502A pdb=" N LEU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 236 through 268 removed outlier: 4.754A pdb=" N SER B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Proline residue: B 251 - end of helix removed outlier: 5.656A pdb=" N ARG B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 55 removed outlier: 3.599A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.646A pdb=" N ARG E 77 " --> pdb=" O PRO E 73 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 78 " --> pdb=" O ASN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.528A pdb=" N LEU E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'E' and resid 168 through 182 Processing helix chain 'E' and resid 195 through 209 removed outlier: 4.152A pdb=" N VAL E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 243 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.622A pdb=" N THR E 256 " --> pdb=" O ILE E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 278 through 289 removed outlier: 3.691A pdb=" N SER E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.592A pdb=" N SER E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 removed outlier: 3.553A pdb=" N ARG E 371 " --> pdb=" O PHE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 386 Processing helix chain 'E' and resid 394 through 397 Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 407 through 417 removed outlier: 4.176A pdb=" N ASP E 417 " --> pdb=" O GLN E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 438 removed outlier: 3.713A pdb=" N ILE E 432 " --> pdb=" O GLN E 428 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 463 removed outlier: 3.561A pdb=" N ASP E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 92 through 104 Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 136 through 150 Processing helix chain 'C' and resid 166 through 185 Processing helix chain 'C' and resid 194 through 202 removed outlier: 4.277A pdb=" N ALA C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.871A pdb=" N ARG C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 92 through 104 Proline residue: D 100 - end of helix Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.866A pdb=" N ASN D 126 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 128 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.760A pdb=" N LEU D 135 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 4.563A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 185 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.512A pdb=" N LEU D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 262 through 271 removed outlier: 4.144A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.596A pdb=" N ILE D 299 " --> pdb=" O TYR D 296 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 300 " --> pdb=" O GLN D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 300' Processing helix chain 'D' and resid 331 through 336 Processing sheet with id=AA1, first strand: chain 'E' and resid 62 through 69 removed outlier: 6.308A pdb=" N LEU E 33 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA E 65 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E 35 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL E 67 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE E 37 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU E 69 " --> pdb=" O PHE E 37 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR E 39 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL E 93 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER E 36 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA E 95 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR E 38 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP E 97 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY E 350 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 150 " --> pdb=" O GLY E 350 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU E 352 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 272 through 275 Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 23 removed outlier: 5.161A pdb=" N ARG C 21 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS C 11 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 