Starting phenix.real_space_refine on Thu May 15 22:15:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ja7_36125/05_2025/8ja7_36125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ja7_36125/05_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_36125/05_2025/8ja7_36125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ja7_36125/05_2025/8ja7_36125.map" model { file = "/net/cci-nas-00/data/ceres_data/8ja7_36125/05_2025/8ja7_36125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ja7_36125/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.69, per 1000 atoms: 0.64 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 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: 1.46 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: 4.12 Time building geometry restraints manager: 4.04 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: 4.130 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- 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 : 1.613 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: 0.2345 time to fit residues: 48.5197 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 : 1.371 ------------------------------------------------------------------------------- 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 = 57)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063871 restraints weight = 38539.956| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.42 r_work: 0.2826 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 5.54218 ( 1806) glycosidic custom : bond 0.01087 ( 1) glycosidic custom : angle 0.71698 ( 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 : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9007 (t0) cc_final: 0.8730 (t0) REVERT: A 244 TYR cc_start: 0.9419 (t80) cc_final: 0.9214 (t80) REVERT: A 262 ASP cc_start: 0.9094 (m-30) cc_final: 0.8725 (m-30) REVERT: A 293 LYS cc_start: 0.9268 (tppp) cc_final: 0.8749 (tppt) REVERT: B 170 MET cc_start: 0.8877 (tpp) cc_final: 0.8469 (tpp) REVERT: E 75 GLU cc_start: 0.9078 (pt0) cc_final: 0.8720 (pm20) REVERT: E 92 ASP cc_start: 0.8627 (m-30) cc_final: 0.8377 (m-30) REVERT: C 13 TYR cc_start: 0.8653 (m-10) cc_final: 0.8372 (m-80) REVERT: C 17 HIS cc_start: 0.8265 (t-90) cc_final: 0.8009 (t-90) REVERT: C 145 MET cc_start: 0.9239 (mtm) cc_final: 0.8571 (mtm) REVERT: C 168 LYS cc_start: 0.9314 (ptmm) cc_final: 0.9083 (pptt) REVERT: C 199 MET cc_start: 0.9421 (mmm) cc_final: 0.9109 (mmm) REVERT: C 240 MET cc_start: 0.8822 (ptp) cc_final: 0.8527 (ptp) REVERT: C 321 TYR cc_start: 0.9072 (m-80) cc_final: 0.8864 (m-80) REVERT: C 369 LEU cc_start: 0.8852 (pp) cc_final: 0.8480 (mp) REVERT: D 85 TYR cc_start: 0.8520 (m-10) cc_final: 0.8159 (m-10) REVERT: D 199 MET cc_start: 0.8672 (mtp) cc_final: 0.8260 (mmp) outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.2393 time to fit residues: 50.8118 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 : 1.419 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.105914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.062961 restraints weight = 39142.936| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.41 r_work: 0.2830 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1580 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= 0.142 Angle : 0.575 10.058 18947 Z= 0.291 Chirality : 0.043 0.164 2252 Planarity : 0.004 0.040 2437 Dihedral : 4.735 61.114 1962 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -1.34 (0.20), residues: 1774 helix: 0.02 (0.18), residues: 836 sheet: -1.40 (0.35), residues: 167 loop : -1.76 (0.22), residues: 771 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 0.03922 ( 627) hydrogen bonds : angle 5.20643 ( 1806) glycosidic custom : bond 0.00293 ( 1) glycosidic custom : angle 1.35952 ( 3) covalent geometry : bond 0.00315 (13886) covalent geometry : angle 0.57441 (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 : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9032 (t0) cc_final: 