Starting phenix.real_space_refine on Sun Nov 17 02:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/11_2024/8hpn_34934.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/11_2024/8hpn_34934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/11_2024/8hpn_34934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/11_2024/8hpn_34934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/11_2024/8hpn_34934.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/11_2024/8hpn_34934.cif" } resolution = 4.55 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= 0.009 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 23 5.16 5 C 7862 2.51 5 N 2078 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12329 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2009 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 269} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1904 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 248} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2563 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2577 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3191 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 31, 'TRANS': 404} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 90 Chain: "G" 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 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.56, per 1000 atoms: 0.69 Number of scatterers: 12329 At special positions: 0 Unit cell: (81.18, 89.38, 167.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 6 15.00 O 2360 8.00 N 2078 7.00 C 7862 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 G 1 " - " GLC G 2 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 13 sheets defined 57.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 76 through 111 removed outlier: 3.771A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 4.022A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 191 removed outlier: 4.855A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.927A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 219 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.878A pdb=" N PHE A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.537A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 292 removed outlier: 4.087A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.522A pdb=" N VAL B 42 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 97 removed outlier: 4.063A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.453A pdb=" N LEU B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 4.059A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 137 through 163 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.552A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 208 Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 255 - end of helix removed outlier: 3.736A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 270 removed outlier: 4.131A pdb=" N ILE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.668A pdb=" N ASN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.552A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 156 removed outlier: 3.640A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 188 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 266 through 276 removed outlier: 4.013A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 140 through 154 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 189 Processing helix chain 'D' and resid 198 through 206 removed outlier: 4.023A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'E' and resid 40 through 56 removed outlier: 3.797A pdb=" N PHE E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN E 54 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 127 through 135 removed outlier: 3.604A pdb=" N LEU E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.916A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 removed outlier: 4.764A pdb=" N ALA E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.556A pdb=" N LYS E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.548A pdb=" N GLY E 308 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 305 through 309' Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 372 through 382 removed outlier: 4.044A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 413 removed outlier: 3.816A pdb=" N THR E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 436 Processing helix chain 'E' and resid 437 through 441 removed outlier: 3.983A pdb=" N ILE E 441 " --> pdb=" O ILE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 460 removed outlier: 3.646A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 31 removed outlier: 6.459A pdb=" N ALA C 23 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER C 12 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS C 25 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR C 10 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 6 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG C 66 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG C 8 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU C 64 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 85 removed outlier: 3.710A pdb=" N ASP C 163 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 261 through 264 removed outlier: 3.581A pdb=" N GLY C 261 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 293 removed outlier: 4.044A pdb=" N GLU C 366 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 314 through 317 Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.305A pdb=" N LYS D 11 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.305A pdb=" N LYS D 11 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D 9 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 62 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 85 removed outlier: 6.662A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 261 through 264 removed outlier: 3.667A pdb=" N GLY D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AB2, first strand: chain 'D' and resid 314 through 317 Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 66 removed outlier: 10.691A pdb=" N VAL E 31 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N VAL E 90 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN E 33 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA E 92 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR E 35 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY E 347 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 147 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 272 728 hydrogen bonds defined for protein. 2043 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: 4.01 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2097 1.29 - 1.42: 3083 1.42 - 1.55: 7337 1.55 - 1.68: 20 1.68 - 1.82: 42 Bond restraints: 12579 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C LEU A 262 " pdb=" O LEU A 262 " ideal model delta sigma weight residual 1.234 1.173 0.062 8.30e-03 1.45e+04 5.52e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.36e+01 ... (remaining 12574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 16635 3.91 - 7.83: 600 7.83 - 11.74: 13 11.74 - 15.65: 0 15.65 - 19.56: 4 Bond angle restraints: 17252 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.31 19.56 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.52 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.53 16.30 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.67e+01 ... (remaining 17247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6924 17.98 - 35.96: 485 35.96 - 53.95: 79 53.95 - 71.93: 29 71.93 - 89.91: 5 Dihedral angle restraints: 7522 sinusoidal: 2608 harmonic: 4914 Sorted by residual: dihedral pdb=" CA ASP E 121 " pdb=" C ASP E 121 " pdb=" N ALA E 122 " pdb=" CA ALA E 122 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA TRP E 106 " pdb=" C TRP E 106 " pdb=" N ALA E 107 " pdb=" CA ALA E 107 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ARG D 134 " pdb=" C ARG D 134 " pdb=" N LYS D 135 " pdb=" CA LYS D 135 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 7519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1319 0.085 - 0.169: 593 0.169 - 0.254: 136 0.254 - 0.338: 28 0.338 - 0.423: 7 Chirality restraints: 2083 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.92e+01 chirality pdb=" CA LEU A 262 " pdb=" N LEU A 262 " pdb=" C LEU A 262 " pdb=" CB LEU A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA LYS C 109 " pdb=" N LYS C 109 " pdb=" C LYS C 109 " pdb=" CB LYS C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 2080 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 402 " -0.120 2.00e-02 2.50e+03 6.83e-02 9.33e+01 pdb=" CG TYR E 402 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 402 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 402 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR E 402 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR E 402 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 402 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 402 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 166 " 0.128 2.00e-02 2.50e+03 5.95e-02 8.85e+01 pdb=" CG TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP E 166 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 166 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 166 " 0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 166 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP E 166 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 234 " -0.113 2.00e-02 2.50e+03 6.91e-02 8.35e+01 pdb=" CG