9 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 58 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 190 through 191 removed outlier: 6.507A pdb=" N ILE C 34 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET C 208 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 36 " --> pdb=" O MET C 208 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN C 215 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR C 209 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 241 through 245 removed outlier: 3.581A pdb=" N ILE C 279 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AA8, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.734A pdb=" N GLN C 288 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 26 through 27 removed outlier: 5.637A pdb=" N LEU D 6 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG D 62 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS D 8 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU D 60 " --> pdb=" O HIS D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 188 through 189 removed outlier: 3.503A pdb=" N LEU D 33 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL D 206 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 34 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 258 removed outlier: 3.553A pdb=" N VAL D 278 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 287 through 289 removed outlier: 5.079A pdb=" N VAL D 308 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR D 323 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 289 removed outlier: 5.079A pdb=" N VAL D 308 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR D 323 " --> pdb=" O VAL D 308 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1806 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: 3.85 Time building geometry restraints manager: 4.27 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: 4486 1.34 - 1.46: 2871 1.46 - 1.58: 6449 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 13886 Sorted by residual: bond pdb=" C1 GLC F 1 " pdb=" O5 GLC F 1 " ideal model delta sigma weight residual 1.402 1.507 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.402 1.483 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sigma weight residual 1.412 1.484 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C2 GLC F 2 " pdb=" C3 GLC F 2 " ideal model delta sigma weight residual 1.528 1.463 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.415 1.477 -0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 13881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 18444 1.61 - 3.22: 402 3.22 - 4.84: 74 4.84 - 6.45: 21 6.45 - 8.06: 3 Bond angle restraints: 18944 Sorted by residual: angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" C GLN E 76 " ideal model delta sigma weight residual 111.28 105.73 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ASP E 43 " pdb=" C ASP E 43 " pdb=" O ASP E 43 " ideal model delta sigma weight residual 121.32 118.15 3.17 1.16e+00 7.43e-01 7.46e+00 angle pdb=" CA ARG E 421 " pdb=" C ARG E 421 " pdb=" O ARG E 421 " ideal model delta sigma weight residual 120.96 117.99 2.97 1.09e+00 8.42e-01 7.40e+00 angle pdb=" O GLN E 76 " pdb=" C GLN E 76 " pdb=" N ARG E 77 " ideal model delta sigma weight residual 122.12 124.89 -2.77 1.06e+00 8.90e-01 6.85e+00 angle pdb=" C PRO E 315 " pdb=" N SER E 316 " pdb=" CA SER E 316 " ideal model delta sigma weight residual 120.89 117.11 3.78 1.50e+00 4.44e-01 6.35e+00 ... (remaining 18939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 7589 17.50 - 35.00: 634 35.00 - 52.50: 76 52.50 - 70.00: 25 70.00 - 87.50: 16 Dihedral angle restraints: 8340 sinusoidal: 3204 harmonic: 5136 Sorted by residual: dihedral pdb=" CA LYS D 11 " pdb=" C LYS D 11 " pdb=" N SER D 12 " pdb=" CA SER D 12 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA SER E 316 " pdb=" C SER E 316 " pdb=" N ASP E 317 " pdb=" CA ASP E 317 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER E 242 " pdb=" C SER E 242 " pdb=" N VAL E 243 " pdb=" CA VAL E 243 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1992 0.070 - 0.141: 252 0.141 - 0.211: 7 0.211 - 0.282: 0 0.282 - 0.352: 1 