0.8624 (t0) REVERT: A 205 ASP cc_start: 0.9151 (m-30) cc_final: 0.8823 (t0) REVERT: A 293 LYS cc_start: 0.9286 (tppp) cc_final: 0.8756 (tppt) REVERT: B 165 GLU cc_start: 0.9218 (tt0) cc_final: 0.8674 (mt-10) REVERT: B 170 MET cc_start: 0.8846 (tpp) cc_final: 0.8378 (tpp) REVERT: C 13 TYR cc_start: 0.8709 (m-10) cc_final: 0.8311 (m-80) REVERT: C 145 MET cc_start: 0.9221 (mtm) cc_final: 0.8616 (mtm) REVERT: C 199 MET cc_start: 0.9425 (mmm) cc_final: 0.9122 (mmm) REVERT: C 240 MET cc_start: 0.8718 (ptp) cc_final: 0.8387 (ptp) REVERT: C 321 TYR cc_start: 0.9081 (m-80) cc_final: 0.8873 (m-80) REVERT: C 369 LEU cc_start: 0.8875 (pp) cc_final: 0.8571 (mp) REVERT: D 85 TYR cc_start: 0.8416 (m-10) cc_final: 0.8046 (m-10) REVERT: D 199 MET cc_start: 0.8622 (mtp) cc_final: 0.8290 (mmp) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 0.2231 time to fit residues: 50.0852 Evaluate side-chains 120 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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: 5.9990 chunk 114 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 chunk 157 optimal weight: 0.0170 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 96 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.107214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064996 restraints weight = 38891.045| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.44 r_work: 0.2869 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1930 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= 0.107 Angle : 0.561 8.165 18947 Z= 0.281 Chirality : 0.043 0.268 2252 Planarity : 0.004 0.059 2437 Dihedral : 4.434 56.519 1962 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.05 % Allowed : 13.36 % Favored : 85.58 % 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: -1.05 (0.20), residues: 1774 helix: 0.27 (0.18), residues: 836 sheet: -1.23 (0.37), residues: 158 loop : -1.64 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 139 HIS 0.004 0.001 HIS C 8 PHE 0.011 0.001 PHE C 322 TYR 0.022 0.001 TYR C 223 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 627) hydrogen bonds : angle 4.96973 ( 1806) glycosidic custom : bond 0.00115 ( 1) glycosidic custom : angle 0.91607 ( 3) covalent geometry : bond 0.00224 (13886) covalent geometry : angle 0.56103 (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 146 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9001 (t0) cc_final: 0.8549 (t0) REVERT: A 205 ASP cc_start: 0.9071 (m-30) cc_final: 0.8790 (t0) REVERT: A 293 LYS cc_start: 0.9273 (tppp) cc_final: 0.8930 (tppt) REVERT: B 170 MET cc_start: 0.8811 (tpp) cc_final: 0.8334 (tpp) REVERT: E 75 GLU cc_start: 0.9142 (pt0) cc_final: 0.8909 (pm20) REVERT: C 1 MET cc_start: 0.7020 (ptt) cc_final: 0.6112 (mpp) REVERT: C 13 TYR cc_start: 0.8710 (m-10) cc_final: 0.8342 (m-80) REVERT: C 145 MET cc_start: 0.9217 (mtm) cc_final: 0.8632 (mtm) REVERT: C 199 MET cc_start: 0.9442 (mmm) cc_final: 0.9141 (mmm) REVERT: C 240 MET cc_start: 0.8812 (ptp) cc_final: 0.8485 (ptp) REVERT: C 321 TYR cc_start: 0.9051 (m-80) cc_final: 0.8851 (m-80) REVERT: C 369 LEU cc_start: 0.8962 (pp) cc_final: 0.8641 (mp) REVERT: D 85 TYR cc_start: 0.8489 (m-10) cc_final: 0.8108 (m-10) REVERT: D 199 MET cc_start: 0.8593 (mtp) cc_final: 0.8320 (mmp) REVERT: D 208 MET cc_start: 0.8752 (mmm) cc_final: 0.8527 (mmm) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.2356 time to fit residues: 52.5502 Evaluate side-chains 117 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 391 VAL Chi-restraints excluded: chain C residue 308 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN E 298 ASN C 90 HIS ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.106881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064261 restraints weight = 39307.237| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.44 r_work: 0.2865 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13887 Z= 0.114 Angle : 0.565 9.992 18947 Z= 0.283 Chirality : 0.043 