PHE C 234 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE C 234 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE C 234 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE C 234 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 234 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE C 234 " -0.063 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1278 2.77 - 3.31: 14649 3.31 - 3.84: 21082 3.84 - 4.37: 24636 4.37 - 4.90: 39194 Nonbonded interactions: 100839 Sorted by model distance: nonbonded pdb=" OD2 ASP B 175 " pdb=" OH TYR C 92 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLN E 150 " pdb=" CE2 TYR E 333 " model vdw 2.302 3.340 nonbonded pdb=" O ASP E 440 " pdb=" OD1 ASP E 440 " model vdw 2.349 3.040 nonbonded pdb=" CD2 LEU A 185 " pdb=" CD1 ILE A 223 " model vdw 2.408 3.880 nonbonded pdb=" O ILE B 132 " pdb=" N LEU B 134 " model vdw 2.424 3.120 ... (remaining 100834 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' and (resid 2 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 124 or (resid 125 through 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 152 or (resid 153 and (name N or name CA or name C or name O or name CB \ )) or resid 154 through 193 or (resid 194 and (name N or name CA or name C or n \ ame O or name CB )) or resid 195 through 204 or (resid 205 and (name N or name C \ A or name C or name O or name CB )) or resid 206 through 261 or (resid 262 and ( \ name N or name CA or name C or name O or name CB )) or resid 263 through 286 or \ (resid 287 and (name N or name CA or name C or name O or name CB )) or resid 288 \ through 313 or (resid 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 376 or (resid 377 and (name N or name CA or name C or n \ ame O or name CB )) or resid 378 through 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB )) or resid 387 or (resid 388 and (name N or na \ me CA or name C or name O or name CB )) or resid 389 through 391 or resid 501)) selection = (chain 'D' and (resid 2 through 50 or (resid 51 through 52 and (name N or name C \ A or name C or name O or name CB )) or resid 53 through 57 or (resid 58 and (nam \ e N or name CA or name C or name O or name CB )) or resid 59 through 77 or (resi \ d 78 and (name N or name CA or name C or name O or name CB )) or resid 79 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 126 or (resid 127 through 128 and (name N or name \ CA or name C or name O or name CB )) or resid 129 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 174 o \ r (resid 175 through 179 and (name N or name CA or name C or name O or name CB ) \ ) or resid 180 through 195 or (resid 196 and (name N or name CA or name C or nam \ e O or name CB )) or resid 197 through 285 or (resid 286 through 287 and (name N \ or name CA or name C or name O or name CB )) or resid 288 through 289 or (resid \ 290 and (name N or name CA or name C or name O or name CB )) or resid 291 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 378 or (resid 379 and (name N or name CA or name C or name O \ or name CB )) or resid 380 or (resid 381 through 383 and (name N or name CA or n \ ame C or name O or name CB )) or resid 384 through 391 or resid 501)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.720 Find NCS groups from input model: 0.310 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.012 0.134 12579 Z= 0.806 Angle : 1.814 19.565 17252 Z= 1.224 Chirality : 0.098 0.423 2083 Planarity : 0.013 0.105 2235 Dihedral : 13.611 89.910 4346 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.28 % Favored : 92.48 % Rotamer: Outliers : 0.35 % Allowed : 6.92 % Favored : 92.73 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 2.11 % 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: -2.64 (0.18), residues: 1689 helix: -1.78 (0.14), residues: 859 sheet: -1.41 (0.39), residues: 126 loop : -1.56 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.128 0.017 TRP E 166 HIS 0.011 0.003 HIS D 290 PHE 0.113 0.017 PHE C 234 TYR 0.120 0.021 TYR E 402 ARG 0.014 0.001 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 310 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9486 (m-80) cc_final: 0.8927 (m-80) REVERT: A 162 GLN cc_start: 0.9526 (tt0) cc_final: 0.9069 (tp40) REVERT: A 166 LEU cc_start: 0.9803 (mt) cc_final: 0.9551 (mt) REVERT: A 176 LYS cc_start: 0.9433 (tptp) cc_final: 0.9090 (tppt) REVERT: A 233 ASP cc_start: 0.8725 (m-30) cc_final: 0.8246 (m-30) REVERT: A 260 ASP cc_start: 0.9013 (t0) cc_final: 0.8443 (t0) REVERT: A 261 ASN cc_start: 0.9085 (m-40) cc_final: 0.8870 (m-40) REVERT: A 289 TYR cc_start: 0.9466 (m-80) cc_final: 0.9217 (m-10) REVERT: A 291 LYS cc_start: 0.8916 (tptt) cc_final: 0.8671 (mmtp) REVERT: B 113 ILE cc_start: 0.9423 (pt) cc_final: 0.9186 (mm) REVERT: B 116 PHE cc_start: 0.8800 (m-80) cc_final: 0.8216 (m-80) REVERT: B 127 ASN cc_start: 0.9537 (m-40) cc_final: 0.9106 (m110) REVERT: B 144 PRO cc_start: 0.9529 (Cg_exo) cc_final: 0.9253 (Cg_endo) REVERT: B 148 PHE cc_start: 0.9528 (m-80) cc_final: 0.9290 (m-80) REVERT: B 174 MET cc_start: 0.9284 (mtp) cc_final: 0.9063 (ttt) REVERT: C 163 ASP cc_start: 0.8276 (m-30) cc_final: 0.7966 (t0) REVERT: C 239 ILE cc_start: 0.8991 (tp) cc_final: 0.8666 (pt) REVERT: D 177 MET cc_start: 0.9143 (mmm) cc_final: 0.8689 (mmp) REVERT: D 269 MET cc_start: 0.8702 (mtt) cc_final: 0.8221 (mmm) REVERT: E 91 MET cc_start: 0.8946 (ptp) cc_final: 0.8689 (ptp) REVERT: E 153 TRP cc_start: 0.8691 (m100) cc_final: 0.8438 (m100) REVERT: E 154 TYR cc_start: 0.8947 (p90) cc_final: 0.8233 (p90) outliers start: 4 outliers final: 0 residues processed: 313 average time/residue: 0.2653 time to fit residues: 116.8503 Evaluate side-chains 203 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 201 GLN B 72 ASN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 218 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 174 ASN E 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12579 Z= 0.272 Angle : 0.786 10.606 17252 Z= 0.419 Chirality : 0.047 0.190 2083 Planarity : 0.006 0.068 2235 Dihedral : 8.151 73.258 1908 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 0.52 % Allowed : 4.33 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -1.16 (0.20), residues: 1689 helix: -0.32 (0.17), residues: 866 sheet: -1.14 (0.34), residues: 158 loop : -1.12 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 97 HIS 0.006 0.001 HIS C 94 PHE 0.030 0.003 PHE A 263 TYR 0.030 0.002 TYR D 13 ARG 0.013 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 255 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8874 (t80) cc_final: 0.8543 (t80) REVERT: A 139 TYR cc_start: 0.9510 (m-80) cc_final: 0.9021 (m-80) REVERT: A 150 ASN cc_start: 0.8609 (t0) cc_final: 0.8210 (m-40) REVERT: A 162 GLN cc_start: 0.9647 (tt0) cc_final: 0.8937 (tp40) REVERT: A 166 LEU cc_start: 0.9831 (mt) cc_final: 0.9601 (mt) REVERT: A 176 LYS cc_start: 0.9475 (tptp) cc_final: 0.9115 (tppt) REVERT: A 198 ASN cc_start: 0.9580 (m110) cc_final: 0.9203 (m110) REVERT: A 201 GLN cc_start: 0.9573 (OUTLIER) cc_final: 0.8935 (mm-40) REVERT: A 229 PHE cc_start: 0.9037 (t80) cc_final: 0.8689 (t80) REVERT: A 260 ASP cc_start: 0.9214 (t0) cc_final: 0.8701 (t0) REVERT: A 261 ASN cc_start: 0.9370 (m-40) cc_final: 0.9143 (m-40) REVERT: B 90 MET cc_start: 0.8204 (mmp) cc_final: 0.7615 (tmm) REVERT: B 118 HIS cc_start: 0.9149 (m-70) cc_final: 0.8714 (m-70) REVERT: B 121 LEU cc_start: 0.9451 (mm) cc_final: 0.8914 (mm) REVERT: B 127 ASN cc_start: 0.9559 (m-40) cc_final: 0.8871 (m110) REVERT: B 128 MET cc_start: 0.9445 (mmt) cc_final: 0.8916 (mmp) REVERT: B 203 PHE cc_start: 0.9535 (t80) cc_final: 0.9263 (t80) REVERT: C 244 MET cc_start: 0.8524 (tpp) cc_final: 0.8095 (tpt) REVERT: D 138 GLN cc_start: 0.7909 (mt0) cc_final: 0.7571 (tm-30) REVERT: E 91 MET cc_start: 0.8849 (ptp) cc_final: 0.8626 (ptp) REVERT: E 166 TRP cc_start: 0.8574 (m100) cc_final: 0.8051 (m100) REVERT: E 262 LEU cc_start: 0.9636 (tp) cc_final: 0.9340 (tp) outliers start: 6 outliers final: 1 residues processed: 258 average time/residue: 0.2240 time to fit residues: 85.7551 Evaluate side-chains 187 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS C 99 GLN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12579 Z= 0.269 Angle : 0.725 8.422 17252 Z= 0.383 Chirality : 0.046 0.192 2083 Planarity : 0.005 0.058 2235 Dihedral : 7.549 77.483 1908 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 0.26 % Allowed : 4.50 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.87 (0.20), residues: 1689 helix: 0.02 (0.17), residues: 872 sheet: -0.89 (0.34), residues: 165 loop : -1.18 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 79 HIS 0.005 0.001 HIS C 94 PHE 0.024 0.002 PHE A 263 TYR 0.017 0.002 TYR D 13 ARG 0.006 0.001 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9540 (m-80) cc_final: 0.9028 (m-80) REVERT: A 150 ASN cc_start: 0.8586 (t0) cc_final: 0.8158 (m-40) REVERT: A 161 ASP cc_start: 0.9405 (m-30) cc_final: 0.9180 (m-30) REVERT: A 162 GLN cc_start: 0.9629 (tt0) cc_final: 0.8632 (tp40) REVERT: A 176 LYS cc_start: 0.9499 (tptp) cc_final: 0.9159 (tppt) REVERT: A 260 ASP cc_start: 0.9182 (t0) cc_final: 0.8779 (t0) REVERT: A 261 ASN cc_start: 0.9369 (m-40) cc_final: 0.9135 (m-40) REVERT: A 291 LYS cc_start: 0.9031 (tptt) cc_final: 0.8820 (pttm) REVERT: B 90 MET cc_start: 0.8193 (mmp) cc_final: 0.7683 (tmm) REVERT: B 118 HIS cc_start: 0.9170 (m-70) cc_final: 0.8681 (m-70) REVERT: B 127 ASN cc_start: 0.9536 (m-40) cc_final: 0.9143 (m110) REVERT: B 145 TYR cc_start: 0.9274 (m-10) cc_final: 0.8661 (m-80) REVERT: B 168 LEU cc_start: 0.9431 (pt) cc_final: 