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C1 GLC F 1 " pdb=" C2 GLC F 1 " pdb=" O5 GLC F 1 " pdb=" O1 GLC F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 5.16e+00 chirality pdb=" C1 GLC F 2 " pdb=" C2 GLC F 2 " pdb=" O1 GLC F 2 " pdb=" O5 GLC F 2 " both_signs ideal model delta sigma weight residual False -2.04 -2.39 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA GLN E 76 " pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CB GLN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2249 not shown) Planarity restraints: 2437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 165 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 166 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 254 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 255 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 75 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C GLU E 75 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU E 75 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN E 76 " 0.010 2.00e-02 2.50e+03 ... (remaining 2434 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 483 2.71 - 3.25: 15049 3.25 - 3.80: 22644 3.80 - 4.35: 28717 4.35 - 4.90: 46789 Nonbonded interactions: 113682 Sorted by model distance: nonbonded pdb=" O LYS E 241 " pdb=" OG1 THR E 245 " model vdw 2.158 3.040 nonbonded pdb=" O ILE A 91 " pdb=" OG SER A 95 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR E 442 " pdb=" OE1 GLU E 443 " model vdw 2.172 3.040 nonbonded pdb=" OG SER E 215 " pdb=" O ASP E 217 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLN D 305 " pdb=" OG SER D 366 " model vdw 2.182 3.040 ... (remaining 113677 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 'C' selection = chain 'D' } 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=0.00 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: 3.890 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 0.105 13887 Z= 0.197 Angle : 0.627 8.060 18947 Z= 0.343 Chirality : 0.044 0.352 2252 Planarity : 0.004 0.042 2437 Dihedral : 13.424 87.499 5028 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.18), residues: 1774 helix: -1.53 (0.16), residues: 817 sheet: -2.26 (0.36), residues: 131 loop : -2.54 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 109 HIS 0.004 0.001 HIS D 286 PHE 0.010 0.001 PHE A 231 TYR 0.016 0.001 TYR E 427 ARG 0.002 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.18085 ( 627) hydrogen bonds : angle 6.95710 ( 1806) glycosidic custom : bond 0.06405 ( 1) glycosidic custom : angle 2.07204 ( 3) covalent geometry : bond 0.00414 (13886) covalent geometry : angle 0.62623 (18944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.8216 (m-30) cc_final: 0.7492 (m-30) REVERT: A 235 ASP cc_start: 0.8732 (t70) cc_final: 0.8470 (t0) REVERT: A 262 ASP cc_start: 0.8324 (m-30) cc_final: 0.8038 (m-30) REVERT: A 293 LYS cc_start: 0.9010 (tppp) cc_final: 0.8614 (tppt) REVERT: B 170 MET cc_start: 0.9032 (tpp) cc_final: 0.8574 (tpp) REVERT: E 92 ASP cc_start: 0.8241 (m-30) cc_final: 0.8026 (m-30) REVERT: E 257 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6563 (mm-30) REVERT: E 283 MET cc_start: 0.8607 (tpt) cc_final: 0.8225 (tpp) REVERT: C 17 HIS cc_start: 0.8031 (t70) cc_final: 0.7757 (t-90) REVERT: C 145 MET cc_start: 0.9077 (mtm) cc_final: 0.8660 (mtm) REVERT: C 209 TYR cc_start: 0.9051 (t80) cc_final: 0.8836 (t80) REVERT: C 321 TYR cc_start: 0.9059 (m-80) cc_final: 0.8721 (m-80) REVERT: C 369 LEU cc_start: 0.8799 (pp) cc_final: 0.8323 (mp) REVERT: D 85 TYR cc_start: 0.8132 (m-10) cc_final: 0.7882 (m-10) REVERT: D 158 MET cc_start: 0.7432 (mtp) cc_final: 0.7113 (ttm) REVERT: D 240 MET cc_start: 0.7835 (ttp) cc_final: 0.7431 (mtm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2509 time to fit residues: 52.4224 Evaluate side-chains 110 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN B 52 ASN B 68 ASN E 52 GLN E 55 ASN E 238 GLN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN E 378 ASN E 379 GLN E 402 GLN E 414 GLN C 17 HIS C 241 ASN C 266 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN C 386 ASN D 10 ASN D 69 ASN D 96 ASN D 134 GLN D 141 GLN D 272 HIS ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.106476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063892 restraints weight = 38539.971| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.42 r_work: 0.2825 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13887 Z= 0.131 Angle : 0.613 10.665 18947 Z= 0.311 Chirality : 0.044 0.197 2252 Planarity : 0.004 0.040 2437 Dihedral : 4.996 64.112 1962 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.70 % Allowed : 9.28 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1774 helix: -0.43 (0.18), residues: 830 sheet: -1.64 (0.34), residues: 158 loop : -2.00 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.018 0.002 HIS D 8 PHE 0.018 0.001 PHE C 379 TYR 0.018 0.002 TYR E 427 ARG 0.009 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 627) hydrogen bonds : angle 5.54217 ( 1806) glycosidic custom : bond 0.01086 ( 1) glycosidic custom : angle 0.71705 ( 3) covalent geometry : bond 0.00285 (13886) covalent geometry : angle 0.61295 (18944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9011 (t0) cc_final: 0.8727 (t0) REVERT: A 244 TYR cc_start: 0.9412 (t80) cc_final: 0.9206 (t80) REVERT: A 262 ASP cc_start: 0.9094 (m-30) cc_final: 0.8726 (m-30) REVERT: A 293 LYS cc_start: 0.9264 (tppp) cc_final: 0.8744 (tppt) REVERT: B 170 MET cc_start: 0.8862 (tpp) cc_final: 0.8456 (tpp) REVERT: E 75 GLU cc_start: 0.9086 (pt0) cc_final: 0.8703 (pm20) REVERT: E 92 ASP cc_start: 0.8616 (m-30) cc_final: 0.8352 (m-30) REVERT: C 13 TYR cc_start: 0.8656 (m-10) cc_final: 0.8376 (m-80) REVERT: C 17 HIS cc_start: 0.8270 (t-90) cc_final: 0.8015 (t-90) REVERT: C 145 MET cc_start: 0.9231 (mtm) cc_final: 0.8559 (mtm) REVERT: C 168 LYS cc_start: 0.9322 (ptmm) cc_final: 0.9094 (pptt) REVERT: C 199 MET cc_start: 0.9426 (mmm) cc_final: 0.9121 (mmm) REVERT: C 240 MET cc_start: 0.8850 (ptp) cc_final: 0.8555 (ptp) REVERT: C 321 TYR cc_start: 0.9072 (m-80) cc_final: 0.8866 (m-80) REVERT: C 369 LEU cc_start: 0.8848 (pp) cc_final: 0.8484 (mp) REVERT: D 85 TYR cc_start: 0.8513 (m-10) cc_final: 0.8145 (m-10) REVERT: D 199 MET cc_start: 0.8668 (mtp) cc_final: 0.8257 (mmp) outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.2375 time to fit residues: 50.4834 Evaluate side-chains 121 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064047 restraints weight = 39047.574| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.43 r_work: 0.2838 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13887 Z= 0.130 Angle : 0.569 10.066 18947 Z= 0.288 Chirality : 0.043 0.161 2252 Planarity : 0.004 0.040 2437 Dihedral : 4.694 60.740 1962 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.34 % Allowed : 11.81 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1774 helix: 0.04 (0.18), residues: 835 sheet: -1.38 (0.35), residues: 167 loop : -1.74 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.005 0.001 HIS D 286 PHE 0.012 0.001 PHE C 379 TYR 0.023 0.001 TYR B 8 ARG 0.012 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 627) hydrogen bonds : angle 5.17198 ( 1806) glycosidic custom : bond 0.00248 ( 1) glycosidic custom : angle 1.20994 ( 3) covalent geometry : bond 0.00291 (13886) covalent geometry : angle 0.56916 (18944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8996 (t0) cc_final: 0.8586 (t0) REVERT: A 205 ASP cc_start: 0.9132 (m-30) cc_final: 0.8808 (t0) REVERT: A 293 LYS cc_start: 0.9285 (tppp) cc_final: 0.8748 (tppt) REVERT: B 165 GLU cc_start: 0.9212 (tt0) cc_final: 0.8715 (mt-10) REVERT: B 170 MET cc_start: 0.8827 (tpp) cc_final: 0.8364 (tpp) REVERT: C 1 MET cc_start: 0.7156 (ptt) cc_final: 0.6785 (mtm) REVERT: C 13 TYR cc_start: 0.8717 (m-10) cc_final: 0.8323 (m-80) REVERT: C 145 MET cc_start: 0.9200 (mtm) cc_final: 0.8592 (mtm) REVERT: C 199 MET cc_start: 0.9424 (mmm) cc_final: 0.9127 (mmm) REVERT: C 240 MET cc_start: 0.8740 (ptp) cc_final: 0.8403 (ptp) REVERT: C 321 TYR cc_start: 0.9083 (m-80) cc_final: 0.8879 (m-80) REVERT: C 369 LEU cc_start: 0.8871 (pp) cc_final: 0.8573 (mp) REVERT: D 85 TYR cc_start: 0.8427 (m-10) cc_final: 0.8053 (m-10) REVERT: D 199 MET cc_start: 0.8635 (mtp) cc_final: 0.8311 (mmp) REVERT: D 319 TYR cc_start: 0.8450 (m-80) cc_final: 0.8223 (m-80) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 