0.195 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.309 53.317 1962 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.48 % Allowed : 14.14 % Favored : 84.39 % 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: -0.88 (0.20), residues: 1774 helix: 0.43 (0.19), residues: 834 sheet: -1.19 (0.35), residues: 184 loop : -1.54 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 177 HIS 0.004 0.001 HIS C 8 PHE 0.023 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 0.03470 ( 627) hydrogen bonds : angle 4.92011 ( 1806) glycosidic custom : bond 0.00057 ( 1) glycosidic custom : angle 1.07404 ( 3) covalent geometry : bond 0.00256 (13886) covalent geometry : angle 0.56489 (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 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9025 (t70) cc_final: 0.8560 (t0) REVERT: A 205 ASP cc_start: 0.9099 (m-30) cc_final: 0.8757 (t0) REVERT: A 293 LYS cc_start: 0.9259 (tppp) cc_final: 0.8925 (tppt) REVERT: B 170 MET cc_start: 0.8846 (tpp) cc_final: 0.8348 (tpp) REVERT: E 75 GLU cc_start: 0.9128 (pt0) cc_final: 0.8873 (pm20) REVERT: C 1 MET cc_start: 0.6979 (ptt) cc_final: 0.6080 (mpp) REVERT: C 13 TYR cc_start: 0.8738 (m-10) cc_final: 0.8373 (m-80) REVERT: C 199 MET cc_start: 0.9442 (mmm) cc_final: 0.9153 (mmm) REVERT: C 240 MET cc_start: 0.8825 (ptp) cc_final: 0.8496 (ptp) REVERT: C 369 LEU cc_start: 0.9014 (pp) cc_final: 0.8714 (mp) REVERT: D 85 TYR cc_start: 0.8497 (m-10) cc_final: 0.8105 (m-10) REVERT: D 240 MET cc_start: 0.6516 (mmm) cc_final: 0.5647 (mmm) outliers start: 21 outliers final: 17 residues processed: 141 average time/residue: 0.2250 time to fit residues: 49.2736 Evaluate side-chains 130 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 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 11 LYS 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 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: 5.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 82 optimal weight: 0.0970 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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** C 347 HIS D 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.107774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065524 restraints weight = 39423.824| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.49 r_work: 0.2874 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2389 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= 0.103 Angle : 0.562 8.626 18947 Z= 0.279 Chirality : 0.042 0.159 2252 Planarity : 0.004 0.037 2437 Dihedral : 4.153 48.980 1962 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.76 % Allowed : 14.63 % Favored : 83.61 % 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: -0.68 (0.20), residues: 1774 helix: 0.63 (0.19), residues: 826 sheet: -1.22 (0.35), residues: 190 loop : -1.42 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 177 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 0.002 0.000 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 627) hydrogen bonds : angle 4.79917 ( 1806) glycosidic custom : bond 0.00372 ( 1) glycosidic custom : angle 0.89712 ( 3) covalent geometry : bond 0.00222 (13886) covalent geometry : angle 0.56193 (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 150 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8983 (t70) cc_final: 0.8494 (t0) REVERT: A 205 ASP cc_start: 0.9081 (m-30) cc_final: 0.8740 (t0) REVERT: A 293 LYS cc_start: 0.9241 (tppp) cc_final: 0.8890 (tppt) REVERT: B 170 MET cc_start: 0.8831 (tpp) cc_final: 0.8311 (tpp) REVERT: E 75 GLU cc_start: 0.9122 (pt0) cc_final: 0.8844 (pm20) REVERT: C 1 MET cc_start: 0.6890 (ptt) cc_final: 0.5998 (mpp) REVERT: C 13 TYR cc_start: 0.8763 (m-10) cc_final: 0.8437 (m-80) REVERT: C 17 HIS cc_start: 0.8329 (t-90) cc_final: 0.8000 (t-90) REVERT: C 199 MET cc_start: 0.9434 (mmm) cc_final: 0.9202 (mmm) REVERT: C 240 MET cc_start: 0.8822 (ptp) cc_final: 0.8507 (ptp) REVERT: C 321 TYR cc_start: 