0.9197 (mm) REVERT: B 174 MET cc_start: 0.9329 (mtp) cc_final: 0.9105 (mtt) REVERT: B 203 PHE cc_start: 0.9505 (t80) cc_final: 0.9229 (t80) REVERT: C 244 MET cc_start: 0.8570 (tpp) cc_final: 0.8053 (tpt) REVERT: D 177 MET cc_start: 0.9061 (mmp) cc_final: 0.8409 (mmp) REVERT: D 212 MET cc_start: 0.7643 (tpp) cc_final: 0.7199 (tpt) REVERT: E 40 GLU cc_start: 0.9258 (tt0) cc_final: 0.8737 (tt0) REVERT: E 91 MET cc_start: 0.8994 (ptp) cc_final: 0.8789 (ptp) REVERT: E 101 PHE cc_start: 0.9343 (m-80) cc_final: 0.9134 (m-80) REVERT: E 159 MET cc_start: 0.8372 (ppp) cc_final: 0.8132 (ppp) outliers start: 3 outliers final: 0 residues processed: 246 average time/residue: 0.2223 time to fit residues: 81.6830 Evaluate side-chains 190 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN E 359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12579 Z= 0.223 Angle : 0.670 8.126 17252 Z= 0.350 Chirality : 0.045 0.189 2083 Planarity : 0.005 0.053 2235 Dihedral : 7.413 80.144 1908 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.32 % Favored : 95.50 % Rotamer: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.54 (0.20), residues: 1689 helix: 0.38 (0.17), residues: 872 sheet: -0.89 (0.34), residues: 155 loop : -1.11 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 79 HIS 0.004 0.001 HIS C 268 PHE 0.029 0.002 PHE A 229 TYR 0.020 0.002 TYR A 41 ARG 0.004 0.000 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8839 (t80) cc_final: 0.8371 (t80) REVERT: A 139 TYR cc_start: 0.9539 (m-80) cc_final: 0.9082 (m-80) REVERT: A 150 ASN cc_start: 0.8636 (t0) cc_final: 0.8220 (m-40) REVERT: A 162 GLN cc_start: 0.9555 (tt0) cc_final: 0.8939 (tp40) REVERT: A 176 LYS cc_start: 0.9478 (tptp) cc_final: 0.9119 (tppt) REVERT: A 260 ASP cc_start: 0.9153 (t0) cc_final: 0.8754 (t0) REVERT: A 261 ASN cc_start: 0.9337 (m-40) cc_final: 0.9099 (m-40) REVERT: A 279 PHE cc_start: 0.9645 (t80) cc_final: 0.9382 (t80) REVERT: B 90 MET cc_start: 0.8142 (mmp) cc_final: 0.7681 (tmm) REVERT: B 118 HIS cc_start: 0.9084 (m-70) cc_final: 0.8733 (m-70) REVERT: B 127 ASN cc_start: 0.9517 (m-40) cc_final: 0.8862 (m110) REVERT: B 128 MET cc_start: 0.9495 (mmt) cc_final: 0.9012 (mmm) REVERT: B 168 LEU cc_start: 0.9401 (pt) cc_final: 0.9140 (mm) REVERT: B 203 PHE cc_start: 0.9443 (t80) cc_final: 0.9187 (t80) REVERT: B 238 PHE cc_start: 0.8956 (m-10) cc_final: 0.8751 (m-10) REVERT: C 194 TYR cc_start: 0.8458 (t80) cc_final: 0.8035 (t80) REVERT: C 244 MET cc_start: 0.8612 (tpp) cc_final: 0.8080 (tpt) REVERT: D 86 PHE cc_start: 0.9419 (t80) cc_final: 0.9155 (t80) REVERT: E 44 PHE cc_start: 0.9136 (m-80) cc_final: 0.8597 (m-80) REVERT: E 91 MET cc_start: 0.8971 (ptp) cc_final: 0.8743 (ptp) REVERT: E 101 PHE cc_start: 0.9359 (m-80) cc_final: 0.9111 (m-80) REVERT: E 159 MET cc_start: 0.8396 (ppp) cc_final: 0.8097 (ppp) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.2321 time to fit residues: 88.4115 Evaluate side-chains 187 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 112 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.0050 chunk 146 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN B 72 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12579 Z= 0.178 Angle : 0.655 7.590 17252 Z= 0.332 Chirality : 0.045 0.214 2083 Planarity : 0.005 0.054 2235 Dihedral : 7.218 80.512 1908 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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 (0.21), residues: 1689 helix: 0.65 (0.18), residues: 871 sheet: -1.01 (0.34), residues: 176 loop : -0.99 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 97 HIS 0.004 0.001 HIS D 290 PHE 0.026 0.002 PHE A 229 TYR 0.021 0.002 TYR A 41 ARG 0.005 0.000 ARG E 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8765 (t80) cc_final: 0.8322 (t80) REVERT: A 58 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8922 (tm-30) REVERT: A 139 TYR cc_start: 0.9521 (m-80) cc_final: 0.9178 (m-80) REVERT: A 162 GLN cc_start: 0.9577 (tt0) cc_final: 0.8985 (tp-100) REVERT: A 176 LYS cc_start: 0.9456 (tptp) cc_final: 0.9138 (tppt) REVERT: A 260 ASP cc_start: 0.9098 (t0) cc_final: 0.8711 (t0) REVERT: A 279 PHE cc_start: 0.9563 (t80) cc_final: 0.9348 (t80) REVERT: B 32 LEU cc_start: 0.9623 (mm) cc_final: 0.9361 (mm) REVERT: B 36 LEU cc_start: 0.9590 (mm) cc_final: 0.8903 (mm) REVERT: B 58 LYS cc_start: 0.9710 (ptpp) cc_final: 0.9408 (mmtt) REVERT: B 90 MET cc_start: 0.8111 (mmp) cc_final: 0.7708 (tmm) REVERT: B 93 TYR cc_start: 0.9387 (t80) cc_final: 0.9127 (t80) REVERT: B 118 HIS cc_start: 0.9226 (m-70) cc_final: 0.8672 (m-70) REVERT: B 127 ASN cc_start: 0.9520 (m-40) cc_final: 0.8881 (m110) REVERT: B 128 MET cc_start: 0.9549 (mmt) cc_final: 0.8919 (mmt) REVERT: B 135 PHE cc_start: 0.8793 (t80) cc_final: 0.8467 (t80) REVERT: B 168 LEU cc_start: 0.9357 (pt) cc_final: 0.9054 (mm) REVERT: B 203 PHE cc_start: 0.9405 (t80) cc_final: 0.8920 (t80) REVERT: C 194 TYR cc_start: 0.8518 (t80) cc_final: 0.8003 (t80) REVERT: C 244 MET cc_start: 0.8577 (tpp) cc_final: 0.8121 (tpt) REVERT: D 86 PHE cc_start: 0.9417 (t80) cc_final: 0.9178 (t80) REVERT: D 177 MET cc_start: 0.9354 (mmp) cc_final: 0.9108 (mmm) REVERT: D 224 ASP cc_start: 0.9543 (t0) cc_final: 0.9129 (p0) REVERT: E 40 GLU cc_start: 0.9042 (tt0) cc_final: 0.8728 (tt0) REVERT: E 91 MET cc_start: 0.8960 (ptp) cc_final: 0.8522 (pmm) REVERT: E 106 TRP cc_start: 0.8553 (m-10) cc_final: 0.8005 (m-10) REVERT: E 159 MET cc_start: 0.8524 (ppp) cc_final: 0.8178 (ppp) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.2277 time to fit residues: 86.3441 Evaluate side-chains 192 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.0060 chunk 163 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12579 Z= 0.269 Angle : 0.664 7.171 17252 Z= 0.348 Chirality : 0.044 0.190 2083 Planarity : 0.005 0.052 2235 Dihedral : 7.189 83.195 1908 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.31 (0.21), residues: 1689 helix: 0.66 (0.18), residues: 873 sheet: -1.09 (0.32), residues: 189 loop : -1.03 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 79 HIS 0.003 0.001 HIS D 94 PHE 0.024 0.002 PHE A 98 TYR 0.017 0.002 TYR E 333 ARG 0.004 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8855 (t80) cc_final: 0.8504 (t80) REVERT: A 137 TRP cc_start: 0.9324 (m100) cc_final: 0.8971 (m100) REVERT: A 139 TYR cc_start: 0.9537 (m-80) cc_final: 0.9035 (m-80) REVERT: A 162 GLN cc_start: 0.9587 (tt0) cc_final: 0.8921 (tp40) REVERT: A 176 LYS cc_start: 0.9507 (tptp) cc_final: 0.9149 (tppt) REVERT: A 260 ASP cc_start: 0.9106 (t0) cc_final: 0.8727 (t0) REVERT: A 291 LYS cc_start: 0.9211 (tptt) cc_final: 0.8985 (pttm) REVERT: B 32 LEU cc_start: 0.9649 (mm) cc_final: 0.9336 (mm) REVERT: B 36 LEU cc_start: 0.9602 (mm) cc_final: 0.8783 (mm) REVERT: B 90 MET cc_start: 0.8199 (mmp) cc_final: 0.7777 (tmm) REVERT: B 118 HIS cc_start: 0.9138 (m-70) cc_final: 0.8677 (m-70) REVERT: B 127 ASN cc_start: 0.9542 (m-40) cc_final: 0.8964 (m-40) REVERT: B 128 MET cc_start: 0.9648 (mmt) cc_final: 0.9165 (mmm) REVERT: B 168 LEU cc_start: 0.9364 (pt) cc_final: 0.9040 (mm) REVERT: B 203 PHE cc_start: 0.9447 (t80) cc_final: 0.9185 (t80) REVERT: C 194 TYR cc_start: 0.8147 (t80) cc_final: 0.7608 (t80) REVERT: D 86 PHE cc_start: 0.9461 (t80) cc_final: 0.9221 (t80) REVERT: D 212 MET cc_start: 0.6317 (tpt) cc_final: 0.5845 (tpp) REVERT: D 224 ASP cc_start: 0.9551 (t0) cc_final: 0.9099 (p0) REVERT: D 244 MET cc_start: 0.5293 (tpt) cc_final: 0.4850 (tpp) REVERT: E 40 GLU cc_start: 0.9058 (tt0) cc_final: 0.8757 (tt0) REVERT: E 159 MET cc_start: 0.8371 (ppp) cc_final: 0.8041 (ppp) REVERT: E 270 GLU cc_start: 0.9221 (pm20) cc_final: 0.8829 (pm20) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.2306 time to fit residues: 83.1290 Evaluate side-chains 181 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN E 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12579 Z= 0.178 Angle : 0.631 7.385 17252 Z= 0.322 Chirality : 0.044 0.218 2083 Planarity : 0.005 0.051 2235 Dihedral : 7.016 81.708 1908 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.08 (0.21), residues: 1689 helix: 0.80 (0.18), residues: 878 sheet: -0.73 (0.34), residues: 177 loop : -0.98 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 97 HIS 0.002 0.001 HIS D 290 PHE 0.018 0.001 PHE A 229 TYR 0.018 0.002 TYR A 41 ARG 0.006 0.000 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TRP cc_start: 0.9282 (m100) cc_final: 0.9020 (m100) REVERT: A 139 TYR cc_start: 0.9532 (m-80) cc_final: 0.9116 (m-80) REVERT: A 150 ASN cc_start: 0.8492 (t0) cc_final: 0.8290 (m-40) REVERT: A 162 GLN cc_start: 0.9561 (tt0) cc_final: 0.8874 (tp40) REVERT: A 176 LYS cc_start: 0.9487 (tptp) cc_final: 0.9174 (tppt) REVERT: A 260 ASP cc_start: 0.9071 (t0) cc_final: 0.8680 (t0) REVERT: A 279 PHE cc_start: 0.9658 (t80) cc_final: 0.9419 (t80) REVERT: A 291 LYS cc_start: 0.9207 (tptt) cc_final: 0.8964 (pttm) REVERT: B 32 LEU cc_start: 0.9617 (mm) cc_final: 0.9325 (mm) REVERT: B 36 LEU cc_start: 0.9616 (mm) cc_final: 0.8987 (mm) REVERT: B 57 TYR cc_start: 0.9141 (m-80) cc_final: 0.8858 (m-80) REVERT: B 58 LYS cc_start: 0.9725 (ptpp) cc_final: 0.9405 (mmtt) REVERT: B 90 MET cc_start: 0.8209 (mmp) cc_final: 0.7758 (tmm) REVERT: B 93 TYR cc_start: 0.9383 (t80) cc_final: 0.9167 (t80) REVERT: B 118 HIS cc_start: 0.9181 (m-70) cc_final: 0.8658 (m-70) REVERT: B 127 ASN cc_start: 0.9496 (m-40) cc_final: 0.9065 (m110) REVERT: B 168 LEU cc_start: 0.9316 (pt) cc_final: 0.8962 (mm) REVERT: B 203 PHE cc_start: 0.9417 (t80) cc_final: 0.8876 (t80) REVERT: C 194 TYR cc_start: 0.8189 (t80) cc_final: 0.7674 (t80) REVERT: C 244 MET cc_start: 0.8669 (tpp) cc_final: 