0.2347 time to fit residues: 52.8678 Evaluate side-chains 119 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 157 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063585 restraints weight = 38775.260| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.56 r_work: 0.2850 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13887 Z= 0.119 Angle : 0.566 8.471 18947 Z= 0.284 Chirality : 0.043 0.256 2252 Planarity : 0.004 0.056 2437 Dihedral : 4.513 57.584 1962 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.20 % Allowed : 13.50 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1774 helix: 0.25 (0.18), residues: 837 sheet: -1.29 (0.35), residues: 176 loop : -1.65 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 139 HIS 0.004 0.001 HIS C 8 PHE 0.010 0.001 PHE C 322 TYR 0.022 0.001 TYR B 8 ARG 0.019 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 627) hydrogen bonds : angle 5.01730 ( 1806) glycosidic custom : bond 0.00009 ( 1) glycosidic custom : angle 1.03898 ( 3) covalent geometry : bond 0.00264 (13886) covalent geometry : angle 0.56589 (18944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9044 (t0) cc_final: 0.8581 (t0) REVERT: A 205 ASP cc_start: 0.9079 (m-30) cc_final: 0.8775 (t0) REVERT: A 262 ASP cc_start: 0.9100 (m-30) cc_final: 0.8713 (m-30) REVERT: A 293 LYS cc_start: 0.9274 (tppp) cc_final: 0.8922 (tppt) REVERT: B 170 MET cc_start: 0.8853 (tpp) cc_final: 0.8361 (tpp) REVERT: E 75 GLU cc_start: 0.9141 (pt0) cc_final: 0.8889 (pm20) REVERT: C 13 TYR cc_start: 0.8752 (m-10) cc_final: 0.8372 (m-80) REVERT: C 145 MET cc_start: 0.9239 (mtm) cc_final: 0.8636 (mtm) REVERT: C 199 MET cc_start: 0.9442 (mmm) cc_final: 0.9150 (mmm) REVERT: C 240 MET cc_start: 0.8852 (ptp) cc_final: 0.8533 (ptp) REVERT: C 369 LEU cc_start: 0.8948 (pp) cc_final: 0.8644 (mp) REVERT: D 85 TYR cc_start: 0.8486 (m-10) cc_final: 0.8111 (m-10) REVERT: D 199 MET cc_start: 0.8619 (mtp) cc_final: 0.8346 (mmp) REVERT: D 208 MET cc_start: 0.8710 (mmm) cc_final: 0.8489 (mmm) REVERT: D 319 TYR cc_start: 0.8358 (m-80) cc_final: 0.8123 (m-80) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 0.2257 time to fit residues: 49.6972 Evaluate side-chains 122 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS D 309 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063844 restraints weight = 39166.803| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.55 r_work: 0.2838 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13887 Z= 0.133 Angle : 0.575 7.992 18947 Z= 0.288 Chirality : 0.043 0.193 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.416 55.059 1962 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 14.28 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1774 helix: 0.39 (0.19), residues: 838 sheet: -1.22 (0.35), residues: 182 loop : -1.57 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 9 HIS 0.004 0.001 HIS C 8 PHE 0.022 0.001 PHE D 230 TYR 0.022 0.001 TYR B 8 ARG 0.002 0.000 ARG E 421 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 627) hydrogen bonds : angle 4.95804 ( 1806) glycosidic custom : bond 0.00053 ( 1) glycosidic custom : angle 1.19463 ( 3) covalent geometry : bond 0.00303 (13886) covalent geometry : angle 0.57490 (18944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9047 (t70) cc_final: 0.8564 (t0) REVERT: A 205 ASP cc_start: 0.9107 (m-30) cc_final: 0.8747 (t0) REVERT: A 293 LYS cc_start: 0.9268 (tppp) cc_final: 0.8930 (tppt) REVERT: B 170 MET cc_start: 0.8851 (tpp) cc_final: 0.8351 (tpp) REVERT: E 75 GLU cc_start: 0.9136 (pt0) cc_final: 0.8919 (pm20) REVERT: C 1 MET cc_start: 0.7028 (ptt) cc_final: 0.6064 (mpp) REVERT: C 13 TYR cc_start: 0.8763 (m-10) cc_final: 0.8391 (m-80) REVERT: C 145 MET cc_start: 0.9233 (mtm) cc_final: 0.8636 (mtm) REVERT: C 199 MET cc_start: 0.9451 (mmm) cc_final: 0.9153 (mmm) REVERT: C 240 MET cc_start: 0.8880 (ptp) cc_final: 0.8565 (ptp) REVERT: C 321 TYR cc_start: 0.8995 (m-80) cc_final: 0.8729 (t80) REVERT: C 369 LEU cc_start: 0.8948 (pp) cc_final: 0.8644 (mp) REVERT: D 85 TYR cc_start: 0.8501 (m-10) cc_final: 0.8120 (m-10) REVERT: D 199 MET cc_start: 0.8595 (mtp) cc_final: 0.8354 (mmp) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.2238 