Starting phenix.real_space_refine on Sun Nov 17 12:06:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/11_2024/8ja7_36125.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/11_2024/8ja7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/11_2024/8ja7_36125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/11_2024/8ja7_36125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/11_2024/8ja7_36125.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja7_36125/11_2024/8ja7_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13601 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2164 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2043 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 16, 'TRANS': 254} Chain: "E" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3335 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 410} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3018 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 372} Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3018 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 372} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.80, per 1000 atoms: 0.72 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: 3.63 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: 1.68 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: 4.31 Time building geometry restraints manager: 4.02 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: 4.020 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.180 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- 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 13886 Z= 0.274 Angle : 0.626 8.060 18944 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 *********************** 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 : 1.566 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: 0.2480 time to fit residues: 51.7428 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 : 1.640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 13886 Z= 0.189 Angle : 0.613 10.665 18944 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 *********************** 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 : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8369 (p0) cc_final: 0.8126 (p0) REVERT: A 262 ASP cc_start: 0.8344 (m-30) cc_final: 0.7969 (m-30) REVERT: A 293 LYS cc_start: 0.8991 (tppp) cc_final: 0.8599 (tppt) REVERT: B 170 MET cc_start: 0.8946 (tpp) cc_final: 0.8560 (tpp) REVERT: C 145 MET cc_start: 0.8974 (mtm) cc_final: 0.8485 (mtm) REVERT: C 168 LYS cc_start: 0.9000 (ptmm) cc_final: 0.8783 (pptt) REVERT: C 199 MET cc_start: 0.9278 (mmm) cc_final: 0.8906 (mmm) REVERT: C 240 MET cc_start: 0.8525 (ptp) cc_final: 0.8136 (ptp) REVERT: C 321 TYR cc_start: 0.9090 (m-80) cc_final: 0.8797 (m-80) REVERT: C 369 LEU cc_start: 0.8805 (pp) cc_final: 0.8336 (mp) REVERT: D 85 TYR cc_start: 0.8206 (m-10) cc_final: 0.7911 (m-10) REVERT: D 199 MET cc_start: 0.8721 (mtp) cc_final: 0.8295 (mmp) REVERT: D 321 TYR cc_start: 0.9464 (m-80) cc_final: 0.9174 (m-80) outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.2348 time to fit residues: 49.5623 Evaluate side-chains 119 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 89 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13886 Z= 0.271 Angle : 0.603 13.643 18944 Z= 0.302 Chirality : 0.044 0.167 2252 Planarity : 0.004 0.041 2437 Dihedral : 4.847 61.836 1962 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.62 % Allowed : 12.45 % Favored : 85.94 % 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: -1.38 (0.20), residues: 1774 helix: -0.01 (0.18), residues: 833 sheet: -1.42 (0.35), residues: 168 loop : -1.76 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 109 HIS 0.005 0.001 HIS D 286 PHE 0.013 0.001 PHE C 379 TYR 0.023 0.002 TYR B 8 ARG 0.006 0.000 ARG A 232 *********************** 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 138 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9110 (m-30) cc_final: 0.8636 (t0) REVERT: A 293 LYS cc_start: 0.9025 (tppp) cc_final: 0.8604 (tppt) REVERT: B 165 GLU cc_start: 0.8954 (tt0) cc_final: 0.8501 (mt-10) REVERT: B 170 MET cc_start: 0.8903 (tpp) cc_final: 0.8460 (tpp) REVERT: C 145 MET cc_start: 0.8981 (mtm) cc_final: 0.8505 (mtm) REVERT: C 199 MET cc_start: 0.9288 (mmm) cc_final: 0.8925 (mmm) REVERT: C 240 MET cc_start: 0.8485 (ptp) cc_final: 