0.8379 (tpt) REVERT: D 86 PHE cc_start: 0.9460 (t80) cc_final: 0.9217 (t80) REVERT: D 212 MET cc_start: 0.6393 (tpt) cc_final: 0.5649 (tpt) REVERT: D 224 ASP cc_start: 0.9532 (t0) cc_final: 0.9095 (p0) REVERT: D 244 MET cc_start: 0.4741 (tpt) cc_final: 0.4228 (tpp) REVERT: E 40 GLU cc_start: 0.9088 (tt0) cc_final: 0.8797 (tt0) REVERT: E 106 TRP cc_start: 0.8565 (m-10) cc_final: 0.8321 (m-10) REVERT: E 159 MET cc_start: 0.8401 (ppp) cc_final: 0.8032 (ppp) REVERT: E 270 GLU cc_start: 0.9205 (pm20) cc_final: 0.8842 (pm20) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2204 time to fit residues: 78.9235 Evaluate side-chains 185 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.0170 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12579 Z= 0.167 Angle : 0.636 7.429 17252 Z= 0.323 Chirality : 0.044 0.241 2083 Planarity : 0.005 0.050 2235 Dihedral : 6.791 83.263 1908 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.01 (0.21), residues: 1689 helix: 0.88 (0.18), residues: 876 sheet: -0.62 (0.34), residues: 177 loop : -0.99 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 97 HIS 0.003 0.001 HIS D 290 PHE 0.024 0.001 PHE A 98 TYR 0.017 0.002 TYR E 333 ARG 0.018 0.001 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9521 (m-80) cc_final: 0.9169 (m-80) REVERT: A 162 GLN cc_start: 0.9557 (tt0) cc_final: 0.8850 (tp-100) REVERT: A 176 LYS cc_start: 0.9484 (tptp) cc_final: 0.9209 (tppt) REVERT: A 260 ASP cc_start: 0.9076 (t0) cc_final: 0.8699 (t0) REVERT: A 291 LYS cc_start: 0.9248 (tptt) cc_final: 0.8990 (pttm) REVERT: B 32 LEU cc_start: 0.9619 (mm) cc_final: 0.9367 (mm) REVERT: B 36 LEU cc_start: 0.9634 (mm) cc_final: 0.8960 (mm) REVERT: B 57 TYR cc_start: 0.9124 (m-80) cc_final: 0.8861 (m-80) REVERT: B 58 LYS cc_start: 0.9726 (ptpp) cc_final: 0.9411 (mmtt) REVERT: B 90 MET cc_start: 0.8171 (mmp) cc_final: 0.7776 (tmm) REVERT: B 118 HIS cc_start: 0.9189 (m-70) cc_final: 0.8636 (m-70) REVERT: B 127 ASN cc_start: 0.9503 (m-40) cc_final: 0.9070 (m110) REVERT: B 168 LEU cc_start: 0.9280 (pt) cc_final: 0.8924 (mm) REVERT: B 203 PHE cc_start: 0.9413 (t80) cc_final: 0.8903 (t80) REVERT: C 194 TYR cc_start: 0.8278 (t80) cc_final: 0.7838 (t80) REVERT: C 244 MET cc_start: 0.8664 (tpp) cc_final: 0.8346 (tpt) REVERT: D 39 LEU cc_start: 0.9530 (tp) cc_final: 0.9328 (tp) REVERT: D 86 PHE cc_start: 0.9451 (t80) cc_final: 0.9192 (t80) REVERT: D 212 MET cc_start: 0.6286 (tpt) cc_final: 0.5606 (tpt) REVERT: D 224 ASP cc_start: 0.9509 (t0) cc_final: 0.9069 (p0) REVERT: D 244 MET cc_start: 0.4777 (tpt) cc_final: 0.4531 (tpp) REVERT: E 40 GLU cc_start: 0.9098 (tt0) cc_final: 0.8821 (tt0) REVERT: E 106 TRP cc_start: 0.8352 (m-10) cc_final: 0.8133 (m-10) REVERT: E 159 MET cc_start: 0.8419 (ppp) cc_final: 0.8088 (ppp) REVERT: E 270 GLU cc_start: 0.9202 (pm20) cc_final: 0.8804 (pm20) REVERT: E 402 TYR cc_start: 0.8782 (t80) cc_final: 0.8573 (t80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2078 time to fit residues: 73.7565 Evaluate side-chains 183 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 160 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12579 Z= 0.164 Angle : 0.619 7.296 17252 Z= 0.312 Chirality : 0.043 0.243 2083 Planarity : 0.005 0.050 2235 Dihedral : 6.600 84.231 1908 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 0.04 (0.21), residues: 1689 helix: 0.90 (0.18), residues: 877 sheet: -0.54 (0.34), residues: 177 loop : -0.96 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 79 HIS 0.003 0.001 HIS D 290 PHE 0.018 0.001 PHE A 83 TYR 0.018 0.002 TYR A 41 ARG 0.008 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8837 (t80) cc_final: 0.8353 (t80) REVERT: A 139 TYR cc_start: 0.9513 (m-80) cc_final: 0.9175 (m-80) REVERT: A 162 GLN cc_start: 0.9564 (tt0) cc_final: 0.8853 (tp40) REVERT: A 176 LYS cc_start: 0.9485 (tptp) cc_final: 0.9232 (tppt) REVERT: A 260 ASP cc_start: 0.9082 (t0) cc_final: 0.8770 (t0) REVERT: A 291 LYS cc_start: 0.9308 (tptt) cc_final: 0.9047 (pttm) REVERT: B 32 LEU cc_start: 0.9627 (mm) cc_final: 0.9308 (mm) REVERT: B 36 LEU cc_start: 0.9623 (mm) cc_final: 0.9012 (mm) REVERT: B 37 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8466 (mmmm) REVERT: B 57 TYR cc_start: 0.9135 (m-80) cc_final: 0.8901 (m-80) REVERT: B 58 LYS cc_start: 0.9727 (ptpp) cc_final: 0.9426 (mmtt) REVERT: B 90 MET cc_start: 0.8193 (mmp) cc_final: 0.7800 (tmm) REVERT: B 118 HIS cc_start: 0.9166 (m-70) cc_final: 0.8538 (m-70) REVERT: B 127 ASN cc_start: 0.9476 (m-40) cc_final: 0.8878 (m110) REVERT: B 128 MET cc_start: 0.9580 (mmt) cc_final: 0.8937 (mmt) REVERT: B 135 PHE cc_start: 0.8595 (t80) cc_final: 0.8297 (t80) REVERT: B 168 LEU cc_start: 0.9246 (pt) cc_final: 0.8864 (mm) REVERT: B 203 PHE cc_start: 0.9398 (t80) cc_final: 0.8907 (t80) REVERT: B 207 TRP cc_start: 0.8650 (t60) cc_final: 