0.9015 (m-80) cc_final: 0.8741 (t80) REVERT: C 369 LEU cc_start: 0.8980 (pp) cc_final: 0.8685 (mp) REVERT: D 85 TYR cc_start: 0.8518 (m-10) cc_final: 0.8146 (m-10) REVERT: D 199 MET cc_start: 0.8738 (mmp) cc_final: 0.8400 (mmm) outliers start: 25 outliers final: 17 residues processed: 147 average time/residue: 0.2234 time to fit residues: 50.7661 Evaluate side-chains 136 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 61 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 74 optimal weight: 0.0870 chunk 81 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.107827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065548 restraints weight = 39166.540| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.45 r_work: 0.2882 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13887 Z= 0.103 Angle : 0.552 8.420 18947 Z= 0.275 Chirality : 0.042 0.160 2252 Planarity : 0.004 0.037 2437 Dihedral : 4.058 45.907 1962 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.48 % Allowed : 15.05 % Favored : 83.47 % 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: -0.59 (0.20), residues: 1774 helix: 0.71 (0.19), residues: 827 sheet: -1.19 (0.35), residues: 193 loop : -1.39 (0.23), residues: 754 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 0.014 0.001 PHE D 230 TYR 0.020 0.001 TYR A 156 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 627) hydrogen bonds : angle 4.73519 ( 1806) glycosidic custom : bond 0.00272 ( 1) glycosidic custom : angle 0.97651 ( 3) covalent geometry : bond 0.00224 (13886) covalent geometry : angle 0.55238 (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 146 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9015 (t70) cc_final: 0.8487 (t0) REVERT: A 205 ASP cc_start: 0.9077 (m-30) cc_final: 0.8733 (t0) REVERT: A 293 LYS cc_start: 0.9222 (tppp) cc_final: 0.8868 (tppt) REVERT: B 95 GLU cc_start: 0.8620 (mp0) cc_final: 0.8246 (pp20) REVERT: B 170 MET cc_start: 0.8835 (tpp) cc_final: 0.8324 (tpp) REVERT: E 75 GLU cc_start: 0.9103 (pt0) cc_final: 0.8798 (pm20) REVERT: E 266 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8493 (mt-10) REVERT: E 407 MET cc_start: 0.9005 (pmm) cc_final: 0.8710 (ptp) REVERT: C 1 MET cc_start: 0.6800 (ptt) cc_final: 0.5982 (mpp) REVERT: C 13 TYR cc_start: 0.8777 (m-10) cc_final: 0.8424 (m-80) REVERT: C 199 MET cc_start: 0.9478 (mmm) cc_final: 0.9180 (mmm) REVERT: C 240 MET cc_start: 0.8821 (ptp) cc_final: 0.8501 (ptp) REVERT: C 321 TYR cc_start: 0.9033 (m-80) cc_final: 0.8774 (t80) REVERT: C 369 LEU cc_start: 0.9002 (pp) cc_final: 0.8721 (mp) REVERT: D 85 TYR cc_start: 0.8564 (m-10) cc_final: 0.8228 (m-10) outliers start: 21 outliers final: 18 residues processed: 143 average time/residue: 0.2182 time to fit residues: 48.3994 Evaluate side-chains 137 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 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 C residue 329 VAL Chi-restraints excluded: chain D residue 13 TYR 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: 4.9990 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 144 optimal weight: 0.3980 chunk 55 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.107683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065187 restraints weight = 39289.514| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.52 r_work: 0.2887 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2621 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= 0.103 Angle : 0.560 10.598 18947 Z= 0.275 Chirality : 0.042 0.159 2252 Planarity : 0.004 0.037 2437 Dihedral : 4.006 43.264 1962 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 15.82 % Favored : 82.77 % 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: -0.52 (0.20), residues: 1774 helix: 0.77 (0.19), residues: 832 sheet: -1.13 (0.36), residues: 194 loop : -1.37 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.004 0.001 HIS C 8 PHE 0.013 0.001 PHE D 230 TYR 0.025 0.001 TYR B 8 ARG 0.002 