0.8072 (ptp) REVERT: C 321 TYR cc_start: 0.9102 (m-80) cc_final: 0.8822 (m-80) REVERT: C 369 LEU cc_start: 0.8829 (pp) cc_final: 0.8448 (mp) REVERT: D 85 TYR cc_start: 0.8099 (m-10) cc_final: 0.7807 (m-10) REVERT: D 199 MET cc_start: 0.8678 (mtp) cc_final: 0.8357 (mmp) REVERT: D 319 TYR cc_start: 0.8706 (m-80) cc_final: 0.8374 (m-80) REVERT: D 321 TYR cc_start: 0.9468 (m-80) cc_final: 0.9257 (m-80) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 0.2393 time to fit residues: 48.9469 Evaluate side-chains 119 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 21 LEU 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 13 TYR 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 159 optimal weight: 20.0000 chunk 121 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13886 Z= 0.322 Angle : 0.621 11.129 18944 Z= 0.311 Chirality : 0.045 0.271 2252 Planarity : 0.004 0.041 2437 Dihedral : 4.860 60.257 1962 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.55 % Allowed : 14.35 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1774 helix: 0.12 (0.18), residues: 832 sheet: -1.37 (0.35), residues: 175 loop : -1.64 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.004 0.001 HIS C 8 PHE 0.010 0.001 PHE E 280 TYR 0.020 0.002 TYR E 427 ARG 0.010 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8352 (m-30) cc_final: 0.7980 (m-30) REVERT: A 293 LYS cc_start: 0.8992 (tppp) cc_final: 0.8560 (tppt) REVERT: B 170 MET cc_start: 0.8908 (tpp) cc_final: 0.8441 (tpp) REVERT: C 168 LYS cc_start: 0.8943 (ptmm) cc_final: 0.8712 (pptt) REVERT: C 169 LEU cc_start: 0.9500 (mt) cc_final: 0.9249 (mt) REVERT: C 199 MET cc_start: 0.9303 (mmm) cc_final: 0.8962 (mmm) REVERT: C 240 MET cc_start: 0.8522 (ptp) cc_final: 0.8097 (ptp) REVERT: C 321 TYR cc_start: 0.9075 (m-80) cc_final: 0.8811 (m-80) REVERT: C 369 LEU cc_start: 0.8921 (pp) cc_final: 0.8494 (mp) REVERT: D 85 TYR cc_start: 0.8137 (m-10) cc_final: 0.7858 (m-10) REVERT: D 199 MET cc_start: 0.8677 (mtp) cc_final: 0.8394 (mmp) REVERT: D 208 MET cc_start: 0.8528 (mmm) cc_final: 0.8323 (mmm) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 0.2409 time to fit residues: 52.6392 Evaluate side-chains 121 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 34 VAL Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 241 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13886 Z= 0.229 Angle : 0.591 10.284 18944 Z= 0.296 Chirality : 0.044 0.221 2252 Planarity : 0.004 0.040 2437 Dihedral : 4.658 57.659 1962 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.69 % Allowed : 15.05 % Favored : 83.26 % 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: -1.04 (0.20), residues: 1774 helix: 0.30 (0.19), residues: 833 sheet: -1.33 (0.35), residues: 183 loop : -1.61 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 169 HIS 0.004 0.001 HIS C 8 PHE 0.020 0.001 PHE D 230 TYR 0.022 0.002 TYR C 223 ARG 0.003 0.000 ARG A 232 *********************** 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 146 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9069 (m-30) cc_final: 0.8801 (t0) REVERT: A 293 LYS cc_start: 0.8979 (tppp) cc_final: 0.8559 (tppt) REVERT: B 170 MET cc_start: 0.8898 (tpp) cc_final: 0.8433 (tpp) REVERT: C 168 LYS cc_start: 0.8908 (ptmm) cc_final: 0.8689 (pptt) REVERT: C 169 LEU cc_start: 0.9479 (mt) cc_final: 0.9204 (mt) REVERT: C 199 MET cc_start: 0.9288 (mmm) cc_final: 0.8940 (mmm) REVERT: C 240 MET cc_start: 0.8561 (ptp) cc_final: 0.8163 (ptp) REVERT: C 321 TYR cc_start: 0.9036 (m-80) cc_final: 0.8771 (m-80) REVERT: C 369 LEU cc_start: 0.8942 (pp) cc_final: 0.8518 (mp) REVERT: D 85 TYR cc_start: 0.8117 (m-10) cc_final: 0.7843 (m-10) REVERT: D 199 MET cc_start: 0.8612 (mtp) cc_final: 0.8399 (mmp) outliers start: 24 outliers final: 21 residues processed: 144 average time/residue: 0.2325 time to fit residues: 51.4879 Evaluate side-chains 131 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 13 TYR 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 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 Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 298 ASN C 90 HIS ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13886 Z= 0.162 Angle : 0.574 8.714 18944 Z= 0.286 Chirality : 0.043 0.188 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.383 52.967 1962 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.97 % Allowed : 15.19 % Favored : 82.84 % 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: -0.80 (0.20), residues: 1774 helix: 0.52 (0.19), residues: 829 sheet: -1.15 (0.36), residues: 182 loop : -1.52 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.004 0.001 HIS C 8 PHE 0.016 0.001 PHE D 230 TYR 0.017 0.001 TYR E 427 ARG 0.007 0.000 ARG A 232 *********************** 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 158 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9068 (m-30) cc_final: 0.8804 (t0) REVERT: A 262 ASP cc_start: 0.8293 (m-30) cc_final: 0.7934 (m-30) REVERT: A 293 LYS cc_start: 0.8934 (tppp) cc_final: 0.8678 (tppt) REVERT: B 170 MET cc_start: 0.8874 (tpp) cc_final: 0.8438 (tpp) REVERT: C 1 MET cc_start: 0.5862 (mpp) cc_final: 0.5426 (mpp) REVERT: C 145 MET cc_start: 0.8936 (mtm) cc_final: 0.8505 (mtm) REVERT: C 168 LYS cc_start: 0.8901 (ptmm) cc_final: 0.8692 (pptt) REVERT: C 169 LEU cc_start: 0.9482 (mt) cc_final: 0.9220 (mt) REVERT: C 199 MET cc_start: 0.9281 (mmm) cc_final: 0.8933 (mmm) REVERT: C 240 MET cc_start: 0.8573 (ptp) cc_final: 0.8192 (ptp) REVERT: C 321 TYR cc_start: 0.9011 (m-80) cc_final: 0.8742 (m-80) REVERT: C 369 LEU cc_start: 0.8971 (pp) cc_final: 0.8565 (mp) REVERT: D 85 TYR cc_start: 0.8094 (m-10) cc_final: 0.7846 (m-10) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 0.2372 time to fit residues: 56.9631 Evaluate side-chains 132 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 13 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13886 Z= 0.200 Angle : 0.583 8.227 18944 Z= 0.290 Chirality : 0.043 0.227 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.363 50.677 1962 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.62 % Allowed : 16.24 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1774 helix: 0.57 (0.19), residues: 827 sheet: -1.23 (0.35), residues: 188 loop : -1.48 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.005 0.001 HIS C 272 PHE 0.013 0.001 PHE D 230 TYR 0.023 0.002 TYR A 156 ARG 0.002 0.000 ARG A 232 *********************** 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 141 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9071 (m-30) cc_final: 0.8802 (t0) REVERT: A 262 ASP cc_start: 0.8303 (m-30) cc_final: 0.7933 (m-30) REVERT: A 293 LYS cc_start: 0.8943 (tppp) cc_final: 0.8676 (tppt) REVERT: B 170 MET cc_start: 0.8864 (tpp) cc_final: 0.8430 (tpp) REVERT: E 407 MET cc_start: 0.8565 (pmm) cc_final: 0.8154 (ptp) REVERT: C 169 LEU cc_start: 0.9471 (mt) cc_final: 0.9199 (mt) REVERT: C 199 MET cc_start: 0.9276 (mmm) cc_final: 0.8943 (mmm) REVERT: C 240 MET cc_start: 0.8582 (ptp) cc_final: 0.8199 (ptp) REVERT: C 321 TYR cc_start: 0.9015 (m-80) cc_final: 0.8755 (m-80) REVERT: C 369 LEU cc_start: 0.8978 (pp) cc_final: 0.8581 (mp) REVERT: D 85 TYR cc_start: 0.8107 (m-10) cc_final: 0.7891 (m-10) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 0.2349 time to fit residues: 50.6822 Evaluate side-chains 132 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** D 309 ASN D 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13886 Z= 0.204 Angle : 0.585 8.444 18944 Z= 0.292 Chirality : 0.043 0.194 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.353 48.639 1962 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.55 % Allowed : 16.67 % Favored : 81.79 % 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: -0.71 (0.20), residues: 1774 helix: 0.63 (0.19), residues: 827 sheet: -1.23 (0.35), residues: 186 loop : -1.48 (0.23), residues: 761 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 0.018 0.001 PHE E 280 TYR 0.024 0.001 TYR B 8 ARG 0.003 0.000 ARG A 232 *********************** 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 140 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9038 (m-30) cc_final: 0.8788 (t0) REVERT: A 262 ASP cc_start: 0.8300 (m-30) cc_final: 0.7922 (m-30) REVERT: A 293 LYS cc_start: 0.8938 (tppp) cc_final: 0.8674 (tppt) REVERT: B 170 MET cc_start: 0.8863 (tpp) cc_final: 0.8428 (tpp) REVERT: E 407 MET cc_start: 0.8546 (pmm) cc_final: 0.8156 (ptp) REVERT: C 199 MET cc_start: 0.9274 (mmm) cc_final: 0.8949 (mmm) REVERT: C 240 MET cc_start: 0.8602 (ptp) cc_final: 0.8220 (ptp) REVERT: C 321 TYR cc_start: 0.9027 (m-80) cc_final: 0.8763 (m-80) REVERT: C 369 LEU cc_start: 0.8973 (pp) cc_final: 0.8585 (mp) outliers start: 22 outliers final: 20 residues processed: 139 average time/residue: 0.2265 