0.8435 (t60) REVERT: C 194 TYR cc_start: 0.8326 (t80) cc_final: 0.7936 (t80) REVERT: C 244 MET cc_start: 0.8678 (tpp) cc_final: 0.8370 (tpt) REVERT: D 39 LEU cc_start: 0.9515 (tp) cc_final: 0.9304 (tp) REVERT: D 86 PHE cc_start: 0.9462 (t80) cc_final: 0.9204 (t80) REVERT: D 212 MET cc_start: 0.6363 (tpt) cc_final: 0.5872 (tpt) REVERT: D 224 ASP cc_start: 0.9520 (t0) cc_final: 0.9088 (p0) REVERT: D 244 MET cc_start: 0.4871 (tpt) cc_final: 0.4331 (tpp) REVERT: E 40 GLU cc_start: 0.9119 (tt0) cc_final: 0.8823 (tt0) REVERT: E 64 ARG cc_start: 0.9657 (mmp-170) cc_final: 0.9329 (mmm160) REVERT: E 106 TRP cc_start: 0.8342 (m-10) cc_final: 0.8128 (m-10) REVERT: E 159 MET cc_start: 0.8472 (ppp) cc_final: 0.8144 (ppp) REVERT: E 402 TYR cc_start: 0.8755 (t80) cc_final: 0.8429 (t80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2267 time to fit residues: 79.0715 Evaluate side-chains 185 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 134 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12579 Z= 0.184 Angle : 0.627 7.187 17252 Z= 0.318 Chirality : 0.044 0.252 2083 Planarity : 0.005 0.050 2235 Dihedral : 6.559 85.574 1908 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 0.08 (0.21), residues: 1689 helix: 0.93 (0.18), residues: 882 sheet: -0.54 (0.34), residues: 177 loop : -0.95 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 79 HIS 0.005 0.001 HIS D 290 PHE 0.025 0.002 PHE A 98 TYR 0.017 0.002 TYR A 41 ARG 0.008 0.000 ARG D 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8847 (t80) cc_final: 0.8394 (t80) REVERT: A 139 TYR cc_start: 0.9502 (m-80) cc_final: 0.9142 (m-80) REVERT: A 162 GLN cc_start: 0.9573 (tt0) cc_final: 0.8871 (tp40) REVERT: A 168 ILE cc_start: 0.9658 (mm) cc_final: 0.9438 (mm) REVERT: A 176 LYS cc_start: 0.9500 (tptp) cc_final: 0.9246 (tppt) REVERT: A 260 ASP cc_start: 0.9116 (t0) cc_final: 0.8744 (t0) REVERT: A 279 PHE cc_start: 0.9614 (t80) cc_final: 0.9397 (t80) REVERT: A 291 LYS cc_start: 0.9329 (tptt) cc_final: 0.9076 (pttm) REVERT: B 36 LEU cc_start: 0.9609 (mm) cc_final: 0.9042 (mm) REVERT: B 37 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8460 (mmmm) REVERT: B 90 MET cc_start: 0.8156 (mmp) cc_final: 0.7744 (tmm) REVERT: B 118 HIS cc_start: 0.9131 (m-70) cc_final: 0.8472 (m-70) REVERT: B 127 ASN cc_start: 0.9497 (m-40) cc_final: 0.8811 (m110) REVERT: B 128 MET cc_start: 0.9619 (mmt) cc_final: 0.8983 (mmm) REVERT: B 135 PHE cc_start: 0.8294 (t80) cc_final: 0.8002 (t80) REVERT: B 168 LEU cc_start: 0.9255 (pt) cc_final: 0.8866 (mm) REVERT: B 203 PHE cc_start: 0.9429 (t80) cc_final: 0.8908 (t80) REVERT: B 216 LEU cc_start: 0.9257 (tp) cc_final: 0.9031 (tp) REVERT: C 194 TYR cc_start: 0.8270 (t80) cc_final: 0.7887 (t80) REVERT: C 244 MET cc_start: 0.8731 (tpp) cc_final: 0.8415 (tpt) REVERT: D 39 LEU cc_start: 0.9523 (tp) cc_final: 0.9316 (tp) REVERT: D 86 PHE cc_start: 0.9466 (t80) cc_final: 0.9215 (t80) REVERT: D 224 ASP cc_start: 0.9521 (t0) cc_final: 0.9082 (p0) REVERT: D 244 MET cc_start: 0.4841 (tpt) cc_final: 0.4564 (tpp) REVERT: E 40 GLU cc_start: 0.9112 (tt0) cc_final: 0.8817 (tt0) REVERT: E 64 ARG cc_start: 0.9569 (mmp-170) cc_final: 0.9348 (mmm160) REVERT: E 159 MET cc_start: 0.8490 (ppp) cc_final: 0.8155 (ppp) REVERT: E 262 LEU cc_start: 0.8891 (mm) cc_final: 0.8617 (mm) REVERT: E 270 GLU cc_start: 0.9098 (pm20) cc_final: 0.8778 (pm20) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2146 time to fit residues: 73.9196 Evaluate side-chains 182 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.0470 chunk 123 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 134 optimal weight: 0.0370 chunk 56 optimal weight: 0.0070 chunk 137 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 overall best weight: 0.0952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** 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 = 0.3358 r_free = 0.3358 target = 0.064504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048349 restraints weight = 81253.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049746 restraints weight = 59045.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050849 restraints weight = 45845.956| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12579 Z= 0.168 Angle : 0.652 7.673 17252 Z= 0.324 Chirality : 0.044 0.271 2083 Planarity : 0.005 0.058 2235 Dihedral : 6.436 82.935 1908 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 0.08 (0.21), residues: 1689 helix: 0.91 (0.18), residues: 877 sheet: -0.53 (0.35), residues: 176 loop : -0.89 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 137 HIS 0.003 0.001 HIS D 290 PHE 0.020 0.001 PHE B 126 TYR 0.019 0.002 TYR A 41 ARG 0.017 0.001 ARG D 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.33 seconds wall clock time: 51 minutes 43.15 seconds (3103.15 seconds total)