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 627) hydrogen bonds : angle 4.66897 ( 1806) glycosidic custom : bond 0.00221 ( 1) glycosidic custom : angle 0.98144 ( 3) covalent geometry : bond 0.00229 (13886) covalent geometry : angle 0.55949 (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 143 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9029 (t70) cc_final: 0.8485 (t0) REVERT: A 205 ASP cc_start: 0.9069 (m-30) cc_final: 0.8711 (t0) REVERT: A 262 ASP cc_start: 0.9053 (m-30) cc_final: 0.8695 (m-30) REVERT: A 293 LYS cc_start: 0.9225 (tppp) cc_final: 0.8871 (tppt) REVERT: B 170 MET cc_start: 0.8802 (tpp) cc_final: 0.8288 (tpp) REVERT: E 75 GLU cc_start: 0.9113 (pt0) cc_final: 0.8822 (pm20) REVERT: E 407 MET cc_start: 0.8981 (pmm) cc_final: 0.8731 (ptp) REVERT: C 1 MET cc_start: 0.6812 (ptt) cc_final: 0.5985 (mpp) REVERT: C 13 TYR cc_start: 0.8808 (m-10) cc_final: 0.8460 (m-80) REVERT: C 199 MET cc_start: 0.9470 (mmm) cc_final: 0.9180 (mmm) REVERT: C 240 MET cc_start: 0.8882 (ptp) cc_final: 0.8559 (ptp) REVERT: C 321 TYR cc_start: 0.9022 (m-80) cc_final: 0.8769 (t80) REVERT: C 369 LEU cc_start: 0.8993 (pp) cc_final: 0.8741 (mp) REVERT: D 85 TYR cc_start: 0.8628 (m-10) cc_final: 0.8336 (m-10) outliers start: 20 outliers final: 17 residues processed: 141 average time/residue: 0.2245 time to fit residues: 49.2449 Evaluate side-chains 137 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 21 LEU 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 C residue 329 VAL Chi-restraints excluded: chain D residue 13 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 0.6980 chunk 126 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.107680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065144 restraints weight = 38944.159| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.49 r_work: 0.2878 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2693 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= 0.109 Angle : 0.555 9.528 18947 Z= 0.275 Chirality : 0.042 0.161 2252 Planarity : 0.004 0.037 2437 Dihedral : 4.003 41.722 1962 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.48 % Allowed : 15.54 % 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: -0.43 (0.20), residues: 1774 helix: 0.83 (0.19), residues: 832 sheet: -1.10 (0.36), residues: 194 loop : -1.30 (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 D 230 TYR 0.018 0.001 TYR A 156 ARG 0.007 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 627) hydrogen bonds : angle 4.64998 ( 1806) glycosidic custom : bond 0.00152 ( 1) glycosidic custom : angle 1.00083 ( 3) covalent geometry : bond 0.00245 (13886) covalent geometry : angle 0.55519 (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 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9049 (t70) cc_final: 0.8483 (t0) REVERT: A 205 ASP cc_start: 0.9078 (m-30) cc_final: 0.8733 (t0) REVERT: A 262 ASP cc_start: 0.9070 (m-30) cc_final: 0.8709 (m-30) REVERT: A 293 LYS cc_start: 0.9223 (tppp) cc_final: 0.8861 (tppt) REVERT: B 95 GLU cc_start: 0.8589 (mp0) cc_final: 0.8190 (pp20) REVERT: B 170 MET cc_start: 0.8787 (tpp) cc_final: 0.8295 (tpp) REVERT: E 75 GLU cc_start: 0.9114 (pt0) cc_final: 0.8830 (pm20) REVERT: E 219 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.8934 (tpp80) REVERT: E 407 MET cc_start: 0.8978 (pmm) cc_final: 0.8740 (ptp) REVERT: C 1 MET cc_start: 0.6843 (ptt) cc_final: 0.6010 (mpp) REVERT: C 13 TYR cc_start: 0.8831 (m-10) cc_final: 0.8488 (m-80) REVERT: C 199 MET cc_start: 0.9471 (mmm) cc_final: 0.9177 (mmm) REVERT: C 240 MET cc_start: 0.8901 (ptp) cc_final: 0.8572 (ptp) REVERT: C 321 TYR cc_start: 0.8974 (m-80) cc_final: 0.8717 (t80) REVERT: C 369 LEU cc_start: 0.8971 (pp) cc_final: 0.8730 (mp) outliers start: 21 outliers final: 18 residues processed: 142 average time/residue: 0.2219 time to fit residues: 49.1223 Evaluate side-chains 138 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 B residue 197 LEU 