time to fit residues: 49.1156 Evaluate side-chains 139 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 150 optimal weight: 0.0970 chunk 104 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13886 Z= 0.316 Angle : 0.632 9.266 18944 Z= 0.314 Chirality : 0.044 0.185 2252 Planarity : 0.004 0.039 2437 Dihedral : 4.556 48.467 1962 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.83 % Allowed : 16.74 % Favored : 81.43 % 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: -0.71 (0.20), residues: 1774 helix: 0.60 (0.19), residues: 825 sheet: -1.22 (0.35), residues: 189 loop : -1.44 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.003 0.001 HIS C 8 PHE 0.017 0.001 PHE D 230 TYR 0.029 0.002 TYR A 156 ARG 0.004 0.000 ARG E 421 *********************** 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 148 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9031 (m-30) cc_final: 0.8742 (t0) REVERT: A 262 ASP cc_start: 0.8339 (m-30) cc_final: 0.7949 (m-30) REVERT: B 170 MET cc_start: 0.8871 (tpp) cc_final: 0.8403 (tpp) REVERT: E 407 MET cc_start: 0.8575 (pmm) cc_final: 0.8221 (ptp) REVERT: C 199 MET cc_start: 0.9298 (mmm) cc_final: 0.9087 (mmm) REVERT: C 240 MET cc_start: 0.8645 (ptp) cc_final: 0.8263 (ptp) REVERT: C 321 TYR cc_start: 0.9007 (m-80) cc_final: 0.8749 (m-80) REVERT: C 369 LEU cc_start: 0.8983 (pp) cc_final: 0.8611 (mp) outliers start: 26 outliers final: 22 residues processed: 145 average time/residue: 0.2339 time to fit residues: 53.5073 Evaluate side-chains 138 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 109 TRP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 391 VAL 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 231 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 102 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 30.0000 chunk 162 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 111 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13886 Z= 0.167 Angle : 0.619 12.288 18944 Z= 0.301 Chirality : 0.043 0.196 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.321 45.230 1962 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.27 % Allowed : 17.65 % Favored : 81.08 % 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: -0.64 (0.20), residues: 1774 helix: 0.67 (0.19), residues: 829 sheet: -1.23 (0.36), residues: 192 loop : -1.41 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 203 HIS 0.004 0.001 HIS C 8 PHE 0.021 0.001 PHE E 280 TYR 0.027 0.002 TYR A 156 ARG 0.002 0.000 ARG C 375 ********************** 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 147 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.9009 (m-30) cc_final: 0.8808 (t70) REVERT: A 262 ASP cc_start: 0.8283 (m-30) cc_final: 0.7913 (m-30) REVERT: B 170 MET cc_start: 0.8820 (tpp) cc_final: 0.8416 (tpp) REVERT: E 407 MET cc_start: 0.8509 (pmm) cc_final: 0.8124 (ptp) REVERT: C 240 MET cc_start: 0.8627 (ptp) cc_final: 0.8237 (ptp) REVERT: C 321 TYR cc_start: 0.8983 (m-80) cc_final: 0.8740 (m-80) REVERT: C 369 LEU cc_start: 0.8995 (pp) cc_final: 0.8640 (mp) outliers start: 18 outliers final: 17 residues processed: 145 average time/residue: 0.2511 time to fit residues: 56.8305 Evaluate side-chains 138 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 391 VAL 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 231 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 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 17 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.107833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065286 restraints weight = 38635.764| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.39 r_work: 0.2861 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13886 Z= 0.162 Angle : 0.610 10.911 18944 Z= 0.297 Chirality : 0.043 0.184 2252 Planarity : 0.004 0.038 2437 Dihedral : 4.174 42.225 1962 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.27 % Allowed : 17.79 % Favored : 80.94 % 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: -0.50 (0.20), residues: 1774 helix: 0.80 (0.19), residues: 825 sheet: -1.19 (0.36), residues: 193 loop : -1.33 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.009 0.001 HIS D 90 PHE 0.017 0.001 PHE D 230 TYR 0.026 0.002 TYR A 156 ARG 0.007 0.000 ARG E 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.63 seconds wall clock time: 54 minutes 16.41 seconds (3256.41 seconds total)