time to fit residues: 47.4303 Evaluate side-chains 133 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 106 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 54 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 298 ASN C 90 HIS ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.106970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064154 restraints weight = 39313.062| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.41 r_work: 0.2862 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13887 Z= 0.110 Angle : 0.562 8.041 18947 Z= 0.280 Chirality : 0.042 0.167 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.281 51.736 1962 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.83 % Allowed : 14.28 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1774 helix: 0.56 (0.19), residues: 828 sheet: -1.11 (0.36), residues: 182 loop : -1.53 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 139 HIS 0.004 0.001 HIS C 8 PHE 0.017 0.001 PHE D 230 TYR 0.023 0.001 TYR B 8 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 627) hydrogen bonds : angle 4.86990 ( 1806) glycosidic custom : bond 0.00044 ( 1) glycosidic custom : angle 0.99523 ( 3) covalent geometry : bond 0.00243 (13886) covalent geometry : angle 0.56182 (18944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9009 (t70) cc_final: 0.8528 (t0) REVERT: A 205 ASP cc_start: 0.9093 (m-30) cc_final: 0.8746 (t0) REVERT: A 293 LYS cc_start: 0.9238 (tppp) cc_final: 0.8899 (tppt) REVERT: B 165 GLU cc_start: 0.9182 (tt0) cc_final: 0.8784 (mt-10) REVERT: B 170 MET cc_start: 0.8848 (tpp) cc_final: 0.8333 (tpp) REVERT: E 74 ASN cc_start: 0.8686 (p0) cc_final: 0.8427 (p0) REVERT: E 75 GLU cc_start: 0.9093 (pt0) cc_final: 0.8853 (pm20) REVERT: C 1 MET cc_start: 0.6887 (ptt) cc_final: 0.6014 (mpp) REVERT: C 13 TYR cc_start: 0.8750 (m-10) cc_final: 0.8395 (m-80) REVERT: C 199 MET cc_start: 0.9446 (mmm) cc_final: 0.9157 (mmm) REVERT: C 240 MET cc_start: 0.8852 (ptp) cc_final: 0.8525 (ptp) REVERT: C 321 TYR cc_start: 0.9043 (m-80) cc_final: 0.8782 (t80) REVERT: C 369 LEU cc_start: 0.8996 (pp) cc_final: 0.8707 (mp) REVERT: D 85 TYR cc_start: 0.8506 (m-10) cc_final: 0.8109 (m-10) outliers start: 26 outliers final: 21 residues processed: 148 average time/residue: 0.2198 time to fit residues: 50.9008 Evaluate side-chains 136 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 137 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.106167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.063185 restraints weight = 39056.506| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.43 r_work: 0.2834 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13887 Z= 0.146 Angle : 0.582 8.020 18947 Z= 0.290 Chirality : 0.043 0.171 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.333 49.677 1962 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.62 % Allowed : 15.40 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1774 helix: 0.60 (0.19), residues: 827 sheet: -1.18 (0.35), residues: 187 loop : -1.49 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 9 HIS 0.004 0.001 HIS C 272 PHE 0.017 0.001 PHE E 280 TYR 0.024 0.001 TYR B 8 ARG 0.002 0.000 ARG E 421 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 627) hydrogen bonds : angle 4.85930 ( 1806) glycosidic custom : bond 0.00021 ( 1) glycosidic custom : angle 1.14739 ( 3) covalent geometry : bond 0.00339 (13886) covalent geometry : angle 0.58232 (18944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9054 (t70) cc_final: 0.8538 (t0) REVERT: A 205 ASP cc_start: 0.9113 (m-30) cc_final: 0.8737 (t0) REVERT: A 262 ASP cc_start: 0.9087 (m-30) cc_final: 0.8722 (m-30) REVERT: A 293 LYS cc_start: 0.9228 (tppp) cc_final: 0.8948 (tppt) REVERT: B 170 MET cc_start: 0.8870 (tpp) cc_final: 0.8334 (tpp) REVERT: E 75 GLU cc_start: 0.9126 (pt0) cc_final: 0.8838 (pm20) REVERT: E 407 MET cc_start: 0.9024 (pmm) cc_final: 0.8737 (ptp) REVERT: C 1 MET cc_start: 0.6917 (ptt) cc_final: 0.6062 (mpp) REVERT: C 13 TYR cc_start: 0.8806 (m-10) cc_final: 0.8464 (m-80) REVERT: C 17 HIS cc_start: 0.8369 (t-90) cc_final: 0.8026 (t-90) REVERT: C 199 MET cc_start: 0.9444 (mmm) cc_final: 0.9152 (mmm) REVERT: C 240 MET cc_start: 0.8884 (ptp) cc_final: 0.8570 (ptp) REVERT: C 321 TYR cc_start: 0.9046 (m-80) cc_final: 0.8788 (t80) REVERT: C 369 LEU cc_start: 0.8985 (pp) cc_final: 0.8702 (mp) REVERT: D 1 MET cc_start: 0.7318 (mpp) cc_final: 0.6951 (mmt) REVERT: D 85 TYR cc_start: 0.8547 (m-10) cc_final: 0.8182 (m-10) outliers start: 23 outliers final: 20 residues processed: 142 average time/residue: 0.2583 time to fit residues: 57.2677 Evaluate side-chains 136 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 144 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.107206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064724 restraints weight = 39314.136| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.49 r_work: 0.2852 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13887 Z= 0.111 Angle : 0.571 10.488 18947 Z= 0.283 Chirality : 0.042 0.165 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.169 46.381 1962 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.69 % Allowed : 15.40 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1774 helix: 0.68 (0.19), residues: 831 sheet: -1.34 (0.35), residues: 195 loop : -1.42 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.004 0.001 HIS C 8 PHE 0.019 0.001 PHE E 280 TYR 0.027 0.001 TYR A 156 ARG 0.004 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 627) hydrogen bonds : angle 4.76176 ( 1806) glycosidic custom : bond 0.00028 ( 1) glycosidic custom : angle 0.94942 ( 3) covalent geometry : bond 0.00250 (13886) covalent geometry : angle 0.57052 (18944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9019 (t70) cc_final: 0.8487 (t0) REVERT: A 205 ASP cc_start: 0.9075 (m-30) cc_final: 0.8718 (t0) REVERT: A 262 ASP cc_start: 0.9086 (m-30) cc_final: 0.8700 (m-30) REVERT: A 293 LYS cc_start: 0.9240 (tppp) cc_final: 0.8861 (tppt) REVERT: B 95 GLU cc_start: 0.8587 (mp0) cc_final: 0.8184 (pp20) REVERT: B 170 MET cc_start: 0.8814 (tpp) cc_final: 0.8293 (tpp) REVERT: E 75 GLU cc_start: 0.9121 (pt0) cc_final: 0.8841 (pm20) REVERT: E 266 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8494 (mt-10) REVERT: E 407 MET cc_start: 0.9001 (pmm) cc_final: 0.8693 (ptp) REVERT: C 1 MET cc_start: 0.6911 (ptt) cc_final: 0.6070 (mpp) REVERT: C 13 TYR cc_start: 0.8814 (m-10) cc_final: 0.8475 (m-80) REVERT: C 17 HIS cc_start: 0.8325 (t-90) cc_final: 0.8024 (t-90) REVERT: C 208 MET cc_start: 0.7931 (tpp) cc_final: 0.7729 (tpt) REVERT: C 240 MET cc_start: 0.8896 (ptp) cc_final: 0.8587 (ptp) REVERT: C 321 TYR cc_start: 0.8997 (m-80) cc_final: 0.8746 (t80) REVERT: C 369 LEU cc_start: 0.8981 (pp) cc_final: 0.8711 (mp) REVERT: D 85 TYR cc_start: 0.8573 (m-10) cc_final: 0.8243 (m-10) REVERT: D 314 LEU cc_start: 0.8952 (tt) cc_final: 0.8746 (tp) outliers start: 24 outliers final: 19 residues processed: 151 average time/residue: 0.2128 time to fit residues: 50.4981 Evaluate side-chains 141 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064326 restraints weight = 38873.689| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.48 r_work: 0.2854 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13887 Z= 0.113 Angle : 0.573 9.004 18947 Z= 0.283 Chirality : 0.042 0.165 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.120 44.066 1962 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.34 % Allowed : 15.68 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1774 helix: 0.74 (0.19), residues: 831 sheet: -1.28 (0.35), residues: 195 loop : -1.34 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 177 HIS 0.004 0.001 HIS C 8 PHE 0.019 0.001 PHE E 280 TYR 0.024 0.001 TYR B 8 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 627) hydrogen bonds : angle 4.72333 ( 1806) glycosidic custom : bond 0.00091 ( 1) glycosidic custom : angle 1.06002 ( 3) covalent geometry : bond 0.00257 (13886) covalent geometry : angle 0.57322 (18944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9035 (t70) cc_final: 0.8482 (t0) REVERT: A 183 MET cc_start: 0.9021 (tpp) cc_final: 0.8778 (ttm) REVERT: A 205 ASP cc_start: 0.9081 (m-30) cc_final: 0.8739 (t0) REVERT: A 262 ASP cc_start: 0.9082 (m-30) cc_final: 0.8698 (m-30) REVERT: A 293 LYS cc_start: 0.9233 (tppp) cc_final: 0.8866 (tppt) REVERT: B 95 GLU cc_start: 0.8549 (mp0) cc_final: 0.8219 (pp20) REVERT: B 170 MET cc_start: 0.8795 (tpp) cc_final: 0.8277 (tpp) REVERT: E 75 GLU cc_start: 0.9139 (pt0) cc_final: 0.8837 (pm20) REVERT: E 407 MET cc_start: 0.9012 (pmm) cc_final: 0.8741 (ptp) REVERT: C 1 MET cc_start: 0.6901 (ptt) cc_final: 0.6076 (mpp) REVERT: C 13 TYR cc_start: 0.8850 (m-10) cc_final: 0.8500 (m-80) REVERT: C 240 MET cc_start: 0.8920 (ptp) cc_final: 0.8595 (ptp) REVERT: C 321 TYR cc_start: 0.9006 (m-80) cc_final: 0.8750 (t80) REVERT: C 369 LEU cc_start: 0.8982 (pp) cc_final: 0.8739 (mp) REVERT: D 85 TYR cc_start: 0.8641 (m-10) cc_final: 0.8360 (m-10) outliers start: 19 outliers final: 19 residues processed: 142 average time/residue: 0.2195 time to fit residues: 48.5469 Evaluate side-chains 140 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 161 optimal weight: 30.0000 chunk 88 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.107716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.065180 restraints weight = 38805.166| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.49 r_work: 0.2882 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13887 Z= 0.104 Angle : 0.577 11.339 18947 Z= 0.283 Chirality : 0.042 0.166 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.027 41.380 1962 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.41 % Allowed : 16.10 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1774 helix: 0.83 (0.19), residues: 832 sheet: -1.21 (0.36), residues: 195 loop : -1.29 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.004 0.001 HIS C 8 PHE 0.018 0.001 PHE D 230 TYR 0.023 0.001 TYR B 8 ARG 0.002 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 627) hydrogen bonds : angle 4.66839 ( 1806) glycosidic custom : bond 0.00203 ( 1) glycosidic custom : angle 0.95843 ( 3) covalent geometry : bond 0.00230 (13886) covalent geometry : angle 0.57710 (18944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9017 (t70) cc_final: 0.8458 (t0) REVERT: A 205 ASP cc_start: 0.9093 (m-30) cc_final: 0.8771 (t0) REVERT: A 262 ASP cc_start: 0.9082 (m-30) cc_final: 0.8686 (m-30) REVERT: A 293 LYS cc_start: 0.9221 (tppp) cc_final: 0.8869 (tppt) REVERT: B 95 GLU cc_start: 0.8518 (mp0) cc_final: 0.8234 (pp20) REVERT: B 170 MET cc_start: 0.8781 (tpp) cc_final: 0.8297 (tpp) REVERT: E 75 GLU cc_start: 0.9148 (pt0) cc_final: 0.8835 (pm20) REVERT: E 407 MET cc_start: 0.8991 (pmm) cc_final: 0.8728 (ptp) REVERT: C 1 MET cc_start: 0.6792 (ptt) cc_final: 0.6012 (mpp) REVERT: C 13 TYR cc_start: 0.8902 (m-10) cc_final: 0.8553 (m-80) REVERT: C 240 MET cc_start: 0.8920 (ptp) cc_final: 0.8588 (ptp) REVERT: C 321 TYR cc_start: 0.9016 (m-80) cc_final: 0.8741 (t80) REVERT: C 369 LEU cc_start: 0.8977 (pp) cc_final: 0.8731 (mp) REVERT: D 85 TYR cc_start: 0.8685 (m-10) cc_final: 0.8415 (m-80) outliers start: 20 outliers final: 19 residues processed: 147 average time/residue: 0.2180 time to fit residues: 49.9512 Evaluate side-chains 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 138 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 122 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065234 restraints weight = 39509.185| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.53 r_work: 0.2867 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13887 Z= 0.106 Angle : 0.583 12.197 18947 Z= 0.286 Chirality : 0.042 0.162 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.000 40.105 1962 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.41 % Allowed : 16.46 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1774 helix: 0.87 (0.19), residues: 833 sheet: -1.16 (0.36), residues: 195 loop : -1.25 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.004 0.001 HIS C 8 PHE 0.022 0.001 PHE E 280 TYR 0.023 0.001 TYR A 156 ARG 0.006 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 627) hydrogen bonds : angle 4.62240 ( 1806) glycosidic custom : bond 0.00165 ( 1) glycosidic custom : angle 0.97292 ( 3) covalent geometry : bond 0.00238 (13886) covalent geometry : angle 0.58338 (18944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8156.50 seconds wall clock time: 139 minutes 54.51 seconds (8394.51 seconds total)