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 C residue 329 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 36 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 172 optimal weight: 40.0000 chunk 167 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.108098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065965 restraints weight = 39230.214| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.53 r_work: 0.2889 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13887 Z= 0.103 Angle : 0.559 9.488 18947 Z= 0.278 Chirality : 0.042 0.161 2252 Planarity : 0.004 0.037 2437 Dihedral : 3.989 40.270 1962 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.20 % Allowed : 15.61 % Favored : 83.19 % 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: -0.35 (0.20), residues: 1774 helix: 0.91 (0.19), residues: 829 sheet: -1.06 (0.36), residues: 194 loop : -1.26 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 156 HIS 0.004 0.001 HIS C 8 PHE 0.020 0.001 PHE D 230 TYR 0.035 0.002 TYR D 13 ARG 0.006 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 627) hydrogen bonds : angle 4.60331 ( 1806) glycosidic custom : bond 0.00342 ( 1) glycosidic custom : angle 0.88757 ( 3) covalent geometry : bond 0.00228 (13886) covalent geometry : angle 0.55939 (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 139 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9038 (t70) cc_final: 0.8471 (t0) REVERT: A 205 ASP cc_start: 0.9075 (m-30) cc_final: 0.8735 (t0) REVERT: A 262 ASP cc_start: 0.9019 (m-30) cc_final: 0.8639 (m-30) REVERT: A 293 LYS cc_start: 0.9214 (tppp) cc_final: 0.8855 (tppt) REVERT: B 95 GLU cc_start: 0.8588 (mp0) cc_final: 0.8224 (pp20) REVERT: B 170 MET cc_start: 0.8759 (tpp) cc_final: 0.8282 (tpp) REVERT: E 75 GLU cc_start: 0.9116 (pt0) cc_final: 0.8819 (pm20) REVERT: E 219 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.8898 (tpp80) REVERT: E 407 MET cc_start: 0.8957 (pmm) cc_final: 0.8717 (ptp) REVERT: C 13 TYR cc_start: 0.8869 (m-10) cc_final: 0.8523 (m-80) REVERT: C 199 MET cc_start: 0.9463 (mmm) cc_final: 0.9163 (mmm) REVERT: C 240 MET cc_start: 0.8884 (ptp) cc_final: 0.8569 (ptp) REVERT: C 321 TYR cc_start: 0.8978 (m-80) cc_final: 0.8720 (t80) REVERT: C 369 LEU cc_start: 0.8970 (pp) cc_final: 0.8735 (mp) REVERT: D 85 TYR cc_start: 0.8437 (m-10) cc_final: 0.8204 (m-10) outliers start: 17 outliers final: 17 residues processed: 137 average time/residue: 0.2292 time to fit residues: 48.6150 Evaluate side-chains 139 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 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 C residue 329 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: 1.9990 chunk 92 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 138 optimal weight: 40.0000 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.107845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065238 restraints weight = 39652.410| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.51 r_work: 0.2877 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13887 Z= 0.108 Angle : 0.556 9.329 18947 Z= 0.275 Chirality : 0.042 0.163 2252 Planarity : 0.004 0.037 2437 Dihedral : 3.971 39.478 1962 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.20 % Allowed : 15.75 % Favored : 83.05 % 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: -0.28 (0.20), residues: 1774 helix: 0.94 (0.19), residues: 832 sheet: -1.01 (0.36), residues: 190 loop : -1.21 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 156 HIS 0.004 0.001 HIS C 8 PHE 0.017 0.001 PHE D 230 TYR 0.025 0.001 TYR D 13 ARG 0.005 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 627) hydrogen bonds : angle 4.58602 ( 1806) glycosidic custom : bond 0.00172 ( 1) glycosidic custom : angle 1.00263 ( 3) covalent geometry : bond 0.00245 (13886) covalent geometry : angle 0.55608 (18944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8432.77 seconds wall clock time: 146 minutes 0.68 seconds (8760.68 seconds total)